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Wang W, Liu Y, Kang Y, Liu W, Li S, Wang Z, Xia X, Chen X, Qian L, Xiong X, Liu Z, Guan C, He X. Genome-wide characterization of LEA gene family reveals a positive role of BnaA.LEA6.a in freezing tolerance in rapeseed (Brassica napus L.). BMC Plant Biol 2024; 24:433. [PMID: 38773359 PMCID: PMC11106994 DOI: 10.1186/s12870-024-05111-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND Freezing stress is one of the major abiotic stresses that causes extensive damage to plants. LEA (Late embryogenesis abundant) proteins play a crucial role in plant growth, development, and abiotic stress. However, there is limited research on the function of LEA genes in low-temperature stress in Brassica napus (rapeseed). RESULTS Total 306 potential LEA genes were identified in B. rapa (79), B. oleracea (79) and B. napus (148) and divided into eight subgroups. LEA genes of the same subgroup had similar gene structures and predicted subcellular locations. Cis-regulatory elements analysis showed that the promoters of BnaLEA genes rich in cis-regulatory elements related to various abiotic stresses. Additionally, RNA-seq and real-time PCR results indicated that the majority of BnaLEA family members were highly expressed in senescent tissues of rapeseed, especially during late stages of seed maturation, and most BnaLEA genes can be induced by salt and osmotic stress. Interestingly, the BnaA.LEA6.a and BnaC.LEA6.a genes were highly expressed across different vegetative and reproductive organs during different development stages, and showed strong responses to salt, osmotic, and cold stress, particularly freezing stress. Further analysis showed that overexpression of BnaA.LEA6.a increased the freezing tolerance in rapeseed, as evidenced by lower relative electrical leakage and higher survival rates compared to the wild-type (WT) under freezing treatment. CONCLUSION This study is of great significance for understanding the functions of BnaLEA genes in freezing tolerance in rapeseed and offers an ideal candidate gene (BnaA.LEA6.a) for molecular breeding of freezing-tolerant rapeseed cultivars.
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Affiliation(s)
- Weiping Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yan Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yu Kang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Wei Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Shun Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Zhonghua Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xiaoyan Xia
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xiaoyu Chen
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Lunwen Qian
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xinghua Xiong
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xin He
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China.
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Balamurugan A, Mallikarjuna MG, Bansal S, Nayaka SC, Rajashekara H, Chellapilla TS, Prakash G. Genome-wide identification and characterization of NBLRR genes in finger millet (Eleusine coracana L.) and their expression in response to Magnaporthe grisea infection. BMC Plant Biol 2024; 24:75. [PMID: 38281915 PMCID: PMC10823742 DOI: 10.1186/s12870-024-04743-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND The nucleotide binding site leucine rich repeat (NBLRR) genes significantly regulate defences against phytopathogens in plants. The genome-wide identification and analysis of NBLRR genes have been performed in several species. However, the detailed evolution, structure, expression of NBLRRs and functional response to Magnaporthe grisea are unknown in finger millet (Eleusine coracana (L.) Gaertn.). RESULTS The genome-wide scanning of the finger millet genome resulted in 116 NBLRR (EcNBLRRs1-116) encompassing 64 CC-NB-LRR, 47 NB-LRR and 5 CCR-NB-LRR types. The evolutionary studies among the NBLRRs of five Gramineae species, viz., purple false brome (Brachypodium distachyon (L.) P.Beauv.), finger millet (E. coracana), rice (Oryza sativa L.), sorghum (Sorghum bicolor L. (Moench)) and foxtail millet (Setaria italica (L.) P.Beauv.) showed the evolution of NBLRRs in the ancestral lineage of the target species and subsequent divergence through gene-loss events. The purifying selection (Ka/Ks < 1) shaped the expansions of NBLRRs paralogs in finger millet and orthologs among the target Gramineae species. The promoter sequence analysis showed various stress- and phytohormone-responsive cis-acting elements besides growth and development, indicating their potential role in disease defence and regulatory mechanisms. The expression analysis of 22 EcNBLRRs in the genotypes showing contrasting responses to Magnaporthe grisea infection revealed four and five EcNBLRRs in early and late infection stages, respectively. The six of these nine candidate EcNBLRRs proteins, viz., EcNBLRR21, EcNBLRR26, EcNBLRR30, EcNBLRR45, EcNBLRR55 and EcNBLRR76 showed CC, NB and LRR domains, whereas the EcNBLRR23, EcNBLRR32 and EcNBLRR83 showed NB and LRR somains. CONCLUSION The identification and expression analysis of EcNBLRRs showed the role of EcNBLRR genes in assigning blast resistance in finger millet. These results pave the foundation for in-depth and targeted functional analysis of EcNBLRRs through genome editing and transgenic approaches.
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Affiliation(s)
- Alexander Balamurugan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Shilpi Bansal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Department of Science and Humanities, SRM Institute of Science and Technology, Modinagar, Uttar Pradesh, 201204, India
| | - S Chandra Nayaka
- Department of Studies in Applied Botany and Biotechnology, University of Mysore, Mysore, 570005, India
| | | | | | - Ganesan Prakash
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Zhang J, Wang J, Wang C. Whole Genome Sequencing and Comparative Analysis of the First Ehrlichia canis Isolate in China. Microorganisms 2024; 12:125. [PMID: 38257951 PMCID: PMC10820421 DOI: 10.3390/microorganisms12010125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Ehrlichia canis, a prominent tick-borne pathogen causing canine monocytic ehrlichiosis (CME), is one of the six recognized Ehrlichia species worldwide. Despite its widespread presence in ticks and host dogs in China, comprehensive genomic information about this pathogen remains limited. This study focuses on an in-depth analysis of E. canis YZ-1, isolated and cultured from an infected dog in China. The complete genome of E. canis YZ-1 was sequenced (1,314,789 bp, 1022 genes, 29% GC content, and 73% coding bases), systematically characterizing its genomic elements and functions. Comparative analysis with representative genomes of Ehrlichia species, including E. canis strain Jake, E. chaffeensis, Ehrlichia spp., E. muris, E. ruminantium, and E. minasensis, revealed conserved genes, indicating potential evolutionary connections with E. ruminantium. The observed reduction in virulence-associated genes, coupled with a type IV secretion system (T4SS), suggests an intricate balance between pathogenicity and host adaptation. The close relationship with E. canis Jake and E. chaffeensis, alongside nuanced genomic variations with E. ruminantium and E. mineirensis, underscores the need to explore emerging strains and advancements in sequencing technologies continuously. This genetic insight opens avenues for innovative medications, studies on probiotic resistance, development of new detection markers, and progress in vaccine development for ehrlichiosis. Further investigations into the functional significance of identified genes and their role in host-pathogen interactions will contribute to a more holistic comprehension of Ehrlichia's biology and its implications for pathogenicity and transmission.
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Affiliation(s)
- Jilei Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- College of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Jiawei Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
| | - Chengming Wang
- College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
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Mallikarjuna MG, Tomar R, Lohithaswa HC, Sahu S, Mishra DC, Rao AR, Chinnusamy V. Genome-wide identification of potassium channels in maize showed evolutionary patterns and variable functional responses to abiotic stresses. Plant Physiol Biochem 2024; 206:108235. [PMID: 38039585 DOI: 10.1016/j.plaphy.2023.108235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Potassium (K) channels are essential components of plant biology, mediating not only K ion (K+) homeostasis but also regulating several physiological processes and stress tolerance. In the current investigation, we identified 27 K+ channels in maize and deciphered the evolution and divergence pattern with four monocots and five dicot species. Chromosomal localization and expansion of K+ channel genes showed uneven distribution and were independent of genome size. The dispersed duplication is the major force in expanding K+ channels in the target genomes. The mean Ka/Ks ratio of <0.5 in paralogs and orthologs indicates horizontal and vertical expansions of K+ channel genes under strong purifying selection. The one-to-one K+ channel orthologs were prominent among the closely related species, with higher synteny between maize and the rest of the monocots. Comprehensive K+ channels promoter analysis revealed various cis-regulatory elements mediating stress tolerance with the predominance of MYB and STRE binding sites. The regulatory network showed AP2-EREBP TFs, miR164 and miR399 are prominent regulatory elements of K+ channels. The qRT-PCR analysis of K+ channels and regulatory miRNAs showed significant expressions in response to drought and waterlogging stresses. The present study expanded the knowledge on K+ channels in maize and will serve as a basis for an in-depth functional analysis.
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Affiliation(s)
| | - Rakhi Tomar
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Sarika Sahu
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Dwijesh Chandra Mishra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Atmakuri Ramakrishna Rao
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR- Indian Agricultural Research Institute, New Delhi, 110012, India
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Duan M, Zong M, Guo N, Han S, Wang G, Miao L, Liu F. Comprehensive Genome-Wide Identification of the RNA-Binding Glycine-Rich Gene Family and Expression Profiling under Abiotic Stress in Brassica oleracea. Plants (Basel) 2023; 12:3706. [PMID: 37960062 PMCID: PMC10649936 DOI: 10.3390/plants12213706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
The RNA-binding glycine-rich proteins (RBGs) of the glycine-rich protein family play vital roles in regulating gene expression both at the transcriptional and post-transcriptional levels. However, the members and functions in response to abiotic stresses of the RBG gene family remain unclear in Brassica oleracea. In this study, a total of 19 BoiRBG genes were identified through genome-wide analysis in broccoli. The characteristics of BoiRBG sequences and their evolution were examined. An analysis of synteny indicated that the expansion of the BoiRBG gene family was primarily driven by whole-genome duplication and tandem duplication events. The BoiRBG expression patterns revealed that these genes are involved in reaction to diverse abiotic stress conditions (i.e., simulated drought, salinity, heat, cold, and abscisic acid) and different organs. In the present research, the up-regulation of BoiRBGA13 expression was observed when subjected to both NaCl-induced and cold stress conditions in broccoli. Moreover, the overexpression of BoiRBGA13 resulted in a noteworthy reduction in taproot lengths under NaCl stress, as well as the inhibition of seed germination under cold stress in broccoli, indicating that RBGs play different roles under various stresses. This study provides insights into the evolution and functions of BoiRBG genes in Brassica oleracea and other Brassicaceae family plants.
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Affiliation(s)
- Mengmeng Duan
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Mei Zong
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Ning Guo
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Shuo Han
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Guixiang Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Liming Miao
- Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China;
| | - Fan Liu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
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Chang L, Liang J, Zhang L, Zhang Z, Cai X, Wu J, Wang X. A complex locus regulates highly lobed-leaf formation in Brassica juncea. Theor Appl Genet 2023; 136:224. [PMID: 37845510 DOI: 10.1007/s00122-023-04473-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023]
Abstract
KEY MESSAGE Lineage-specific evolution of RCO was described in Brassicaceae. BjRCO.1 and BjRCO.2 within the complex locus regulated highly lobed-leaf formation in Brassica juncea. RCO regulates the formation of lobed leaves in Brassicaceae species. RCO originated from the duplication of LMI1-type sequences and evolved through gene duplication and loss within the Brassicaceae. However, the evolutionary process and diversification of RCO in different lineages of Brassicaceae remain unclear. Although the RCO locus in B. juncea has been associated with lobed-leaf formation, its complexity has remained largely unknown. This study involved the identification of 55 LMI1-like genes in 16 species of Brassicaceae through syntenic analysis. We classified these LMI1-like genes into two types, namely LMI1-type and RCO-type, based on their phylogenetic relationship. Additionally, we proposed two independent lineage-specific evolution routes for RCO following the divergence of Aethionema. Our findings revealed that the LMI1-like loci responsible for lobed-leaf formation in Brassica species are located on the LF subgenomes. For B. juncea (T84-66V2), we discovered that the complex locus underwent duplication through segments of nucleic acid sequence containing Exostosin-LMI1-RCO (E-R-L), resulting in the tandem presence of two RCO-type and two LMI1-type genes on chromosome A10. As additional evidence, we successfully mapped the complex locus responsible for highly lobed-leaf formation to chromosome A10 using a B. juncea F2 population, which corroborated the results of our evolutionary analysis. Furthermore, through transcriptome analysis, we clarified that BjRCO.1 and BjRCO.2 within the complex locus are functional genes involved in the regulation of highly lobed-leaf formation. The findings of this study offer valuable insights into the regulation of leaf morphology for the breeding of Brassica crops.
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Affiliation(s)
- Lichun Chang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian, 10081, Beijing, People's Republic of China
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian, 10081, Beijing, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian, 10081, Beijing, People's Republic of China
| | - Zhicheng Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian, 10081, Beijing, People's Republic of China
| | - Xu Cai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian, 10081, Beijing, People's Republic of China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian, 10081, Beijing, People's Republic of China.
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St., Haidian, 10081, Beijing, People's Republic of China.
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Zhang K, Zhang L, Cui Y, Yang Y, Wu J, Liang J, Li X, Zhang X, Zhang Y, Guo Z, Zhang L, Chen S, Ruan J, Freeling M, Wang X, Cheng F. The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids. Proc Natl Acad Sci U S A 2023; 120:e2305208120. [PMID: 37816049 PMCID: PMC10589682 DOI: 10.1073/pnas.2305208120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
Polyploidization is important to the evolution of plants. Subgenome dominance is a distinct phenomenon associated with most allopolyploids. A gene on the dominant subgenome tends to express to higher RNA levels in all organs as compared to the expression of its syntenic paralogue (homoeolog). The mechanism that underlies the formation of subgenome dominance remains unknown, but there is evidence for the involvement of transposon/DNA methylation density differences nearby the genes of parents as being causal. The subgenome with lower density of transposon and methylation near genes is positively associated with subgenome dominance. Here, we generated eight generations of allotetraploid progenies from the merging of parental genomes Brassica rapa and Brassica oleracea. We found that transposon/methylation density differ near genes between the parental (rapa:oleracea) existed in the wide hybrid, persisted in the neotetraploids (the synthetic Brassica napus), but these neotetraploids expressed no expected subgenome dominance. This absence of B. rapa vs. B. oleracea subgenome dominance is particularly significant because, while there is no negative relationship between transposon/methylation level and subgenome dominance in the neotetraploids, the more ancient parental subgenomes for all Brassica did show differences in transposon/methylation densities near genes and did express, in the same samples of cells, biased gene expression diagnostic of subgenome dominance. We conclude that subgenome differences in methylated transposon near genes are not sufficient to initiate the biased gene expressions defining subgenome dominance. Our result was unexpected, and we suggest a "nuclear chimera" model to explain our data.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Yinan Cui
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
- Chengde Academy of Agriculture and Forestry Sciences, Chengde067032, China
| | - Yinqing Yang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Xing Li
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Xin Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Yiyue Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Zhongwei Guo
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518120, China
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720-3102
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
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Huang Y, Guo X, Zhang K, Mandáková T, Cheng F, Lysak MA. The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora. Plant J 2023; 116:446-466. [PMID: 37428465 DOI: 10.1111/tpj.16383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Although the South African Cape flora is one of the most remarkable biodiversity hotspots, its high diversity has not been associated with polyploidy. Here, we report the chromosome-scale genome assembly of an ephemeral cruciferous species Heliophila variabilis (~334 Mb, n = 11) adapted to South African semiarid biomes. Two pairs of differently fractionated subgenomes suggest an allo-octoploid origin of the genome at least 12 million years ago. The ancestral octoploid Heliophila genome (2n = 8x = ~60) has probably originated through hybridization between two allotetraploids (2n = 4x = ~30) formed by distant, intertribal, hybridization. Rediploidization of the ancestral genome was marked by extensive reorganization of parental subgenomes, genome downsizing, and speciation events in the genus Heliophila. We found evidence for loss-of-function changes in genes associated with leaf development and early flowering, and over-retention and sub/neofunctionalization of genes involved in pathogen response and chemical defense. The genomic resources of H. variabilis will help elucidate the role of polyploidization and genome diploidization in plant adaptation to hot arid environments and origin of the Cape flora. The sequenced H. variabilis represents the first chromosome-scale genome assembly of a meso-octoploid representative of the mustard family.
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Affiliation(s)
- Yile Huang
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Xinyi Guo
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
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9
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Wang T, van Dijk ADJ, Bucher J, Liang J, Wu J, Bonnema G, Wang X. Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus. Mol Biol Evol 2023; 40:msad199. [PMID: 37707440 PMCID: PMC10504873 DOI: 10.1093/molbev/msad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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10
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Wei M, Duan P, Zhao S, Gou B, Wang Y, Yang N, Ma Y, Ma Z, Zhang G, Wei B. Genome-wide identification of RUB activating enzyme and conjugating enzyme gene families and their expression analysis under abiotic stresses in Capsicum annuum. Protoplasma 2023; 260:821-837. [PMID: 36322293 DOI: 10.1007/s00709-022-01816-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
NEDD8/RUB, as a ubiquitin-like protein, participates in the post-translational modification of protein and requires unique E1, E2, and E3 enzymes to bind to its substrate. The RUB E1 activating enzyme and E2 conjugating enzyme play a significant role in the neddylation. However, it is unknown whether RUB E1 and E2 exist in pepper and what its function is. In this study, a total of three putative RUB E1 and five RUB E2 genes have been identified in the pepper genome. Subsequently, their physical and chemical properties, gene structure, conserved domains and motifs, phylogenetic relationship, and cis-acting elements were analyzed. The structure and conserved domain of RUB E1 and E2 are similar to that of Arabidopsis and tomato. The RUB E1 and E2 genes were randomly distributed on seven chromosomes, and there were two pairs of collinearity between pepper and Arabidopsis and eight pairs of collinearity between pepper and tomato. Phylogenetic analysis reveals that RUB E1 and E2 genes of pepper have a closer relationship with that of tomato, potato, and Nicotiana attenuate. The cis-elements of RUB E1 and E2 genes contained hormone response and stress response. RUB E1 and E2 genes were expressed in at least one tissue and CaRCE1.3 and CaRCE2.1 were exclusively expressed in flowers and anthers. Moreover, the expression of RUB E1 genes (CaECR1, CaAXR1.1, and CaAXR1.2) and RUB E2 genes (CaRCE1.1, CaRCE1.2, and CaRCE2.1) was increased to varying degrees under low-temperature, drought, salt, ABA, and IAA treatments, while CaRCE1.3 and CaRCE2.2 were down-regulated under low-temperature treatment. In addition, these genes were hardly expressed under MeJA treatment. In summary, this study provides a theoretical foundation to explore the role of RUB E1 and E2 in the response of plants to stress.
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Affiliation(s)
- Min Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Panpan Duan
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Shufang Zhao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Bingdiao Gou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Yongfu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Nan Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Yan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Zhengbao Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Bingqiang Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.
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11
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Zhang K, Yang Y, Zhang X, Zhang L, Fu Y, Guo Z, Chen S, Wu J, Schnable JC, Yi K, Wang X, Cheng F. The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits. Plant Commun 2023; 4:100431. [PMID: 36071668 PMCID: PMC10030322 DOI: 10.1016/j.xplc.2022.100431] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/09/2022] [Accepted: 08/24/2022] [Indexed: 05/04/2023]
Abstract
Orychophragmus violaceus, referred to as "eryuelan" (February orchid) in China, is an early-flowering ornamental plant. The high oil content and abundance of unsaturated fatty acids in O. violaceus seeds make it a potential high-quality oilseed crop. Here, we generated a whole-genome assembly for O. violaceus using Nanopore and Hi-C sequencing technologies. The assembled genome of O. violaceus was ∼1.3 Gb in size, with 12 pairs of chromosomes. Through investigation of ancestral genome evolution, we determined that the genome of O. violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype. Comparisons between the reconstructed subgenomes of O. violaceus identified indicators of subgenome dominance, indicating that subgenomes likely originated via allotetraploidy. O. violaceus was phylogenetically close to the Brassica genus, and tetraploidy in O. violaceus occurred approximately 8.57 million years ago, close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage. However, the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica, as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks. Moreover, identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O. violaceus. These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O. violaceus.
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Affiliation(s)
- Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Yinqing Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Xin Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Lingkui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Yu Fu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Zhongwei Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Shumin Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA.
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China.
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China.
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12
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Chen D, Chen H, Dai G, Zhang H, Liu Y, Shen W, Zhu B, Cui C, Tan C. Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species. BMC Genomics 2023; 24:103. [PMID: 36894869 PMCID: PMC9999611 DOI: 10.1186/s12864-023-09170-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/07/2023] [Indexed: 03/11/2023] Open
Abstract
Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The change of seed coat color of Brassica crops is related to the specific synthesis and accumulation of anthocyanin, and the expression level of structural genes in anthocyanin synthesis pathway is specifically regulated by transcription factors. Despite some previous reports on the regulations of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the trait of Brassica crops is affected by the evolutionary events such as genome triploidization, the regulatory mechanism is still largely unknown. In this study, we identified genes related to anthocyanin synthesis in six Brassica crops in U-triangle at the genome-wide level and performed collinearity analysis. A total of 1119 anthocyanin-related genes were identified, the collinear relationship of anthocyanin-related genes on subgenomic chromosomes was the best in B. napus (AACC) and the worst in B. carinata (BBCC). The comparisons of gene expressions for anthocyanin metabolic pathways in seed coats during seed development revealed differences in its metabolism among these species. Interestingly, the R2R3-MYB transcription factors MYB5 and TT2 were differentially expressed at all eight stages of seed coat development, indicating that they might be the key genes that caused the variation of the seed coat color. The expression curve and trend analyses of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 was likely gene silencing caused by gene structural variation. These results were valuable for the genetic improvement of Brassica seed coat color, and also provided new insights into gene multicopy evolution in Brassica polyploids.
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Affiliation(s)
- Daozong Chen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Haidong Chen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Guoqiang Dai
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Haimei Zhang
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Yi Liu
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Wenjie Shen
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China
| | - Bo Zhu
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China.
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chendu, 610066, China.
| | - Chen Tan
- College of Life Sciences, Ganzhou Key Laboratory of Greenhouse Vegetable, Gannan Normal University, Ganzhou, 341000, China.
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13
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Yang T, Cai B, Jia Z, Wang Y, Wang J, King GJ, Ge X, Li Z. Sinapis genomes provide insights into whole-genome triplication and divergence patterns within tribe Brassiceae. Plant J 2023; 113:246-261. [PMID: 36424891 DOI: 10.1111/tpj.16043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Sinapis alba and Sinapis arvensis are mustard crops within the Brassiceae tribe of the Brassicaceae family, and represent an important genetic resource for crop improvement. We performed the de novo assembly of Brassica nigra, S. alba, and S. arvensis, and conducted comparative genomics to investigate the pattern of genomic evolution since an ancient whole-genome triplication event. Both Sinapis species retained evidence of the Brassiceae whole-genome triplication approximately 20.5 million years ago (Mya), with subgenome dominance observed in gene density, gene expression, and selective constraint. While S. alba diverged from the ancestor of Brassica and Raphanus at approximately 12.5 Mya, the divergence time of S. arvensis and B. nigra was approximately 6.5 Mya. S. arvensis and B. nigra had greater collinearity compared with their relationship to either Brassica rapa or Brassica oleracea. Two chromosomes of S. alba (Sal03 and Sal08) were completely collinear with two ancestral chromosomes proposed in the Ancestral Crucifer Karyotype (ACK) genomic block model, the first time this has been observed in the Brassiceae. These results are consistent with S. alba representing a relatively ancient lineage of the species evolved from the common ancestor of tribe Brassiceae, and suggest that the phylogeny of the Brassica and Sinapis genera requires some revision. Our study provides new insights into the genome evolution and phylogenetic relationships of Brassiceae and provides genomic information for genetic improvement of these plants.
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Affiliation(s)
- Taihua Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bowei Cai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, 2480, Australia
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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14
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Sun X, Feng D, Liu M, Qin R, Li Y, Lu Y, Zhang X, Wang Y, Shen S, Ma W, Zhao J. Single-cell transcriptome reveals dominant subgenome expression and transcriptional response to heat stress in Chinese cabbage. Genome Biol 2022; 23:262. [PMID: 36536447 PMCID: PMC9762029 DOI: 10.1186/s13059-022-02834-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Chinese cabbage (Brassica rapa ssp. pekinensis) experienced a whole-genome triplication event and thus has three subgenomes: least fractioned, medium fractioned, and most fractioned subgenome. Environmental changes affect leaf development, which in turn influence the yield. To improve the yield and resistance to different climate scenarios, a comprehensive understanding of leaf development is required including insights into the full diversity of cell types and transcriptional networks underlying their specificity. RESULTS Here, we generate the transcriptional landscape of Chinese cabbage leaf at single-cell resolution by performing single-cell RNA sequencing of 30,000 individual cells. We characterize seven major cell types with 19 transcriptionally distinct cell clusters based on the expression of the reported marker genes. We find that genes in the least fractioned subgenome are predominantly expressed compared with those in the medium and most fractioned subgenomes in different cell types. Moreover, we generate a single-cell transcriptional map of leaves in response to high temperature. We find that heat stress not only affects gene expression in a cell type-specific manner but also impacts subgenome dominance. CONCLUSIONS Our study highlights the transcriptional networks in different cell types and provides a better understanding of transcriptional regulation during leaf development and transcriptional response to heat stress in Chinese cabbage.
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Affiliation(s)
- Xiaoxue Sun
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Daling Feng
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Mengyang Liu
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Ruixin Qin
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Yan Li
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Yin Lu
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Xiaomeng Zhang
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Yanhua Wang
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Shuxing Shen
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Wei Ma
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
| | - Jianjun Zhao
- grid.274504.00000 0001 2291 4530State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071000 China
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15
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Megha S, Wang Z, Kav NNV, Rahman H. Genome-wide identification of biotin carboxyl carrier subunits of acetyl-CoA carboxylase in Brassica and their role in stress tolerance in oilseed Brassica napus. BMC Genomics 2022; 23:707. [PMID: 36253756 PMCID: PMC9578262 DOI: 10.1186/s12864-022-08920-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
Background Biotin carboxyl carrier protein (BCCP) is a subunit of Acetyl CoA-carboxylase (ACCase) which catalyzes the conversion of acetyl-CoA to malonyl-CoA in a committed step during the de novo biosynthesis of fatty acids. Lipids, lipid metabolites, lipid-metabolizing and -modifying enzymes are known to play a role in biotic and abiotic stress tolerance in plants. In this regard, an understanding of the Brassica napus BCCP genes will aid in the improvement of biotic and abiotic stress tolerance in canola. Results In this study, we identified 43 BCCP genes in five Brassica species based on published genome data. Among them, Brassica rapa, Brassica oleracea, Brassica nigra, Brassica napus and Brassica juncea had six, seven, seven, 10 and 13 BCCP homologs, respectively. Phylogenetic analysis categorized them into five classes, each with unique conserved domains. The promoter regions of all BCCP genes contained stress-related cis-acting elements as determined by cis-element analysis. We identified four and three duplicated gene pairs (segmental) in B. napus and B. juncea respectively, indicating the role of segmental duplication in the expansion of this gene family. The Ka/Ks ratios of orthologous gene pairs between Arabidopsis thaliana and five Brassica species were mostly less than 1.0, implying that purifying selection, i.e., selective removal of deleterious alleles, played a role during the evolution of Brassica genomes. Analysis of 10 BnaBCCP genes using qRT-PCR showed a different pattern of expression because of exposure of the plants to biotic stresses, such as clubroot and sclerotinia diseases, and abiotic stresses such as drought, low temperature and salinity stresses. Conclusions The identification and functional analysis of the Brassica BCCPs demonstrated that some of these genes might play important roles in biotic and abiotic stress responses. Results from this study could lay the foundation for a better understanding of these genes for the improvement of Brassica crops for stress tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08920-y.
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Affiliation(s)
- Swati Megha
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Zhengping Wang
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Nat N V Kav
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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16
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Kaya Y, Aydın ZU, Cai X, Wang X, Dönmez AA. Genome-wide characterization of two Aubrieta taxa: Aubrieta canescens subsp. canescens and Au. macrostyla (Brassicaceae). AoB Plants 2022; 14:plac035. [PMID: 36196394 PMCID: PMC9521481 DOI: 10.1093/aobpla/plac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Aubrieta canescens complex is divided into two subspecies, Au. canescens subsp. canescens, Au. canescens subsp. cilicica and a distinct species, Au. macrostyla, based on molecular phylogeny. We generated a draft assembly of Au. canescens subsp. canescens and Au. macrostyla using paired-end shotgun sequencing. This is the first attempt at genome characterization for the genus. In the presented study, ~165 and ~157 Mbp of the genomes of Au. canescens subsp. canescens and Au. macrostyla were assembled, respectively, and a total of 32 425 and 31 372 gene models were predicted in the genomes of the target taxa, respectively. We corroborated the phylogenomic affinity of taxa with some core Brassicaceae species (Clades A and B) including Arabis alpina. The orthology-based tree suggested that Aubrieta species differentiated from A. alpina 1.3-2.0 mya (million years ago). The genome-wide syntenic comparison of two Aubrieta taxa revealed that Au. canescens subsp. canescens (46 %) and Au. macrostyla (45 %) have an almost identical syntenic gene pair ratio. These novel genome assemblies are the first steps towards the chromosome-level assembly of Au. canescens and understanding the genome diversity within the genus.
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Affiliation(s)
| | - Zübeyde Uğurlu Aydın
- Molecular Plant Systematic Laboratory (MOBIS), Department of Biology, Faculty of Science, Hacettepe University, Ankara 06800, Turkey
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ali A Dönmez
- Molecular Plant Systematic Laboratory (MOBIS), Department of Biology, Faculty of Science, Hacettepe University, Ankara 06800, Turkey
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Akond Z, Rahman H, Ahsan MA, Mosharaf MP, Alam M, Mollah MNH, Borisjuk N. Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.). BioMed Research International 2022; 2022:1-26. [PMID: 36177060 PMCID: PMC9513535 DOI: 10.1155/2022/4955209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are known as the three major gene families that act as the critical components of RNA interference or silencing mechanisms through the noncoding small RNA molecules (miRNA and siRNA) to regulate the expressions of protein-coding genes in eukaryotic organisms. However, most of their characteristics including structures, chromosomal location, subcellular locations, regulatory elements, and gene networking were not rigorously studied. Our analysis identified 7 TaDCL, 39 TaAGO, and 16 TaRDR genes as RNA interference (RNAi) genes from the wheat genome. Phylogenetic analysis of predicted RNAi proteins with the RNAi proteins of Arabidopsis and rice showed that the predicted proteins of TaDCL, TaAGO, and TaRDR groups are clustered into four, eight, and four subgroups, respectively. Domain, 3D protein structure, motif, and exon-intron structure analyses showed that these proteins conserve identical characteristics within groups and maintain differences between groups. The nonsynonymous/synonymous mutation ratio (Ka/Ks) < 1 suggested that these protein sequences conserve some purifying functions. RNAi genes networking with TFs revealed that ERF, MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof are the key transcriptional regulators of the predicted RNAi-related genes. The cis-regulatory element (CREs) analysis detected some important CREs of RNAi genes that are significantly associated with light, stress, and hormone responses. Expression analysis based on an online database exhibited that almost all of the predicted RNAi genes are expressed in different tissues and organs. A case-control study from the gene expression level showed that some RNAi genes significantly responded to the drought and heat stresses. Overall results would therefore provide an excellent basis for in-depth molecular investigation of these genes and their regulatory elements for wheat crop improvement against different stressors.
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18
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Li SF, She HB, Yang LL, Lan LN, Zhang XY, Wang LY, Zhang YL, Li N, Deng CL, Qian W, Gao WJ. Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species. Int J Mol Sci 2022; 23:ijms231710158. [PMID: 36077556 PMCID: PMC9456015 DOI: 10.3390/ijms231710158] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Hong-Bing She
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long-Long Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xin-Yu Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Li-Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wei Qian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (W.Q.); (W.-J.G.)
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Correspondence: (W.Q.); (W.-J.G.)
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19
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Shamloo-Dashtpagerdi R, Lindlöf A, Tahmasebi S. Evidence that miR168a contributes to salinity tolerance of Brassica rapa L. via mediating melatonin biosynthesis. Physiol Plant 2022; 174:e13790. [PMID: 36169653 DOI: 10.1111/ppl.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Melatonin is a master regulator of diverse biological processes, including plant's abiotic stress responses and tolerance. Despite the extensive information on the role of melatonin in response to abiotic stress, how plants regulate endogenous melatonin content under stressful conditions remains largely unknown. In this study, we computationally mined Expressed Sequence Tag (EST) libraries of salinity-exposed Chinese cabbage (Brassica rapa) to identify the most reliable differentially expressed miRNA and its target gene(s). In light of these analyses, we found that miR168a potentially targets a key melatonin biosynthesis gene, namely O-METHYLTRANSFERASE 1 (OMT1). Accordingly, molecular and physiochemical evaluations were performed in a separate salinity experiment using contrasting B. rapa genotypes. Then, the association between B. rapa salinity tolerance and changes in measured molecular and physiochemical characteristics was determined. Results indicated that the expression profiles of miR168a and OMT1 significantly differed between B. rapa genotypes. Moreover, the expression profiles of miR168a and OMT1 significantly correlated with more melatonin content, robust antioxidant activities, and better ion homeostasis during salinity stress. Our results suggest that miR168a plausibly mediates melatonin biosynthesis, mainly through the OMT1 gene, under salinity conditions and thereby contributes to the salinity tolerance of B. rapa. To our knowledge, this is the first report on the role of miR168a and OMT1 in B. rapa salinity response.
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Affiliation(s)
| | | | - Sirous Tahmasebi
- Seed and Plant Improvement Research Department, Fars Agricultural and Natural Resources Research and Education Center, AREEO, Shiraz, Iran
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20
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Fierro Morales JC, Xue Q, Roh-Johnson M. An evolutionary and physiological perspective on cell-substrate adhesion machinery for cell migration. Front Cell Dev Biol 2022; 10:943606. [PMID: 36092727 PMCID: PMC9453864 DOI: 10.3389/fcell.2022.943606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-substrate adhesion is a critical aspect of many forms of cell migration. Cell adhesion to an extracellular matrix (ECM) generates traction forces necessary for efficient migration. One of the most well-studied structures cells use to adhere to the ECM is focal adhesions, which are composed of a multilayered protein complex physically linking the ECM to the intracellular actin cytoskeleton. Much of our understanding of focal adhesions, however, is primarily derived from in vitro studies in Metazoan systems. Though these studies provide a valuable foundation to the cell-substrate adhesion field, the evolution of cell-substrate adhesion machinery across evolutionary space and the role of focal adhesions in vivo are largely understudied within the field. Furthering investigation in these areas is necessary to bolster our understanding of the role cell-substrate adhesion machinery across Eukaryotes plays during cell migration in physiological contexts such as cancer and pathogenesis. In this review, we review studies of cell-substrate adhesion machinery in organisms evolutionary distant from Metazoa and cover the current understanding and ongoing work on how focal adhesions function in single and collective cell migration in an in vivo environment, with an emphasis on work that directly visualizes cell-substrate adhesions. Finally, we discuss nuances that ought to be considered moving forward and the importance of future investigation in these emerging fields for application in other fields pertinent to adhesion-based processes.
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Affiliation(s)
| | | | - Minna Roh-Johnson
- Department of Biochemistry, University of Utah, Salt Lake City, UT, United States
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Kuczynski C, McCorkle S, Keereetaweep J, Shanklin J, Schwender J. An expanded role for the transcription factor WRINKLED1 in the biosynthesis of triacylglycerols during seed development. Front Plant Sci 2022; 13:955589. [PMID: 35991420 PMCID: PMC9389262 DOI: 10.3389/fpls.2022.955589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/28/2022] [Indexed: 06/12/2023]
Abstract
The transcription factor WRINKLED1 (WRI1) is known as a master regulator of fatty acid synthesis in developing oilseeds of Arabidopsis thaliana and other species. WRI1 is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by WRI1. To shortlist possible gene targets for future in-planta experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additional layers of evidence. Upstream regions of protein-encoding genes in A. thaliana were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the in vitro assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase (FRK3) and of phosphoglucose isomerase (PGI1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.
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22
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Muthusamy M, Kim JA, Lee SI. Phylogenomics-Based Reconstruction and Molecular Evolutionary Histories of Brassica Photoreceptor Gene Families. Int J Mol Sci 2022; 23:ijms23158695. [PMID: 35955826 PMCID: PMC9369451 DOI: 10.3390/ijms23158695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/25/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Photosensory proteins known as photoreceptors (PHRs) are crucial for delineating light environments in synchronization with other environmental cues and regulating their physiological variables in plants. However, this has not been well studied in the Brassica genus, which includes several important agricultural and horticultural crops. Herein, we identified five major PHR gene families—phytochrome (PHY), cryptochrome (CRY), phototropin (PHOT), F-box containing flavin binding proteins (ZTL/FKF1/LKP2), and UV RESISTANCE LOCUS 8 (UVR8)—genomic scales and classified them into subfamilies based on their phylogenetic clustering with Arabidopsis homologues. The molecular evolution characteristics of Brassica PHR members indicated indirect expansion and lost one to six gene copies at subfamily levels. The segmental duplication was possibly the driving force of the evolution and amplification of Brassica PHRs. Gene replication retention and gene loss events of CRY, PHY, and PHOT members found in diploid progenitors were highly conserved in their tetraploid hybrids. However, hybridization events were attributed to quantitative changes in UVR8 and ZTL/FKF1/LKP2 members. All PHR members underwent purifying selection. In addition, the transcript expression profiles of PHR genes in different tissue and in response to exogenous ABA, and abiotic stress conditions suggested their multiple biological significance. This study is helpful in understanding the molecular evolution characteristics of Brassica PHRs and lays the foundation for their functional characterization.
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23
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Wang R, Li Y, Gao M, Han M, Liu H. Genome-wide identification and characterization of the bHLH gene family and analysis of their potential relevance to chlorophyll metabolism in Raphanus sativus L. BMC Genomics 2022; 23:548. [PMID: 35915410 DOI: 10.1186/s12864-022-08782-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Green-fleshed radish (Raphanus sativus L.) is an economically important root vegetable of the Brassicaceae family, and chlorophyll accumulates in its root tissues. It was reported that the basic helix-loop-helix (bHLH) transcription factors play vital roles in the process of chlorophyll metabolism. Nevertheless, a comprehensive study on the bHLH gene family has not been performed in Raphanus sativus L. RESULTS In this study, a total of 213 Raphanus sativus L. bHLH (RsbHLH) genes were screened in the radish genome, which were grouped into 22 subfamilies. 204 RsbHLH genes were unevenly distributed on nine chromosomes, and nine RsbHLH genes were located on the scaffolds. Gene structure analysis showed that 25 RsbHLH genes were intron-less. Collineation analysis revealed the syntenic orthologous bHLH gene pairs between radish and Arabidopsis thaliana/Brassica rapa/Brassica oleracea. 162 RsbHLH genes were duplicated and retained from the whole genome duplication event, indicating that the whole genome duplication contributed to the expansion of the RsbHLH gene family. RNA-seq results revealed that RsbHLH genes had a variety of expression patterns at five development stages of green-fleshed radish and white-fleshed radish. In addition, the weighted gene co-expression network analysis confirmed four RsbHLH genes closely related to chlorophyll content. CONCLUSIONS A total of 213 RsbHLH genes were identified, and we systematically analyzed their gene structure, evolutionary and collineation relationships, conserved motifs, gene duplication, cis-regulatory elements and expression patterns. Finally, four bHLH genes closely involved in chlorophyll content were identified, which may be associated with the photosynthesis of the green-fleshed radish. The current study would provide valuable information for further functional exploration of RsbHLH genes, and facilitate clarifying the molecular mechanism underlying photosynthesis process in green-fleshed radish.
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Affiliation(s)
- Ruihua Wang
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China
| | - Yuanyuan Li
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China.
| | - Minggang Gao
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China
| | - Min Han
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China
| | - Huilian Liu
- Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China
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24
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Pelosi B. Developing a bioinformatics pipeline for comparative protein classification analysis. BMC Genom Data 2022; 23:43. [PMID: 35668373 PMCID: PMC9172112 DOI: 10.1186/s12863-022-01045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: data collection, unbalanced classification or labelling of the data.As an alternative, I propose the use of a bioinformatics pipeline to search for and classify information from protein databases. Hence, to evaluate the efficiency and accuracy of the pipeline, I focused on the carotenoid biosynthetic genes and developed a filtering approach to retrieve orthologs clusters in two well-studied plants that belong to the Brassicaceae family: Arabidopsis thaliana and Brassica rapa Pekinensis group. The result obtained has been compared with previous studies on carotenoid biosynthetic genes in B. rapa where phylogenetic analysis was conducted. RESULTS The developed bioinformatics pipeline relies on commercial software and multiple databeses including the use of phylogeny, Gene Ontology terms (GOs) and Protein Families (Pfams) at a protein level. Furthermore, the phylogeny is coupled with "population analysis" to evaluate the potential orthologs. All the steps taken together give a final table of potential orthologs. The phylogenetic tree gives a result of 43 putative orthologs conserved in B. rapa Pekinensis group. Different A. thaliana proteins have more than one syntenic ortholog as also shown in a previous finding (Li et al., BMC Genomics 16(1):1-11, 2015). CONCLUSIONS This study demonstrates that, when the biological features of proteins of interest are not specific, I can rely on a computational approach in filtering steps for classification purposes. The comparison of the results obtained here for the carotenoid biosynthetic genes with previous research confirmed the accuracy of the developed pipeline which can therefore be applied for filtering different types of datasets.
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Affiliation(s)
- Benedetta Pelosi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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25
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Al-Harrasi A, Behl T, Upadhyay T, Chigurupati S, Bhatt S, Sehgal A, Bhatia S, Singh S, Sharma N, Vijayabalan S, Palanimuthu VR, Das S, Kaur R, Aleya L, Bungau S. Targeting natural products against SARS-CoV-2. Environ Sci Pollut Res Int 2022; 29:42404-42432. [PMID: 35362883 PMCID: PMC8972763 DOI: 10.1007/s11356-022-19770-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/13/2022] [Indexed: 06/01/2023]
Abstract
The human coronavirus disease (COVID-19) pandemic is caused by a novel coronavirus; the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). Natural products, secondary metabolites show positive leads with antiviral and immunotherapy treatments using genomic studies in silico docking. In addition, it includes the action of a mechanism targeting the SARS-CoV-2. In this literature, we aimed to evaluate the antiviral movement of the NT-VRL-1 unique terpene definition to Human coronavirus (HCoV-229E). The effects of 19 hydrolysable tannins on the SARS-CoV-2 were therefore theoretically reviewed and analyzed utilising the molecular operating surroundings for their C-Like protease 3CLpro catalytic dyad residues Angiotensin converting enzyme-2 (MOE 09). Pedunculagin, tercatan, and castalin were detected as interacting strongly with SARS-receptor Cov-2's binding site and catalytic dyad (Cys145 and His41). SARS-CoV-2 methods of subunit S1 (ACE2) inhibit the interaction of the receiver with the s-protein once a drug molecule is coupled to the s-protein and prevent it from infecting the target cells in alkaloids. Our review strongly demonstrates the evidence that natural compounds and their derivatives can be used against the human coronavirus and serves as an area of research for future perspective.
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Affiliation(s)
- Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Birkat Al Mawz, Oman
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Tanuj Upadhyay
- Amity Institute of Pharmacy, Amity University, Gwalior, Madhya Pradesh, India
| | - Sridevi Chigurupati
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraidah, Kingdom of Saudi Arabia
| | - Shvetank Bhatt
- Amity Institute of Pharmacy, Amity University, Gwalior, Madhya Pradesh, India
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Center, University of Nizwa, Birkat Al Mawz, Oman
- School of Health Science, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Shantini Vijayabalan
- Faculty of Health and Medical Sciences, School of Pharmacy, Taylor's University, Subang Jaya, Kuala Lumpur, Malaysia
| | - Vasanth Raj Palanimuthu
- Department of Pharmaceutical Biotechnology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Suprava Das
- Department of Pharmacology, Faculty of Medicine, AIMST University, Semeling, Bedong, Kedah, Malaysia
| | - Rajwinder Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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Yang Y, Zhang K, Xiao Y, Zhang L, Huang Y, Li X, Chen S, Peng Y, Yang S, Liu Y, Cheng F. Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei (Rubus corchorifolius). Genomics Proteomics Bioinformatics 2022; 20:1106-1118. [PMID: 35643190 DOI: 10.1016/j.gpb.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022]
Abstract
Rubus corchorifolius (Shanmei or mountain berry, 2n = 14) is widely distributed in China, and its fruits possess high nutritional and medicinal values. Here, we reported a high-quality chromosome-scale genome assembly of Shanmei, with contig size of 215.69 Mb and 26,696 genes. Genome comparison among Rosaceae species showed that Shanmei and Fupenzi (Rubus chingii Hu) were most closely related, followed by blackberry (Rubus occidentalis), and that environmental adaptation-related genes were significantly expanded in the Shanmei genome. Further resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan, Hunan, Jiangxi, and Sichuan in China revealed that the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral population. Moreover, the Yunnan population underwent strong selection based on the nucleotide diversity, linkage disequilibrium, and historical effective population size analyses. Furthermore, genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways, indicating the genetic basis of adaptation of Shanmei to the local environment. The high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.
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Affiliation(s)
- Yinqing Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Ya Xiao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China; Biotechnology Research Center, Xiangxi Academy of Agricultural Sciences, Jishou 416000, China
| | - Lingkui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Yile Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Xing Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Shumin Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China
| | - Yansong Peng
- Lushan Botanical Garden, Chinese Academy of Sciences, Lushan 332900, China
| | - Shuhua Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China.
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China.
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Wu P, Zhang L, Zhang K, Yin Y, Liu A, Zhu Y, Fu Y, Sun F, Zhao S, Feng K, Xu X, Chen X, Cheng F, Li L. The adaptive evolution of Euryale ferox to the aquatic environment through paleo-hexaploidization. Plant J 2022; 110:627-645. [PMID: 35218099 PMCID: PMC9314984 DOI: 10.1111/tpj.15717] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/24/2022] [Accepted: 02/20/2022] [Indexed: 05/25/2023]
Abstract
Occupation of living space is one of the main driving forces of adaptive evolution, especially for aquatic plants whose leaves float on the water surface and thus have limited living space. Euryale ferox, from the angiosperm basal family Nymphaeaceae, develops large, rapidly expanding leaves to compete for space on the water surface. Microscopic observation found that the cell proliferation of leaves is almost completed underwater, while the cell expansion occurs rapidly after they grow above water. To explore the mechanism underlying the specific development of leaves, we performed sequences assembly and analyzed the genome and transcriptome dynamics of E. ferox. Through reconstruction of the three sub-genomes generated from the paleo-hexaploidization event in E. ferox, we revealed that one sub-genome was phylogenetically closer to Victoria cruziana, which also exhibits gigantic floating leaves. Further analysis revealed that while all three sub-genomes promoted the evolution of the specific leaf development in E. ferox, the genes from the sub-genome closer to V. cruziana contributed more to this adaptive evolution. Moreover, we found that genes involved in cell proliferation and expansion, photosynthesis, and energy transportation were over-retained and showed strong expression association with the leaf development stages, such as the expression divergence of SWEET orthologs as energy uploaders and unloaders in the sink and source leaf organs of E. ferox. These findings provide novel insights into the genome evolution through polyploidization, as well as the adaptive evolution regarding the leaf development accomplished through biased gene retention and expression sub-functionalization of multi-copy genes in E. ferox.
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Affiliation(s)
- Peng Wu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Lingkui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Yulai Yin
- Suzhou Academy of Agricultural ScienceSuzhou215000China
| | - Ailian Liu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Yue Zhu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Yu Fu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Fangfang Sun
- Suzhou Academy of Agricultural ScienceSuzhou215000China
| | - Shuping Zhao
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Kai Feng
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Xuewen Xu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Xuehao Chen
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Liangjun Li
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhou225000China
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28
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Zhang K, Yang Y, Wu J, Liang J, Chen S, Zhang L, Lv H, Yin X, Zhang X, Zhang Y, Zhang L, Zhang Y, Freeling M, Wang X, Cheng F. A cluster of transcripts identifies a transition stage initiating leafy head growth in heading morphotypes of Brassica. Plant J 2022; 110:688-706. [PMID: 35118736 PMCID: PMC9314147 DOI: 10.1111/tpj.15695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 05/10/2023]
Abstract
Leaf heading is an important and economically valuable horticultural trait in many vegetables. The formation of a leafy head is a specialized leaf morphogenesis characterized by the emergence of the enlarged incurving leaves. However, the transcriptional regulation mechanisms underlying the transition to leaf heading remain unclear. We carried out large-scale time-series transcriptome assays covering the major vegetative growth phases of two headingBrassica crops, Chinese cabbage and cabbage, with the non-heading morphotype Taicai as the control. A regulatory transition stage that initiated the heading process is identified, accompanied by a developmental switch from rosette leaf to heading leaf in Chinese cabbages. This transition did not exist in the non-heading control. Moreover, we reveal that the heading transition stage is also conserved in the cabbage clade. Chinese cabbage acquired through domestication a leafy head independently from the origins of heading in other cabbages; phylogenetics supports that the ancestor of all cabbages is non-heading. The launch of the transition stage is closely associated with the ambient temperature. In addition, examination of the biological activities in the transition stage identified the ethylene pathway as particularly active, and we hypothesize that this pathway was targeted for selection for domestication to form the heading trait specifically in Chinese cabbage. In conclusion, our findings on the transcriptome transition that initiated the leaf heading in Chinese cabbage and cabbage provide a new perspective for future studies of leafy head crops.
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Affiliation(s)
- Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Yinqing Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Shumin Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Lei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Xiaona Yin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Xin Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Yiyue Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Lingkui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Michael Freeling
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCAUSA
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agricultureand Rural Affairs, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijingChina
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Xiao Y, Li M, Wang J. The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus. BMC Plant Biol 2022; 22:103. [PMID: 35255818 PMCID: PMC8900393 DOI: 10.1186/s12870-022-03485-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Polyploidization promotes species formation and is widespread in angiosperms. Genome changes dramatically bring opportunities and challenges to plants after polyploidy. Methyl-CpG-Binding Domain (MBD) proteins can recognize and bind to methylation sites and they play an important role in the physiological process related to methylation in animals and plants. However, research on the influence of the allopolyploidization process on the MBD gene family is still lacking, so it is necessary to conduct a comprehensive analysis. RESULTS In this study, twenty-two, ten and eleven MBD genes were identified in the genome of allotetraploid B. napus and its diploid ancestors, B. rapa and B. oleracea, respectively. Based on the clades of the MBD gene in Arabidopsis, rice and maize, we divided the new phylogenetic tree into 8 clades. Among them, the true MBD genes in Brassica existed in only 5 clades. Clade IV and Clade VI were unique in term of MBD genes in dicotyledons. Ka/Ks calculations showed that MBD genes underwent purifying selection in Brassica and may retain genes through sequence or functional differentiation early in evolution. In the process of allopolyploidization, the number of MBD gene introns increased, and the protein motifs changed. The MBD proteins had their own special motifs in each clade, and the MBD domains were only conserved in their clades. At the same time, the MBD genes were expressed in flower, leaf, silique, and stem tissues, and the expression levels of the different genes were significantly different, while the tissue specificity was not obvious. The allopolyploidization process may increase the number of cis-acting elements and activate the transposable elements. During allopolyploidization, the expression pattern of the MBD gene changes, which may be regulated by cis-acting elements and transposable elements. The number imbalance of cis-acting elements and transposable elements in An and Cn subgenomes may also lead to biased An subgenome expression of the MBD gene in B. napus. CONCLUSIONS In this study, by evaluating the number, structure, phylogeny and expression of the MBD gene in B. napus and its diploid ancestors, we increased the understanding of MBD genes in allopolyploids and provided a reference for future analysis of allopolyploidization.
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Affiliation(s)
- Yafang Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Xu Y, Zhang H, Zhong Y, Jiang N, Zhong X, Zhang Q, Chai S, Li H, Zhang Z. Comparative genomics analysis of bHLH genes in cucurbits identifies a novel gene regulating cucurbitacin biosynthesis. Hortic Res 2022; 9:uhac038. [PMID: 35184192 PMCID: PMC9071377 DOI: 10.1093/hr/uhac038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/22/2022] [Accepted: 01/30/2022] [Indexed: 05/08/2023]
Abstract
The basic helix-loop-helix (bHLH) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, and have undergone significant expansion during land plant evolution by gene duplications. In cucurbit crops, several bHLH genes have been found to be responsible for the agronomic traits such as bitterness. However, the characterization of bHLH genes across the genomes of cucurbit species has not been reported, and how they have evolved and diverged remains largely unanswered. Here we identified 1160 bHLH genes in seven cucurbit crops and performed a comprehensive comparative genomics analysis. We determined orthologous and paralogous bHLH genes across cucurbit crops by syntenic analysis between or within species. Orthology and phylogenetic analysis of the tandem-duplicated bHLH genes in the Bt cluster which regulate the biosynthesis of cucurbitacins suggest that this cluster is derived from three ancestral genes after the cucurbit-common tetraploidization event. Interestingly, we identified a new conserved cluster paralogous to the Bt cluster that includes two tandem bHLH genes, and the evolutionary history and expression profiles of these two genes in the new cluster suggest the involvement of one gene (Brp) in the regulation of cucurbitacin biosynthesis in roots. Further biochemical and transgenic assays in melon hairy roots support the function of Brp. This study provides useful information for further investigating the functions of bHLH TFs and novel insights into the regulation of cucurbitacin biosynthesis in cucurbit crops and other plants.
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Affiliation(s)
- Yuanchao Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huimin Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yang Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Naiyu Jiang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyun Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiqi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sen Chai
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
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31
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Clark TJ, Schwender J. Elucidation of Triacylglycerol Overproduction in the C 4 Bioenergy Crop Sorghum bicolor by Constraint-Based Analysis. Front Plant Sci 2022; 13:787265. [PMID: 35251073 PMCID: PMC8892208 DOI: 10.3389/fpls.2022.787265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C4 biomass crop Sorghum bicolor (iTJC1414) along with a minimal model for photosynthetic CO2 assimilation, sucrose and TAG biosynthesis in C3 plants. Extending iTJC1414 to a four-cell diel model we simulate C4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.
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Affiliation(s)
- Teresa J. Clark
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Jorg Schwender
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY, United States
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32
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Li H, Wang S, Chai S, Yang Z, Zhang Q, Xin H, Xu Y, Lin S, Chen X, Yao Z, Yang Q, Fei Z, Huang S, Zhang Z. Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nat Commun 2022; 13:682. [PMID: 35115520 DOI: 10.1038/s41467-022-28362-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding. Increasing studies have suggested that single reference genome is insufficient to capture all variations in the genome. Here, the authors report a graph-based cucumber pan-genome by analyzing 12 chromosome-scale assemblies and reveal variations associated with agronomic traits and domestication.
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33
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Chen H, Wang T, He X, Cai X, Lin R, Liang J, Wu J, King G, Wang X. BRAD V3.0: an upgraded Brassicaceae database. Nucleic Acids Res 2022; 50:D1432-D1441. [PMID: 34755871 PMCID: PMC8728314 DOI: 10.1093/nar/gkab1057] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.
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Affiliation(s)
- Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Tianpeng Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Xiaoning He
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Graham King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
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Sun W, Li M, Wang J. Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors. Int J Mol Sci 2022; 23:614. [PMID: 35054810 DOI: 10.3390/ijms23020614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.
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35
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Liu L, Zhang K, Bai J, Lu J, Lu X, Hu J, Pan C, He S, Yuan J, Zhang Y, Zhang M, Guo Y, Wang X, Huang Z, Du Y, Cheng F, Li J. All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter. J Exp Bot 2022; 73:123-138. [PMID: 34490889 PMCID: PMC8730696 DOI: 10.1093/jxb/erab401] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The formation of locule gel is an important process in tomato and is a typical characteristic of berry fruit. In this study, we examined a natural tomato mutant that produces all-flesh fruit (AFF) in which the locule tissue remains in a solid state during fruit development. We constructed different genetic populations to fine-map the causal gene for this trait and identified SlMBP3 as the locus conferring the locule gel formation, which we rename as AFF. We determined the causal mutation as a 416-bp deletion in the promoter region of AFF, which reduces its expression dosage. Generally, this sequence is highly conserved among Solanaceae, as well as within the tomato germplasm. Using BC6 near-isogenic lines, we determined that the reduced expression dosage of AFF did not affect the normal development of seeds, whilst producing unique, non-liquefied locule tissue that was distinct from that of normal tomatoes in terms of metabolic components. Combined analysis using mRNA-seq and metabolomics indicated the importance of AFF in locule tissue liquefaction. Our findings provide insights into fruit-type differentiation in Solanaceae crops and also present the basis for future applications of AFF in tomato breeding programs.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kang Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinrui Bai
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinghua Lu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoxiao Lu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junling Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunyang Pan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shumin He
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiale Yuan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yiyue Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Min Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanmei Guo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoxuan Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zejun Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongchen Du
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Feng Cheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junming Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Lu YH, Alam I, Yang YQ, Yu YC, Chi WC, Chen SB, Chalhoub B, Jiang LX. Evolutionary Analysis of the YABBY Gene Family in Brassicaceae. Plants (Basel) 2021; 10:plants10122700. [PMID: 34961171 PMCID: PMC8704796 DOI: 10.3390/plants10122700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
The YABBY gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 YABBY genes were identified from 37 Brassicaceae genomes, of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these YABBY genes into six compact clades except for a YAB3-like gene identified in Aethionema arabicum. Seventeen Brassicaceae species each contained a complete set of six basic YABBY genes (i.e., 1 FIL, 1 YAB2, 1 YAB3, 1 YAB5, 1 INO and 1 CRC), while 20 others each contained a variable number of YABBY genes (5-25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate YABBY genes changed considerably according to plant species, as well as to YABBY gene type. These YABBY genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of YABBY genes in two Brassica species (B. rapa and B. oleracea). Our study provides valuable insights for understanding the evolutionary story of YABBY genes in Brassicaceae and for further functional characterization of each YABBY gene across the Brassicaceae species.
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Affiliation(s)
- Yun-Hai Lu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
| | - Intikhab Alam
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (I.A.); (Y.-Q.Y.)
| | - Yan-Qing Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (I.A.); (Y.-Q.Y.)
| | - Ya-Cen Yu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
| | - Wen-Chao Chi
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (W.-C.C.); (S.-B.C.)
| | - Song-Biao Chen
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (W.-C.C.); (S.-B.C.)
| | - Boulos Chalhoub
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
| | - Li-Xi Jiang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
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He D, Zhang D, Li T, Liu L, Zhou D, Kang L, Wu J, Liu Z, Yan M. Whole-Genome Identification and Comparative Expression Analysis of Anthocyanin Biosynthetic Genes in Brassica napus. Front Genet 2021; 12:764835. [PMID: 34868247 PMCID: PMC8636775 DOI: 10.3389/fgene.2021.764835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/11/2021] [Indexed: 12/05/2022] Open
Abstract
Anthocyanins contribute to most colors of plants and play protective roles in response to abiotic stresses. Brassica napus is widely cultivated worldwide as both an oilseed and a vegetable. However, only several high anthocyanin-containing cultivars have been reported, and the mechanisms of anthocyanin accumulation have not been well-elucidated in B. napus. Here, the phenotype, comparative whole-genome identification, and gene expression analysis were performed to investigate the dynamic change of the anthocyanin content and the gene expression patterns of anthocyanin biosynthetic genes (ABGs) in B. napus. A total of 152 ABGs were identified in the B. napus reference genome. To screen out the critical genes involved in anthocyanin biosynthesis and accumulation, the RNA-seq of young leaves of two B. napus lines with purple leaves (PL) or green leaves (GL), and their F1 progeny at 41, 91, and 101 days were performed to identify the differentially expressed genes. The comparative expression analysis of these ABGs indicated that the upregulation of TT8 together with its target genes (such as DFR, ANS, UFGT, and TT19) might promote the anthocyanin accumulation in PL at the early developmental stage (41–91 days). While the downregulation of those ABGs and anthocyanin degradation at the late developmental stage (91–101 days) might result in the decrease in anthocyanin accumulation. Our results would enhance the understanding of the regulatory network of anthocyanin dynamic accumulation in B. napus.
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Affiliation(s)
- Dan He
- School of Life Science, Hunan University of Science and Technology, Xiangtan, China.,Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Xiangtan, China
| | - Dawei Zhang
- School of Life Science, Hunan University of Science and Technology, Xiangtan, China.,Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Xiangtan, China
| | - Ting Li
- School of Life Science, Hunan University of Science and Technology, Xiangtan, China.,Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Xiangtan, China
| | - Lili Liu
- School of Life Science, Hunan University of Science and Technology, Xiangtan, China.,Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Xiangtan, China
| | - Dinggang Zhou
- School of Life Science, Hunan University of Science and Technology, Xiangtan, China.,Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Xiangtan, China
| | - Lei Kang
- Oilseed Research Institute, Hunan Agricultural University, Changsha, China
| | - Jinfeng Wu
- School of Life Science, Hunan University of Science and Technology, Xiangtan, China.,Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhongsong Liu
- Oilseed Research Institute, Hunan Agricultural University, Changsha, China
| | - Mingli Yan
- School of Life Science, Hunan University of Science and Technology, Xiangtan, China.,Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Xiangtan, China
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Zhang X, Liu T, Wang J, Wang P, Qiu Y, Zhao W, Pang S, Li X, Wang H, Song J, Zhang W, Yang W, Sun Y, Li X. Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes. Mol Plant 2021; 14:2032-2055. [PMID: 34384905 DOI: 10.1016/j.molp.2021.08.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/27/2021] [Accepted: 08/05/2021] [Indexed: 05/22/2023]
Abstract
Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear mechanisms. Raphanus is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and introgression. Here, we report the de novo sequence assemblies for 11 genomes covering most of the typical sub-species and varieties of domesticated, wild and weedy radishes from East Asia, South Asia, Europe, and America. Divergence among the species, sub-species, and South/East Asian types coincided with Quaternary glaciations. A genus-level pan-genome was constructed with family-based, locus-based, and graph-based methods, and whole-genome comparisons revealed genetic variations ranging from single-nucleotide polymorphisms (SNPs) to inversions and translocations of whole ancestral karyotype (AK) blocks. Extensive gene flow occurred between wild, weedy, and domesticated radishes. High frequencies of genome reshuffling, biased retention, and large-fragment translocation have shaped the genomic diversity. Most variety-specific gene-rich blocks showed large structural variations. Extensive translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich islands. Disease resistance genes mostly resided on specific and dispensable loci. Variations causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive evolution. This study provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improvement of radish crops, biological control of weeds, and protection of wild species' germplasms.
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Affiliation(s)
- Xiaohui Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tongjin Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Horticulture, Jinling Institute of Technology, Nanjing 210038, China
| | - Jinglei Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Peng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Pang
- Berry Genomics Corporation, Beijing 100015, China
| | - Xiaoman Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiping Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangping Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenlin Zhang
- Berry Genomics Corporation, Beijing 100015, China
| | - Wenlong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuyan Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xixiang Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Huang H, Miao Y, Zhang Y, Huang L, Cao J, Lin S. Comprehensive Analysis of Arabinogalactan Protein-Encoding Genes Reveals the Involvement of Three BrFLA Genes in Pollen Germination in Brassica rapa. Int J Mol Sci 2021; 22:ijms222313142. [PMID: 34884948 PMCID: PMC8658186 DOI: 10.3390/ijms222313142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 02/03/2023] Open
Abstract
Arabinogalactan proteins (AGPs) are a superfamily of hydroxyproline-rich glycoproteins that are massively glycosylated, widely implicated in plant growth and development. No comprehensive analysis of the AGP gene family has been performed in Chinese cabbage (Brassica rapa ssp. chinensis). Here, we identified a total of 293 putative AGP-encoding genes in B. rapa, including 25 classical AGPs, three lysine-rich AGPs, 30 AG-peptides, 36 fasciclin-like AGPs (FLAs), 59 phytocyanin-like AGPs, 33 xylogen-like AGPs, 102 other chimeric AGPs, two non-classical AGPs and three AGP/extensin hybrids. Their protein structures, phylogenetic relationships, chromosomal location and gene duplication status were comprehensively analyzed. Based on RNA sequencing data, we found that 73 AGP genes were differentially expressed in the floral buds of the sterile and fertile plants at least at one developmental stage in B. rapa, suggesting a potential role of AGPs in male reproductive development. We further characterized BrFLA2, BrFLA28 and BrFLA32, three FLA members especially expressed in anthers, pollen grains and pollen tubes. BrFLA2, BrFLA28 and BrFLA32 are indispensable for the proper timing of pollen germination under high relative humidity. Our study greatly extends the repertoire of AGPs in B. rapa and reveals a role for three members of the FLA subfamily in pollen germination.
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Affiliation(s)
- Huiting Huang
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou 325000, China; (H.H.); (Y.M.); (Y.Z.)
| | - Yingjing Miao
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou 325000, China; (H.H.); (Y.M.); (Y.Z.)
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China;
| | - Yuting Zhang
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou 325000, China; (H.H.); (Y.M.); (Y.Z.)
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China;
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China;
- Correspondence: (J.C.); (S.L.)
| | - Sue Lin
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou 325000, China; (H.H.); (Y.M.); (Y.Z.)
- Biomedicine Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325000, China
- Correspondence: (J.C.); (S.L.)
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Hu M, Li M, Wang J. Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors. Genes (Basel) 2021; 12:genes12121848. [PMID: 34946800 PMCID: PMC8701781 DOI: 10.3390/genes12121848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.
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Affiliation(s)
- Meimei Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.H.); (M.L.)
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.H.); (M.L.)
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (M.H.); (M.L.)
- Correspondence:
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Han F, Zhang X, Yang L, Zhuang M, Zhang Y, Liu Y, Li Z, Wang Y, Fang Z, Ji J, Lv H. Genome-wide characterization and analysis of the anthocyanin biosynthetic genes in Brassica oleracea. Planta 2021; 254:92. [PMID: 34633541 DOI: 10.1007/s00425-021-03746-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
From Brassica oleracea genome, 88 anthocyanin biosynthetic genes were identified. They expanded via whole-genome or tandem duplication and showed significant expression differentiation. Functional characterization revealed BoMYB113.1 as positive and BoMYBL2.1 as negative regulators responsible for anthocyanin accumulation. Brassica oleracea produces various health-promoting phytochemicals, including glucosinolates, carotenoids, and vitamins. Despite the anthocyanin biosynthetic pathways in the model plant Arabidopsis thaliana being well characterized, little is known about the genetic basis of anthocyanin biosynthesis in B. oleracea. In this study, we identified 88 B. oleracea anthocyanin biosynthetic genes (BoABGs) representing homologs of 46 Arabidopsis anthocyanin biosynthetic genes (AtABGs). Most anthocyanin biosynthetic genes, having expanded via whole-genome duplication and tandem duplication, retained more than one copy in B. oleracea. Expression analysis revealed diverse expression patterns of BoABGs in different tissues, and BoABG duplications showed significant expression differentiation. Additional expression analysis and functional characterization revealed that the positive regulator BoMYB113.1 and negative regulator BoMYBL2.1 may be key genes responsible for anthocyanin accumulation in red cabbage and ornamental kale by upregulating the expression of structural genes. This study paves the way for a better understanding of anthocyanin biosynthetic genes in B. oleracea and should promote breeding for anthocyanin content.
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Affiliation(s)
- Fengqing Han
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Xiaoli Zhang
- Tianjin Kernel Vegetable Research Institute, State Key Laboratory of Vegetable Germplasm Innovation, Jinjing Road, Xiqing District, Tianjin, 300384, China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Yumei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Zhansheng Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Jialei Ji
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China.
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Akhter N, Aqeel M, Hameed M, Sakit Alhaithloul HA, Alghanem SM, Shahnaz MM, Hashem M, Alamri S, Khalid N, Al-Zoubi OM, Iqbal MF, Masood T, Noman A. Foliar architecture and physio-biochemical plasticity determines survival of Typha domingensis pers. Ecotypes in nickel and salt affected soil. Environ Pollut 2021; 286:117316. [PMID: 33990051 DOI: 10.1016/j.envpol.2021.117316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/23/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Six ecotypes of Typha domingensis Pers. Jahlar (E1), Sheikhupura (E2), Sahianwala (E3), Gatwala (E4), Treemu (E5) and Knotti (E6) from different ecological regions were collected to evaluate the leaf anatomical and biochemical attributes under different levels of salinity and nickel stress viz; L0 (control), L1 (100 mM + 50 mg kg-1), L2 (200 mM + 100 mg kg-1) and L3 (300 mM + 150 mg kg-1). Presence of salt and Ni in rooting medium consistently affected growth, anatomical and physio-biochemical attributes in all Typha ecotypes. Discrete anatomical modifications among ecotypes such as reduced leaf thickness, increased parenchyma area, metaxylem cell area, aerenchyma formation and improved metaxylem vessels were recorded with increasing dose of salt and Ni. The minimum anatomical damages were recorded in E1 and E6 ecotypes. In all ecotypes, progressive perturbations in ionic homeostasis (Na+, K+, Cl-, N) due to salt and metal toxicity were evident along with reduction in photosynthetic pigments. Maximum enhancement in Catalase (CAT), Superoxide dismutase (SOD), Peroxidase (POD) and modulated Malondialdehyde (MDA) activity was recorded in E1 and E6 as compared to other ecotypes. Accumulation of large amounts of metabolites such as total soluble sugars, total free amino acids content in Jahlar, Knotti, Treemu and Sahianawala ecotypes under different levels of salt and Ni prevented cellular damages in T. domingensis Pers. The correlation analysis exhibited a close relationship among different levels of salinity and Ni with various plant attributes. PCA-Biplot verified our correlational analysis among various attributes of Typha ecotypes. An obvious separation of Typha characters in response to different salinity and Ni levels was exhibited by PC1. We recommend that genetic potential of T. domingensis Pers. To grow under salt and Ni stresses must be investigated and used for phytoremediation and reclamation of contaminated soil.
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Affiliation(s)
- Noreen Akhter
- Department of Botany, Government College Women University, Faisalabad, 38000, Pakistan
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
| | - Mansoor Hameed
- Department of Botany, University of Agriculture, Faisalabad, 38040, Pakistan
| | | | | | | | - Mohamed Hashem
- Department of Biology, Faculty of Science, King Khalid University, Abha, 61413, Saudi Arabia; Assiut University, Faculty of Science, Botany and Microbiology Department, Assiut, 71516, Egypt
| | - Saad Alamri
- Department of Biology, Faculty of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Noreen Khalid
- Department of Botany, Government College Women University Sialkot, Sialkot, Pakistan
| | | | - Muhammad Faisal Iqbal
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hafei, Anhui, PR China
| | - Tayyaba Masood
- Department of Environmental Sciences, Lahore College for Women University, Lahore, Pakistan
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, Pakistan.
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Babula-Skowrońska D. Functional divergence of Brassica napus BnaABI1 paralogs in the structurally conserved PP2CA gene subfamily of Brassicaceae. Genomics 2021; 113:3185-97. [PMID: 34182082 DOI: 10.1016/j.ygeno.2021.06.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/26/2021] [Accepted: 06/23/2021] [Indexed: 11/21/2022]
Abstract
Group A PP2C (PP2CA) genes form a gene subfamily whose members play an important role in regulating many biological processes by dephosphorylation of target proteins. In this study we examined the effects of evolutionary changes responsible for functional divergence of BnaABI1 paralogs in Brassica napus against the background of the conserved PP2CA gene subfamily in Brassicaceae. We performed comprehensive phylogenetic analyses of 192 PP2CA genes in 15 species in combination with protein structure homology modeling. Fundamentally, the number of PP2CA genes remained relatively constant in these taxa, except in the Brassica genus and Camelina sativa. The expansion of this gene subfamily in these species has resulted from whole genome duplication. We demonstrated a high degree of structural conservation of the PP2CA genes, with a few minor variations between the different PP2CA groups. Furthermore, the pattern of conserved sequence motifs in the PP2CA proteins and their secondary and 3D structures revealed strong conservation of the key ion-binding sites. Syntenic analysis of triplicated regions including ABI1 paralogs revealed significant structural rearrangements of the Brassica genomes. The functional and syntenic data clearly show that triplication of BnaABI1 in B. napus has had an impact on its functions, as well as the positions of adjacent genes in the corresponding chromosomal regions. The expression profiling of BnaABI1 genes showed functional divergence, i.e. subfunctionalization, potentially leading to neofunctionalization. These differences in expression are likely due to changes in the promoters of the BnaABI1 paralogs. Our results highlight the complexity of PP2CA gene subfamily evolution in Brassicaceae.
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Cai X, Chang L, Zhang T, Chen H, Zhang L, Lin R, Liang J, Wu J, Freeling M, Wang X. Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa. Genome Biol 2021; 22:166. [PMID: 34059118 PMCID: PMC8166115 DOI: 10.1186/s13059-021-02383-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/20/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes. RESULTS Herein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes. Among the genes that derive from WGT, 13.42% of polyploidy-derived genes accumulate more transposable elements and non-synonymous mutations than other genes during individual genome evolution. We denote such genes as being "flexible." We construct the Brassica rapa ancestral genome and observe the continuing influence of the dominant subgenome on intraspecific diversification in B. rapa. The gene flexibility is biased to the more fractionated subgenomes (MFs), in contrast to the more intact gene content of the dominant LF (least fractionated) subgenome. Furthermore, polyploidy-derived flexible syntenic genes are implicated in the response to stimulus and the phytohormone auxin; this may reflect adaptation to the environment. Using an integrated graph-based genome, we investigate the structural variation (SV) landscapes in 524 B. rapa genomes. We observe that SVs track morphotype domestication. Four out of 266 candidate genes for Chinese cabbage domestication are speculated to be involved in the leafy head formation. CONCLUSIONS This pan-genome uncovers the possible contributions of allopolyploidization on intraspecific diversification and the possible and underexplored role of SVs in favorable trait domestication. Collectively, our work serves as a rich resource for genome-based B. rapa improvement.
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Affiliation(s)
- Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China
| | - Lichun Chang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China
| | - Tingting Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China
| | - Haixu Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China
| | - Lei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing, 100081, China.
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Li P, Su T, Zhao X, Wang W, Zhang D, Yu Y, Bayer PE, Edwards D, Yu S, Zhang F. Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson. Plant Biotechnol J 2021; 19:966-976. [PMID: 33283404 PMCID: PMC8131043 DOI: 10.1111/pbi.13522] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/11/2020] [Accepted: 12/01/2020] [Indexed: 05/10/2023]
Abstract
Brassica rapa displays a wide range of morphological diversity which is exploited for a variety of food crops. Here we present a high-quality genome assembly for pak choi (Brassica rapa L. subsp. chinensis), an important non-heading leafy vegetable, and comparison with the genomes of heading type Chinese cabbage and the oilseed form, yellow sarson. Gene presence-absence variation (PAV) and genomic structural variations (SV) were identified, together with single nucleotide polymorphisms (SNPs). The structure and expression of genes for leaf morphology and flowering were compared between the three morphotypes revealing candidate genes for these traits in B. rapa. The pak choi genome assembly and its comparison with other B. rapa genome assemblies provides a valuable resource for the genetic improvement of this important vegetable crop and as a model to understand the diversity of morphological variation across Brassica species.
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Affiliation(s)
- Peirong Li
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
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Calderwood A, Hepworth J, Woodhouse S, Bilham L, Jones DM, Tudor E, Ali M, Dean C, Wells R, Irwin JA, Morris RJ. Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars. Quant Plant Biol 2021; 2:e4. [PMID: 37077206 PMCID: PMC10095958 DOI: 10.1017/qpb.2021.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 05/03/2023]
Abstract
Comparative transcriptomics can be used to translate an understanding of gene regulatory networks from model systems to less studied species. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. We find that different curve registration functions are required for different genes, indicating that there is no single common 'developmental time' between Arabidopsis and B. rapa. A detailed comparison between Arabidopsis and B. rapa and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa and highlights the importance of registration methods for the comparison of developmental gene expression data.
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Affiliation(s)
- Alexander Calderwood
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Jo Hepworth
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Shannon Woodhouse
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Lorelei Bilham
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - D. Marc Jones
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
- VIB-UGent Centre for Plant Systems Biology, Gent, Belgium
| | - Eleri Tudor
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Mubarak Ali
- Bangladesh Agricultural Research Institute, Gazipur, Bangladesh
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Rachel Wells
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Judith A. Irwin
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Richard J. Morris
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
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Wang R, Han T, Sun J, Xu L, Fan J, Cao H, Liu C. Genome-wide identification and characterization of the OFP gene family in Chinese cabbage ( Brassica rapa L. ssp. pekinensis). PeerJ 2021; 9:e10934. [PMID: 33717690 PMCID: PMC7938782 DOI: 10.7717/peerj.10934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/21/2021] [Indexed: 11/20/2022] Open
Abstract
Ovate family proteins (OFPs) are a class of proteins with a conserved OVATE domain that contains approximately 70 amino acid residues. OFP proteins are plant-specific transcription factors that participate in regulating plant growth and development and are widely distributed in many plants. Little is known about OFPs in Brassica rapa to date. We identified 29 OFP genes in Brassica rapa and found that they were unevenly distributed on 10 chromosomes. Intron gain events may have occurred during the structural evolution of BraOFP paralogues. Syntenic analysis verified Brassica genome triplication, and whole genome duplication likely contributed to the expansion of the OFP gene family. All BraOFP genes had light responsive- and phytohormone-related cis-acting elements. Expression analysis from RNA-Seq data indicated that there were obvious changes in the expression levels of six OFP genes in the Brassica rapa hybrid, which may contribute to the formation of heterosis. Finally, we found that the paralogous genes had different expression patterns among the hybrid and its parents. These results provide the theoretical basis for the further analysis of the biological functions of OFP genes across the Brassica species.
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Affiliation(s)
- Ruihua Wang
- Biological and Agricultural College, Weifang University, Weifang, China
| | - Taili Han
- Vegetable Research Institute, Weifang Academy of Agricultural Sciences, Weifang, China
| | - Jifeng Sun
- Vegetable Research Institute, Weifang Academy of Agricultural Sciences, Weifang, China
| | - Ligong Xu
- Vegetable Research Institute, Weifang Academy of Agricultural Sciences, Weifang, China
| | - Jingjing Fan
- Biological and Agricultural College, Weifang University, Weifang, China
| | - Hui Cao
- Biological and Agricultural College, Weifang University, Weifang, China
| | - Chunxiang Liu
- Biological and Agricultural College, Weifang University, Weifang, China
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Tian P, Zhang X, Xia R, Liu Y, Wang M, Li B, Liu T, Shi J, Wing RA, Meyers BC, Chen M. Evolution and diversification of reproductive phased small interfering RNAs in Oryza species. New Phytol 2021; 229:2970-2983. [PMID: 33111313 DOI: 10.1111/nph.17035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/12/2020] [Indexed: 05/20/2023]
Abstract
In grasses, two types of phased, small interfering RNAs (phasiRNAs) are expressed largely in young, developing anthers. They are 21 or 24 nucleotides (nt) in length and are triggered by miR2118 or miR2275, respectively. However, most of their functions and activities are not fully understood. We performed comparative genomic analysis of their source loci (PHAS) in five Oryza genomes and combined this with analysis of high-throughput sRNA and degradome datasets. In total, we identified 8216 21-PHAS and 626 24-PHAS loci. Local tandem and segmental duplications mainly contributed to the expansion and supercluster distribution of the 21-PHAS loci. Despite their relatively conserved genomic positions, PHAS sequences diverged rapidly, except for the miR2118/2275 target sites, which were under strong selection for conservation. We found that 21-nt phasiRNAs with a 5'-terminal uridine (U) demonstrated cis-cleavage at PHAS precursors, and these cis-acting sites were also variable among close species. miR2118 could trigger phasiRNA production from its own antisense transcript and the derived phasiRNAs might reversibly regulate miR2118 precursors. We hypothesised that successful initiation of phasiRNA biogenesis is conservatively maintained, while phasiRNA products diverged quickly and are not individually conserved. In particular, phasiRNA production is under the control of multiple reciprocal regulation mechanisms.
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Affiliation(s)
- Peng Tian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xuemei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Meijiao Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Bo Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tieyan Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Shi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Blake C Meyers
- Division of Plant Sciences, 52 Agriculture Laboratory, University of Missouri, Columbia, Missouri, 65211, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
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Restrepo-Montoya D, McClean PE, Osorno JM. Orthology and synteny analysis of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. BMC Genomics 2021; 22:113. [PMID: 33568053 PMCID: PMC7874474 DOI: 10.1186/s12864-021-07384-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses directly involve plasma membrane receptor proteins known as receptor-like kinases and receptor-like proteins. Evaluating the homology relations among RLK and RLP for seven legume species, and exploring their presence among synteny blocks allow an increased understanding of evolutionary relations, physical position, and chromosomal distribution in related species and their shared roles in stress responses. RESULTS Typically, a high proportion of RLK and RLP legume proteins belong to orthologous clusters, which is confirmed in this study, where between 66 to 90% of the RLKs and RLPs per legume species were classified in orthologous clusters. One-third of the evaluated syntenic blocks had shared RLK/RLP genes among both legumes and non-legumes. Among the legumes, between 75 and 98% of the RLK/RLP were present in syntenic blocks. The distribution of chromosomal segments between Phaseolus vulgaris and Vigna unguiculata, two species that diverged ~ 8 mya, were highly similar. Among the RLK/RLP synteny clusters, seven experimentally validated resistance RLK/RLP genes were identified in syntenic blocks. The RLK resistant genes FLS2, BIR2, ERECTA, IOS1, and AtSERK1 from Arabidopsis and SLSERK1 from Solanum lycopersicum were present in different pairwise syntenic blocks among the legume species. Meanwhile, only the LYM1- RLP resistant gene from Arabidopsis shared a syntenic blocks with Glycine max. CONCLUSIONS The orthology analysis of the RLK and RLP suggests a dynamic evolution in the legume family, with between 66 to 85% of RLK and 83 to 88% of RLP belonging to orthologous clusters among the species evaluated. In fact, for the 10-species comparison, a lower number of singleton proteins were reported among RLP compared to RLK, suggesting that RLP positions are more physically conserved compared to RLK. The identification of RLK and RLP genes among the synteny blocks in legumes revealed multiple highly conserved syntenic blocks on multiple chromosomes. Additionally, the analysis suggests that P. vulgaris is an appropriate anchor species for comparative genomics among legumes.
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Affiliation(s)
- Daniel Restrepo-Montoya
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58108-6050, USA.
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
| | - Phillip E McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58108-6050, USA.
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
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Li Y, Liu GF, Ma LM, Liu TK, Zhang CW, Xiao D, Zheng HK, Chen F, Hou XL. A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. Hortic Res 2020; 7:212. [PMID: 33372175 PMCID: PMC7769993 DOI: 10.1038/s41438-020-00449-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/28/2020] [Accepted: 12/09/2020] [Indexed: 05/12/2023]
Abstract
Non-heading Chinese cabbage (NHCC) is an important leafy vegetable cultivated worldwide. Here, we report the first high-quality, chromosome-level genome of NHCC001 based on PacBio, Hi-C, and Illumina sequencing data. The assembled NHCC001 genome is 405.33 Mb in size with a contig N50 of 2.83 Mb and a scaffold N50 of 38.13 Mb. Approximately 53% of the assembled genome is composed of repetitive sequences, among which long terminal repeats (LTRs, 20.42% of the genome) are the most abundant. Using Hi-C data, 97.9% (396.83 Mb) of the sequences were assigned to 10 pseudochromosomes. Genome assessment showed that this B. rapa NHCC001 genome assembly is of better quality than other currently available B. rapa assemblies and that it contains 48,158 protein-coding genes, 99.56% of which are annotated in at least one functional database. Comparative genomic analysis confirmed that B. rapa NHCC001 underwent a whole-genome triplication (WGT) event shared with other Brassica species that occurred after the WGD events shared with Arabidopsis. Genes related to ascorbic acid metabolism showed little variation among the three B. rapa subspecies. The numbers of genes involved in glucosinolate biosynthesis and catabolism were higher in NHCC001 than in Chiifu and Z1, due primarily to tandem duplication. The newly assembled genome will provide an important resource for research on B. rapa, especially B. rapa ssp. chinensis.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gao-Feng Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li-Ming Ma
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Tong-Kun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chang-Wei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Kun Zheng
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Fei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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