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He S, Xu B, Chen S, Li G, Zhang J, Xu J, Wu H, Li X, Yang Z. Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome. BMC Genomics 2024; 25:384. [PMID: 38637729 PMCID: PMC11027378 DOI: 10.1186/s12864-024-10278-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear. RESULTS We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species. CONCLUSIONS These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.
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Affiliation(s)
- Shuilian He
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Bin Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Siyun Chen
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Gengyun Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Jie Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Junqiang Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Hang Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Xuejiao Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
| | - Zhengan Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
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Cai H, Xu R, Tian P, Zhang M, Zhu L, Yin T, Zhang H, Liu X. Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom. Int J Mol Sci 2023; 25:257. [PMID: 38203426 PMCID: PMC10778623 DOI: 10.3390/ijms25010257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687-152,759 bp in length. Each genome contains 126-132 genes, including 81-87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61-64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.
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Affiliation(s)
| | | | | | | | | | - Tuo Yin
- Key Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (H.C.); (R.X.); (P.T.); (M.Z.); (L.Z.); (T.Y.)
| | - Hanyao Zhang
- Key Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (H.C.); (R.X.); (P.T.); (M.Z.); (L.Z.); (T.Y.)
| | - Xiaozhen Liu
- Key Laboratory of Conservation and Utilization of Southwest Mountain Forest Resources, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (H.C.); (R.X.); (P.T.); (M.Z.); (L.Z.); (T.Y.)
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Li X, Li M, Li W, Zhou J, Han Q, Lu W, Luo Q, Zhu S, Xiong A, Tan G, Zheng Y. Comparative Analysis of the Complete Mitochondrial Genomes of Apium graveolens and Apium leptophyllum Provide Insights into Evolution and Phylogeny Relationships. Int J Mol Sci 2023; 24:14615. [PMID: 37834070 PMCID: PMC10572446 DOI: 10.3390/ijms241914615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The genus Apium, belonging to the family Apiaceae, comprises roughly 20 species. Only two species, Apium graveolens and Apium leptophyllum, are available in China and are both rich in nutrients and have favorable medicinal properties. However, the lack of genomic data has severely constrained the study of genetics and evolution in Apium plants. In this study, Illumina NovaSeq 6000 and Nanopore sequencing platforms were employed to identify the mitochondrial genomes of A. graveolens and A. leptophyllum. The complete lengths of the mitochondrial genomes of A. graveolens and A. leptophyllum were 263,017 bp and 260,164 bp, respectively, and contained 39 and 36 protein-coding genes, five and six rRNA genes, and 19 and 20 tRNA genes. Consistent with most angiosperms, both A. graveolens and A. leptophyllum showed a preference for codons encoding leucine (Leu). In the mitochondrial genome of A. graveolens, 335 SSRs were detected, which is higher than the 196 SSRs found in the mitochondrial genome of A. leptophyllum. Studies have shown that the most common RNA editing type is C-to-U, but, in our study, both A. graveolens and A. leptophyllum exhibited the U-C editing type. Furthermore, the transfer of the mitochondrial genomes of A. graveolens and A. leptophyllum into the chloroplast genomes revealed homologous sequences, accounting for 8.14% and 4.89% of the mitochondrial genome, respectively. Lastly, in comparing the mitochondrial genomes of 29 species, it was found that A. graveolens, A. leptophyllum, and Daucus carota form a sister group with a support rate of 100%. Overall, this investigation furnishes extensive insights into the mitochondrial genomes of A. graveolens and A. leptophyllum, thereby enhancing comprehension of the traits and evolutionary patterns within the Apium genus. Additionally, it offers supplementary data for evolutionary and comparative genomic analyses of other species within the Apiaceae family.
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Affiliation(s)
- Xiaoyan Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Weilong Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Jin Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Qiuju Han
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Qin Luo
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Q.L.); (S.Z.)
| | - Shunhua Zhu
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Q.L.); (S.Z.)
| | - Aisheng Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing 611130, China;
| | - Guofei Tan
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Q.L.); (S.Z.)
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
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Zhao M, Zhang J, Yang C, Cui Z, Chen L. Identification of QTLs and Putative Candidate Genes for Plant Architecture of Lotus Revealed by Regional Association Mapping. PLANTS (BASEL, SWITZERLAND) 2023; 12:1221. [PMID: 36986910 PMCID: PMC10051333 DOI: 10.3390/plants12061221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/26/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The lotus (Nelumbo Adans.) is one of the most economically relevant ornamental aquatic plants. Plant architecture (PA) is an important trait for lotus classification, cultivation, breeding, and applications. However, the underlying genetic and molecular basis controlling PA remains poorly understood. In this study, an association study for PA-related traits was performed with 93 genome-wide microsatellite markers (simple sequence repeat, SSR) and 51 insertion-deletion (InDel) markers derived from the candidate regions using a panel of 293 lotus accessions. Phenotypic data analysis of the five PA-related traits revealed a wide normal distribution and high heritability from 2013 to 2016, which indicated that lotus PA-related traits are highly polygenic traits. The population structure (Q-matrix) and the relative kinships (K-matrix) of the association panels were analyzed using 93 SSR markers. The mixed linear model (MLM) taking Q-matrix and K-matrix into account was used to estimate the association between markers and the traits. A total of 26 markers and 65 marker-trait associations were identified by considering associations with p < 0.001 and Q < 0.05. Based on the significant markers, two QTLs on Chromosome 1 were identified, and two candidate genes were preliminarily determined. The results of our study provided useful information for the lotus breeding aiming at different PA phenotypes using a molecular-assisted selection (MAS) method and also laid the foundation for the illustration of the molecular mechanism underlying the major QTL and key markers associated with lotus PA.
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Affiliation(s)
- Mei Zhao
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Jibin Zhang
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Chuxuan Yang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhenhua Cui
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Longqing Chen
- Southwest Landscape Architecture Engineering Research Center (National Forestry and Grassland Administration), Southwest Forestry University, Kunming 650224, China
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Studies on Lotus Genomics and the Contribution to Its Breeding. Int J Mol Sci 2022; 23:ijms23137270. [PMID: 35806274 PMCID: PMC9266308 DOI: 10.3390/ijms23137270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
Lotus (Nelumbo nucifera), under the Nelumbonaceae family, is one of the relict plants possessing important scientific research and economic values. Because of this, much attention has been paid to this species on both its biology and breeding among the scientific community. In the last decade, the genome of lotus has been sequenced, and several high-quality genome assemblies are available, which have significantly facilitated functional genomics studies in lotus. Meanwhile, re-sequencing of the natural and genetic populations along with different levels of omics studies have not only helped to classify the germplasm resources but also to identify the domestication of selected regions and genes controlling different horticultural traits. This review summarizes the latest progress of all these studies on lotus and discusses their potential application in lotus breeding.
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Zhang J, Huang H, Qu C, Meng X, Meng F, Yao X, Wu J, Guo X, Han B, Xing S. Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.). PLANTA 2021; 255:26. [PMID: 34940902 DOI: 10.1007/s00425-021-03812-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
The Albizia julibrissin chloroplasts have a classical chloroplast genome structure, containing 93 coding genes and 34 non-coding genes. Our research provides basic data for plant phylogenetic evolutionary studies. There is limited genomic information available for the important Chinese herb Albizia julibrissin Durazz. In this study, we constructed the chloroplast (Cp) genome of A. julibrissin. The length of the assembled Cp genome was 175,922 bp consisting of four conserved regions: a 5145 bp small single-copy (SSC) region, a 91,323 bp large single-copy (LSC) region, and two identical length-inverted repeat (IR) regions (39,725 bp). This Cp genome included 34 non-coding RNAs and 93 unique genes, the former contains 30 transfer and 4 ribosomal RNA genes. Gene annotation indicated some of the coding genes (82) in the A. julibrissin Cp genome classified in the Leguminosae family, with some to other related families (11). The results show that low GC content (36.9%) and codon bias towards A- or T-terminal codons may affect the frequency of gene codon usage. The sequence analysis identified 30 forward, 18 palindrome, and 1 reverse repeat > 30 bp length, and 149 simple sequence repeats (SSR). Fifty-five RNA editing sites in the Cp of A. julibrissin were predicted, most of which are C-to-U conversions. Analysis of the reverse repeat expansion or contraction and divergence area between several species, including A. julibrissin, was performed. The phylogenetic tree revealed that A. julibrissin was most closely related to Albizia odoratissima and Albizia bracteata, followed by Samanea saman, forming an evolutionary branch with Mimosa pudica and Leucaena trichandra. The research results are helpful for breeding and genetic improvement of A. julibrissin, and also provide valuable information for understanding the evolution of this plant.
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Affiliation(s)
- Jing Zhang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Huizhen Huang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, 421008, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-Aging, Chinese Herbal Medicine, Fuyang Normal University, Fuyang, 236037, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, Minneapolis, 55108, USA
| | - Fei Meng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiaoyan Yao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China
| | - Xiaohu Guo
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Bangxing Han
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, West Anhui University, Lu'an, 237012, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China.
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, 230012, China.
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Characterization of Genomic Variation from Lotus (Nelumbo Adans.) Mutants with Wide and Narrow Tepals. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Compared with rose, chrysanthemum, and water lily, the absence of short-wide and long-narrow tepals of ornamental lotus (Nelumbo Adans.) limits the commercial value of flowers. In this study, the genomes of two groups of lotus mutants with wide-short and narrow-long tepals were resequenced to uncover the genomic variation and candidate genes associated with tepal shape. In group NL (short for N. lutea, containing two mutants and one control of N. lutea), 716,656 single nucleotide polymorphisms (SNPs) and 221,688 insertion-deletion mutations (Indels) were obtained, while 639,953 SNPs and 134,6118 Indels were obtained in group WSH (short for ‘Weishan Hong’, containing one mutant and two controls of N. nucifera ‘Weishan Hong’). Only a small proportion of these SNPs and Indels was mapped to exonic regions of genome: 1.92% and 0.47%, respectively, in the NL group, and 1.66% and 0.48%, respectively, in the WSH group. Gene Ontology (GO) analysis showed that out of 4890 (NL group) and 1272 (WSH group) annotated variant genes, 125 and 62 genes were enriched (Q < 0.05), respectively. Additionally, in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 104 genes (NL group) and 35 genes (WSH group) were selected (p < 0.05). Finally, there were 306 candidate genes that were sieved to determine the development of tepal shape in lotus plants. It will be an essential reference for future identification of tepal-shaped control genes in lotus plants. This is the first comprehensive report of genomic variation controlling tepal shape in lotus, and the mutants in this study are promising materials for breeding novel lotus cultivars with special tepals.
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Cao D, Lin Z, Huang L, Damaris RN, Yang P. Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology. BMC Genomics 2021; 22:171. [PMID: 33750315 PMCID: PMC7945336 DOI: 10.1186/s12864-021-07473-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background The AP2/ERF family is widely present in plants and plays a crucial regulatory role in plant growth and development. As an essential aquatic horticultural model plant, lotus has an increasingly prominent economic and research value. Results We have identified and analysed the AP2/ERF gene family in the lotus. Initially, 121 AP2/ERF family genes were identified. By analysing their gene distribution and protein structure, and their expression patterns during the development of lotus rhizome, combined with previous studies, we obtained an SNP (megascaffold_20:3578539) associated with lotus rhizome phenotype. This SNP was in the NnADAP gene of the AP2 subfamily, and the changes in SNP (C/T) caused amino acid conversion (proline/leucine). We constructed a population of 95 lotus varieties for SNP verification. Through population typing experiments, we found that the group with SNP CC had significantly larger lotus rhizome and higher soluble sugar content among the population. Conclusions In conclusion, we speculate that the alteration of the SNP in the NnADAP can affect the size and sugar content of the lotus rhizome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07473-w.
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Affiliation(s)
- Dingding Cao
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhongyuan Lin
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Longyu Huang
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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Molecular cloning and characterization of a gene encoding soluble starch synthase III (SSSIII) in Lotus (Nelumbo nucifera). Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-019-00341-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Lin Z, Zhang C, Cao D, Damaris RN, Yang P. The Latest Studies on Lotus ( Nelumbo nucifera)-an Emerging Horticultural Model Plant. Int J Mol Sci 2019; 20:E3680. [PMID: 31357582 PMCID: PMC6696627 DOI: 10.3390/ijms20153680] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/12/2019] [Accepted: 07/20/2019] [Indexed: 12/21/2022] Open
Abstract
Lotus (Nelumbo nucifera) is a perennial aquatic basal eudicot belonging to a small family Nelumbonaceace, which contains only one genus with two species. It is an important horticultural plant, with its uses ranging from ornamental, nutritional to medicinal values, and has been widely used, especially in Southeast Asia. Recently, the lotus obtained a lot of attention from the scientific community. An increasing number of research papers focusing on it have been published, which have shed light on the mysteries of this species. Here, we comprehensively reviewed the latest advancement of studies on the lotus, including phylogeny, genomics and the molecular mechanisms underlying its unique properties, its economic important traits, and so on. Meanwhile, current limitations in the research of the lotus were addressed, and the potential prospective were proposed as well. We believe that the lotus will be an important model plant in horticulture with the generation of germplasm suitable for laboratory operation and the establishment of a regeneration and transformation system.
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Affiliation(s)
- Zhongyuan Lin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Cheng Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Dingding Cao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
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Marques A, Moraes L, Aparecida Dos Santos M, Costa I, Costa L, Nunes T, Melo N, Simon MF, Leitch AR, Almeida C, Souza G. Origin and parental genome characterization of the allotetraploid Stylosanthes scabra Vogel (Papilionoideae, Leguminosae), an important legume pasture crop. ANNALS OF BOTANY 2018; 122:1143-1159. [PMID: 29982475 PMCID: PMC6324754 DOI: 10.1093/aob/mcy113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/28/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUNDS AND AIMS The genus Stylosanthes includes nitrogen-fixing and drought-tolerant species of considerable economic importance for perennial pasture, green manure and land recovery. Stylosanthes scabra is adapted to variable soil conditions, being cultivated to improve pastures and soils worldwide. Previous studies have proposed S. scabra as an allotetraploid species (2n = 40) with a putative diploid A genome progenitor S. hamata or S. seabrana (2n = 20) and the B genome progenitor S. viscosa (2n = 20). We aimed to provide conclusive evidence for the origin of S. scabra. METHODS We performed fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) experiments and Illumina paired-end sequencing of S. scabra, S. hamata and S. viscosa genomic DNA, to assemble and compare complete ribosomal DNA (rDNA) units and chloroplast genomes. Plastome- and genome-wide single nucleotide variation detection was also performed. KEY RESULTS GISH and phylogenetic analyses of plastid DNA and rDNA sequences support that S. scabra is an allotetraploid formed from 0.63 to 0.52 million years ago (Mya), from progenitors with a similar genome structure to the maternal donor S. hamata and the paternal donor S. viscosa. FISH revealed a non-additive number of 35S rDNA sites in S. scabra compared with its progenitors, indicating the loss of one locus from A genome origin. In S. scabra, most 5S rDNA units were similar to S. viscosa, while one 5S rDNA site of reduced size most probably came from an A genome species as revealed by GISH and in silico analysis. CONCLUSIONS Our approach combined whole-plastome and rDNA assembly with additional cytogenetic analysis to shed light successfully on the allotetraploid origin of S. scabra. We propose a Middle Pleistocene origin for S. scabra involving species with maternal A and paternal B genomes. Our data also suggest that variation found in rDNA units in S. scabra and its progenitors reveals differences that can be explained by homogenization, deletion and amplification processes that have occurred since its origin.
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Affiliation(s)
- André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, AL, Brazil
| | - Lívia Moraes
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | | | - Iara Costa
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, AL, Brazil
| | - Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Tomáz Nunes
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, AL, Brazil
| | - Natoniel Melo
- Laboratory of Biotechnology, Embrapa Semi-arid, Petrolina, Brazil
| | | | | | - Cicero Almeida
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, AL, Brazil
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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12
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Zhao M, Yang JX, Mao TY, Zhu HH, Xiang L, Zhang J, Chen LQ. Detection of Highly Differentiated Genomic Regions Between Lotus ( Nelumbo nucifera Gaertn.) With Contrasting Plant Architecture and Their Functional Relevance to Plant Architecture. FRONTIERS IN PLANT SCIENCE 2018; 9:1219. [PMID: 30177946 PMCID: PMC6110191 DOI: 10.3389/fpls.2018.01219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/30/2018] [Indexed: 05/13/2023]
Abstract
The lotus (Nelumbo nucifera Gaertn.) is one of the most economically and ornamentally important perennial aquatic plants. Plant architecture is an important trait for lotus classification, cultivation, breeding, and applications. In this study, traits representing plant architecture were measured in 390 lotus germplasms for 3 years. According to the phenotypic distribution, 21 large architecture (LA) and 22 small architecture (SA) germplasms exhibiting extreme phenotypes were selected as representatives of plant architecture. Microscopy analyses revealed that LA lotuses possessed far more vertical cells and longer cell lengths than SA lotuses, and there was a closer linear relationship between vertical cell number and plant architecture than cell length and plant architecture. Furthermore, based on whole genome re-sequencing data from 10 LA and 10 SA lotus germplasms, fixation index (FST) genome scan identified 11.02 Mb of genomic regions that were highly differentiated between the LA and SA lotus groups. Chi-square test revealed that 17,154 single nucleotide polymorphisms (SNPs) and 1,554 insertions and deletions (InDels) showed distinct allelic distribution between the LA and SA lotus groups within these regions. A total of 126 variants with distinct allelic distribution in the highly differentiated region were predicted to cause amino acid changes in 60 genes. Among the 41 genes with functional annotation, the expression patterns of six genes involved in cell division and cell wall construction were confirmed using quantitative reverse-transcription PCR (qRT-PCR). In addition, 34 plant architecture-associated InDel markers were developed and verified in the remaining 11 LA and 12 SA lotus plant architecture representatives. This study identified promising functional markers and candidates for molecular breeding and will facilitate further elucidation of the genetic mechanisms underlying plant architecture in the lotus.
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Affiliation(s)
- Mei Zhao
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Ministry of Education, Wuhan, China
| | - Ju-Xiang Yang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Ministry of Education, Wuhan, China
| | - Tian-Yu Mao
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Ministry of Education, Wuhan, China
| | - Huan-Huan Zhu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Ministry of Education, Wuhan, China
| | - Lin Xiang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Ministry of Education, Wuhan, China
| | - Jie Zhang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Ministry of Education, Wuhan, China
| | - Long-Qing Chen
- Southwest Engineering Technology and Research Center of Landscape Architecture, State Forestry Administration, Southwest Forestry University, Kunming, China
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13
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Gui S, Peng J, Wang X, Wu Z, Cao R, Salse J, Zhang H, Zhu Z, Xia Q, Quan Z, Shu L, Ke W, Ding Y. Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:721-734. [PMID: 29575237 DOI: 10.1111/tpj.13894] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 01/31/2018] [Accepted: 02/21/2018] [Indexed: 05/11/2023]
Abstract
Genetic and physical maps are powerful tools to anchor fragmented draft genome assemblies generated from next-generation sequencing. Currently, two draft assemblies of Nelumbo nucifera, the genomes of 'China Antique' and 'Chinese Tai-zi', have been released. However, there is presently no information on how the sequences are assembled into chromosomes in N. nucifera. The lack of physical maps and inadequate resolution of available genetic maps hindered the assembly of N. nucifera chromosomes. Here, a linkage map of N. nucifera containing 2371 bin markers [217 577 single nucleotide polymorphisms (SNPs)] was constructed using restriction-site associated DNA sequencing data of 181 F2 individuals and validated by adding 197 simple sequence repeat (SSR) markers. Additionally, a BioNano optical map covering 86.20% of the 'Chinese Tai-zi' genome was constructed. The draft assembly of 'Chinese Tai-zi' was improved based on the BioNano optical map, showing an increase of the scaffold N50 from 0.989 to 1.48 Mb. Using a combination of multiple maps, 97.9% of the scaffolds in the 'Chinese Tai-zi' draft assembly and 97.6% of the scaffolds in the 'China Antique' draft assembly were anchored into pseudo-chromosomes, and the centromere regions along the pseudo-chromosomes were identified. An evolutionary scenario was proposed to reach the modern N. nucifera karyotype from the seven ancestral eudicot chromosomes. The present study provides the highest-resolution linkage map, the optical map and chromosome level genome assemblies for N. nucifera, which are valuable for the breeding and cultivation of N. nucifera and future studies of comparative and evolutionary genomics in angiosperms.
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Affiliation(s)
- Songtao Gui
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Peng
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei, 430065, China
| | - Xiaolei Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhihua Wu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Cao
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jérôme Salse
- Paleogenomics & Evolution (PaleoEvo) Group, Génétique Diversité & Ecophysiologie des Céréales (GDEC), Institut National de la Recherché Agronomique UMR 1095, Clermont-Ferrand, 63100, France
| | - Hongyuan Zhang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhixuan Zhu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qiuju Xia
- Key Laboratory of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China
| | - Zhiwu Quan
- Key Laboratory of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China
| | - Liping Shu
- Wuhan Ice-Harbor Biological Technology Co. Ltd, Wuhan, 430040, China
| | - Wedong Ke
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei, 430065, China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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14
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Huang L, Yang M, Li L, Li H, Yang D, Shi T, Yang P. Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:2-15. [PMID: 29052958 DOI: 10.1111/jipb.12606] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/28/2017] [Indexed: 05/11/2023]
Abstract
Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome, seed and flower lotus), one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and an outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation. We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.
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Affiliation(s)
- Longyu Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
| | - Ling Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
| | - Tao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
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15
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Wang W, Yu H, Wang J, Lei W, Gao J, Qiu X, Wang J. The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae). Int J Mol Sci 2017; 18:E2288. [PMID: 29088105 PMCID: PMC5713258 DOI: 10.3390/ijms18112288] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 11/16/2022] Open
Abstract
Forsythia suspensa is an important medicinal plant and traditionally applied for the treatment of inflammation, pyrexia, gonorrhea, diabetes, and so on. However, there is limited sequence and genomic information available for F. suspensa. Here, we produced the complete chloroplast genomes of F. suspensa using Illumina sequencing technology. F. suspensa is the first sequenced member within the genus Forsythia (Oleaceae). The gene order and organization of the chloroplast genome of F. suspensa are similar to other Oleaceae chloroplast genomes. The F. suspensa chloroplast genome is 156,404 bp in length, exhibits a conserved quadripartite structure with a large single-copy (LSC; 87,159 bp) region, and a small single-copy (SSC; 17,811 bp) region interspersed between inverted repeat (IRa/b; 25,717 bp) regions. A total of 114 unique genes were annotated, including 80 protein-coding genes, 30 tRNA, and four rRNA. The low GC content (37.8%) and codon usage bias for A- or T-ending codons may largely affect gene codon usage. Sequence analysis identified a total of 26 forward repeats, 23 palindrome repeats with lengths >30 bp (identity > 90%), and 54 simple sequence repeats (SSRs) with an average rate of 0.35 SSRs/kb. We predicted 52 RNA editing sites in the chloroplast of F. suspensa, all for C-to-U transitions. IR expansion or contraction and the divergent regions were analyzed among several species including the reported F. suspensa in this study. Phylogenetic analysis based on whole-plastome revealed that F. suspensa, as a member of the Oleaceae family, diverged relatively early from Lamiales. This study will contribute to strengthening medicinal resource conservation, molecular phylogenetic, and genetic engineering research investigations of this species.
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Affiliation(s)
- Wenbin Wang
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Huan Yu
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Jiahui Wang
- College of Plant Protection, Northwest Agriculture & Forestry University, Yangling 712100, China.
| | - Wanjun Lei
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Jianhua Gao
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Xiangpo Qiu
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
| | - Jinsheng Wang
- College of Life Science, Shanxi Agricultural University, Taigu 030801, China.
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16
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Shi T, Wang K, Yang P. The evolution of plant microRNAs: insights from a basal eudicot sacred lotus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:442-457. [PMID: 27743419 DOI: 10.1111/tpj.13394] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 10/01/2016] [Accepted: 10/07/2016] [Indexed: 06/06/2023]
Abstract
microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNAs in eukaryotes. However, under which circumstances different miRNAs/miRNA families exhibit different evolutionary trajectories in plants remains unclear. In this study, we sequenced the small RNAs and degradome from a basal eudicot, sacred lotus (Nelumbo nucifera or lotus), to identify miRNAs and their targets. Combining with public miRNAs, we predicted 57 pre-eudicot miRNA families from different evolutionary stages. We found that miRNA families featuring older age, higher copy and target number tend to show lower propensity for miRNA family loss (PGL) and stronger signature of purifying selection during divergence of temperate and tropical lotus. Further analyses of lotus genome revealed that there is an association between loss of miRNA families in descendent plants and in duplicated genomes. Gene dosage balance is crucial in maintaining those preferentially retained MIRNA duplicates by imposing stronger purifying selection. However, these factors and selection influencing miRNA family evolution are not applicable to the putative MIRNA-likes. Additionally, the MIRNAs participating in lotus pollen-pistil interaction, a conserved process in angiosperms, also have a strong signature of purifying selection. Functionally, sequence divergence in MIRNAs escalates expression divergence of their target genes between temperate and tropical lotus during rhizome and leaf growth. Overall, our study unravels several important factors and selection that determine the miRNA family distribution in plants and duplicated genomes, and provides evidence for functional impact of MIRNA sequence evolution.
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Affiliation(s)
- Tao Shi
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, China
| | - Kun Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, China
- School of Life Sciences, Wuhan University, Wuhan, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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17
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He Y, Xiao H, Deng C, Xiong L, Yang J, Peng C. The Complete Chloroplast Genome Sequences of the Medicinal Plant Pogostemon cablin. Int J Mol Sci 2016; 17:ijms17060820. [PMID: 27275817 PMCID: PMC4926354 DOI: 10.3390/ijms17060820] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 01/15/2023] Open
Abstract
Pogostemon cablin, the natural source of patchouli alcohol, is an important herb in the Lamiaceae family. Here, we present the entire chloroplast genome of P. cablin. This genome, with 38.24% GC content, is 152,460 bp in length. The genome presents a typical quadripartite structure with two inverted repeats (each 25,417 bp in length), separated by one small and one large single-copy region (17,652 and 83,974 bp in length, respectively). The chloroplast genome encodes 127 genes, of which 107 genes are single-copy, including 79 protein-coding genes, four rRNA genes, and 24 tRNA genes. The genome structure, GC content, and codon usage of this chloroplast genome are similar to those of other species in the family, except that it encodes less protein-coding genes and tRNA genes. Phylogenetic analysis reveals that P. cablin diverged from the Scutellarioideae clade about 29.45 million years ago (Mya). Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to high AT content in the chloroplast genome. Complete sequences and annotation of P. cablin chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.
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Affiliation(s)
- Yang He
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Hongtao Xiao
- School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China.
- Department of Pharmacy, Hospital of the University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China.
| | - Cao Deng
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu 611731, China.
| | - Liang Xiong
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Jian Yang
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu 611731, China.
| | - Cheng Peng
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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