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Glombik M, Arunkumar R, Burrows S, Mogg SL, Wang X, Borrill P. Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations. Genome Biol 2025; 26:147. [PMID: 40437599 PMCID: PMC12121048 DOI: 10.1186/s13059-025-03598-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 04/29/2025] [Indexed: 06/01/2025] Open
Abstract
BACKGROUND Differences in the relative level of expression of homoeologs, known as homoeolog expression bias, are widely observed in allopolyploids. While the evolution of homoeolog expression bias through hybridization has been characterized, on shorter timescales such as those found in crop breeding programs, the extent to which homoeolog expression bias is preserved or altered between generations remains elusive. RESULTS Here we use biparental mapping populations of hexaploid wheat (Triticum aestivum) with a common "Paragon" parent to explore the inheritance of homoeolog expression bias in the F5 generation. We found that homoeolog expression bias is inherited for 26-27% of triads in both populations. Most triads conserved a similar homoeolog expression bias pattern as one or both parents. Inherited patterns were largely driven by changes in the expression of one homoeolog, allowing homoeolog expression bias in subsequent generations to match parental expression. Novel patterns of homoeolog expression bias occurred more frequently in the biparental population from a landrace × elite cross, than in the population with two elite parents. CONCLUSIONS These results demonstrate that there is significant reprogramming and stabilization of homoeolog expression bias within a small number of generations that differs significantly based on the parental lines used in the crossing.
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Affiliation(s)
- Marek Glombik
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ramesh Arunkumar
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Germany
| | - Samuel Burrows
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sophie Louise Mogg
- School of Biosciences, University of Birmingham, Birmingham, B15 2 TT, UK
- School of Biological Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Xiaoming Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Philippa Borrill
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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Guo W, Banerjee AK, Feng H, Ng WL, Wu H, Li W, Yuan Y, Huang Y. Recent allopolyploidization and transcriptomic asymmetry in the mangrove shrub Acanthus tetraploideus. BMC Genomics 2025; 26:438. [PMID: 40316933 PMCID: PMC12046671 DOI: 10.1186/s12864-025-11557-2] [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: 12/10/2024] [Accepted: 04/01/2025] [Indexed: 05/04/2025] Open
Abstract
BACKGROUND Mangrove species are vital to the ecosystems of tropical and subtropical coastlines worldwide. Despite the underexplored role of polyploidization in these species, deciphering its impact on gene expression is essential for understanding the connection between polyploidization and species diversification. Our initial investigation, integrating multiple nuclear loci with morphological and cytological data, indicates that the tetraploid Acanthus tetraploideus likely originated from allopolyploidization events involving the diploid species A. ilicifolius and A. ebracteatus. Expanding on these insights, this study utilizes genome-wide evidence to confirm the divergence patterns among extant Acanthus mangrove diploids and to investigate the origin and transcriptome asymmetry of the tetraploid A. tetraploideus. RESULTS Phylogenetic analysis and molecular dating revealed a closer evolutionary relationship between A. ebracteatus and A. volubilis than between A. ebracteatus and A. ilicifolius, diverged approximately 6.92 Mya and 9.59 Mya, respectively. Analysis of individual whole transcriptomes revealed that homeologous sequences in A. tetraploideus were preferentially clustered with A. ilicifolius and A. ebracteatus, rather than A. volubilis, in a roughly 1:1 ratio. The high similarity in nucleotide sequences and homologous polymorphisms between the tetraploid A. tetraploideus and its two parental diploids, A. ebracteatus and A. ilicifolius, supports the hypothesis of a recent allopolyploid origin for A. tetraploideus. Estimation of homeolog expression revealed a general attenuation of homeolog expression divergence in A. tetraploideus compared to the in silico parental mix, with 22.87% and 67.66% of genes exhibiting biased homeolog expression, respectively. Further investigation identified remarkable retention of parental expression dominance in the tetraploid, suggesting that parental genetic legacy substantially influences the reconfiguration of homeolog expression in the derived tetraploid. Meanwhile, the observation of numerous novel expression patterns between the two homeolog sets suggests that the transcriptome shock (i.e., the transcriptomic changes induced by interspecific hybridization) associated with allopolyploidization and subsequent post-polyploid evolutionary processes also significantly impact transcriptome asymmetry in A. tetraploideus. While no strong evidence directly links transcriptomic changes to specific adaptive traits, the patterns in unbiased and novelly biased genes in A. tetraploideus suggest adaptations to stable polyploidy. Unbiased genes involved in fundamental cellular processes and novelly biased genes related to chromosome dynamics and cell cycle regulation may stabilize polyploid genomes, supporting the species' establishment and long-term success. These findings underscore the role of transcriptomic stability in polyploid adaptation. CONCLUSIONS Our study sheds light on the evolutionary origins and the intricate transcriptional reconfiguration of the tetraploid A. tetraploideus. These insights significantly enhance our comprehension of the pivotal role that polyploidization plays in speciation and adaptative evolution of mangrove species.
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Affiliation(s)
- Wuxia Guo
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, 368 Jinwan Road, Zhuhai, Guangdong, 519041, People's Republic of China.
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
| | - Achyut Kumar Banerjee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
- School of Arts and Sciences, Azim Premji University, Bhopal, Madhya Pradesh, 462010, India
| | - Hui Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, 43900, Malaysia
| | - Haidan Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
| | - Weixi Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
| | - Yang Yuan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
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Fu J, Zhang Y, Yin M, Liu S, Xu Z, Wu M, Ni Z, Li P, Zhu R, Cai G, Wang M, Wang R. A visible seedling-stage screening system for the Brassica napus hybrid breeding by a novel hypocotyl length-regulated gene BnHL. PLANT BIOTECHNOLOGY JOURNAL 2025; 23:442-453. [PMID: 39504251 PMCID: PMC11772316 DOI: 10.1111/pbi.14507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/19/2024] [Accepted: 10/19/2024] [Indexed: 11/08/2024]
Abstract
Rapeseed (Brassica napus) is a globally significant oilseed crop with strong heterosis performance. Recessive genic male sterility (RGMS) is one of the key approaches for utilizing heterosis in B. napus. However, this method faces the inherent challenge of being time-consuming and labour-intensive for removing fertile plants during seed production. Here, we report a hypocotyl length-regulated gene, BnHL, which is closely linked to a known fertility gene, BnMs2, serving as a seedling morphology marker. This marker could be used to identify fertile plants in the breeding of RGMS lines based on hypocotyl traits. By targeting the BnHL gene, both homozygous and heterozygous edited mutants exhibited significantly longer hypocotyls than the wild type (WT). Furthermore, germination experiments revealed that 7 days after seed germination, the difference in hypocotyl length between the mutant and the WT seedlings reached its maximum, effectively distinguishing fertile plants under both white (W) and red/far-red (R/FR) light. Mutations in BnHL did not result in significant changes in main agronomic traits. Thus, this study provides a comprehensive strategy for screening and identifying a new morphological marker gene for early screening in RGMS hybrid breeding with completely non-transgene during the whole production.
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Affiliation(s)
- Jingyan Fu
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Ying Zhang
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Meng Yin
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Sha Liu
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Ziyue Xu
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Mingting Wu
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Zihan Ni
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Peiyao Li
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Ruijia Zhu
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Guangqin Cai
- Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Maolin Wang
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
| | - Rui Wang
- Key Laboratory for Bio‐Resources and Eco‐Environment, College of Life SciencesSichuan UniversityChengduChina
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Prost-Boxoen L, Bafort Q, Van de Vloet A, Almeida-Silva F, Paing YT, Casteleyn G, D’hondt S, De Clerck O, de Peer YV. Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids. THE NEW PHYTOLOGIST 2025; 245:869-884. [PMID: 39501615 PMCID: PMC7616817 DOI: 10.1111/nph.20249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 10/21/2024] [Indexed: 11/18/2024]
Abstract
Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.
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Affiliation(s)
- Lucas Prost-Boxoen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Biology, Ghent University, Ghent, Belgium
| | - Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Biology, Ghent University, Ghent, Belgium
| | - Antoine Van de Vloet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Yunn Thet Paing
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Griet Casteleyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie D’hondt
- Department of Biology, Ghent University, Ghent, Belgium
| | | | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Biology, Ghent University, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
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5
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Huang X, Wang Y, Zhang S, Pei L, You J, Long Y, Li J, Zhang X, Zhu L, Wang M. Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton. Nat Commun 2024; 15:10721. [PMID: 39730363 PMCID: PMC11680999 DOI: 10.1038/s41467-024-55309-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 12/06/2024] [Indexed: 12/29/2024] Open
Abstract
Although epigenetic modification has long been recognized as a vital force influencing gene regulation in plants, the dynamics of chromatin structure implicated in the intertwined transcriptional regulation of duplicated genes in polyploids have yet to be understood. Here, we document the dynamic organization of chromatin structure in two subgenomes of allotetraploid cotton (Gossypium hirsutum) by generating 3D genomic, epigenomic and transcriptomic datasets from 12 major tissues/developmental stages covering the life cycle. We systematically identify a subset of genes that are closely associated with specific tissue functions. Interestingly, these genes exhibit not only higher tissue specificity but also a more pronounced homoeologous bias. We comprehensively elucidate the intricate process of subgenomic collaboration and divergence across various tissues. A comparison among subgenomes in the 12 tissues reveals widespread differences in the reorganization of 3D genome structures, with the Dt subgenome exhibiting a higher extent of dynamic chromatin status than the At subgenome. Moreover, we construct a comprehensive atlas of putative functional genome elements and discover that 37 cis-regulatory elements (CREs) have selection signals acquired during domestication and improvement. These data and analyses are publicly available to the research community through a web portal. In summary, this study provides abundant resources and depicts the regulatory architecture of the genome, which thereby facilitates the understanding of biological processes and guides cotton breeding.
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Affiliation(s)
- Xianhui Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuejin Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sainan Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuexuan Long
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science, Shihezi University, Shihezi, 832003, China.
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6
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Yang L, Qin W, Wei X, Liu R, Yang J, Wang Z, Yan Q, Zhang Y, Hu W, Han X, Gao C, Zhan J, Gao B, Ge X, Li F, Yang Z. Regulatory networks of coresident subgenomes during rapid fiber cell elongation in upland cotton. PLANT COMMUNICATIONS 2024; 5:101130. [PMID: 39257006 PMCID: PMC11671760 DOI: 10.1016/j.xplc.2024.101130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 08/09/2024] [Accepted: 09/05/2024] [Indexed: 09/12/2024]
Abstract
Cotton, an intriguing plant species shaped by polyploidization, evolution, and domestication, holds particular interest due to the complex mechanisms governing fiber traits across its two subgenomes. However, the regulatory elements or transcriptional networks between subgenomes during fiber elongation remain to be fully clarified. Here, we analyzed 1462 cotton fiber samples to reconstruct the gene-expression regulatory networks that influence fiber cell elongation. Inter-subgenome expression quantitative trait loci (eQTLs) largely dictate gene transcription, with a notable tendency for the D subgenome to regulate A-subgenome eGenes. This regulation reveals synchronized homoeologous gene expression driven by co-localized eQTLs and divergent patterns that diminish genetic correlations, thus leading to preferential expression in the A and D subgenomes. Hotspot456 emerged as a key regulator of fiber initiation and elongation, and artificial selection of trans-eQTLs in hotspot456 that positively regulate KCS1 has facilitated cell elongation. Experiments designed to clarify the roles of trans-eQTLs in improved fiber breeding confirmed the inhibition of GhTOL9 by a specific trans-eQTL via GhWRKY28, which negatively affects fiber elongation. We propose a model in which the GhWRKY28-GhTOL9 module regulates this process through the ESCRT (endosomal sorting complex required for transport) pathway. This research significantly advances our understanding of cotton's evolutionary and domestication processes and the intricate regulatory mechanisms that underlie significant plant traits.
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Affiliation(s)
- Lan Yang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wenqiang Qin
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xi Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Rui Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jiaxiang Yang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou Univeristy, Zhengzhou 450000, China
| | - Zhi Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Qingdi Yan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yihao Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou Univeristy, Zhengzhou 450000, China
| | - Wei Hu
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou Univeristy, Zhengzhou 450000, China
| | - Xiao Han
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chenxu Gao
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou Univeristy, Zhengzhou 450000, China
| | - Jingjing Zhan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Baibai Gao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyang Ge
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou Univeristy, Zhengzhou 450000, China.
| | - Fuguang Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou Univeristy, Zhengzhou 450000, China.
| | - Zhaoen Yang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou Univeristy, Zhengzhou 450000, China.
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7
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Hosaka AJ, Sanetomo R, Hosaka K. Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole-genome sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39585203 DOI: 10.1111/tpj.17158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2024] [Revised: 11/06/2024] [Accepted: 11/09/2024] [Indexed: 11/26/2024]
Abstract
Mexican wild diploid potato species are reproductively isolated from A-genome species, including cultivated potatoes; thus, their genomic relationships remain unknown. Solanum stoloniferum Schlechtd. et Bché. (2n = 4x = 48, AABB) is a Mexican allotetraploid species frequently used in potato breeding. We constructed a chromosome-scale assembly of the S. stoloniferum genome using PacBio long-read sequencing and Hi-C scaffolding technologies. The final assembly consisted of 1742 Mb, among which 745 Mb and 713 Mb were anchored to the 12 A-genome and 12 B-genome chromosomes, respectively. Using the RNA-seq datasets, we detected 20 994 and 19 450 genes in the A and B genomes, respectively. Among these genes, 5138 and 3594 were specific to the A and B genomes, respectively, and 15 856 were homoeologous, of which 18.6-25.4% were biasedly expressed. Structural variations such as large pericentromeric inversions were frequently found between the A- and B-genome chromosomes. A comparison of the gene sequences from 38 diverse genomes of the related Solanum species revealed that the S. stoloniferum B genome and Mexican diploid species, with the exception of S. verrucosum, were monophyletically distinct from the S. stoloniferum A genome and the other A-genome species, indicating that the Mexican diploid species share the B genome. The content and divergence of transposable elements (TEs) revealed recent bursts and transpositions of TEs after polyploidization. Thus, the S. stoloniferum genome has undergone dynamic structural differentiation and TE mobilization and reorganization to stabilize the genomic imbalance. This study provides new insights into polyploid evolution and the efficient use of allotetraploid species in potato breeding.
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Affiliation(s)
- Awie J Hosaka
- Nihon BioData Corporation, Takatsu, Kawasaki, Kanagawa, 213-0012, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan
| | - Rena Sanetomo
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Kazuyoshi Hosaka
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
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8
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Rodríguez-Decuadro S, Ramos S, Rodríguez-Ustra MJ, Marques A, Smircich P, Vaio M. Transcriptome analysis of the allotetraploids of the Dilatata group of Paspalum (Poaceae): effects of diploidization on the expression of defensin and Snakin/GASA genes. Funct Integr Genomics 2024; 24:190. [PMID: 39412676 DOI: 10.1007/s10142-024-01466-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 09/27/2024] [Accepted: 09/27/2024] [Indexed: 12/22/2024]
Abstract
Plant Snakin/GASA and defensin peptides are cysteine-rich molecules with a wide range of biological functions. They are included within the large family of plant antimicrobial peptides (AMPs), characterized by their structural stability, broad spectrum of activity, and diverse mechanisms of action. The Dilatata group of Paspalum includes five allotetraploids that share an equivalent genomic formula IIJJ. From RNA-seq data of seedling tissues, we performed an in silico characterization of the defensin and Snakin/GASA genes in these species and diploids with a II and JJ genome formula and studied the evolutionary consequences of polyploidy on the expression of the two AMPs families. A total of 107 defensins (distributed in eight groups) and 145 Snakin/GASA (grouped in three subfamilies) genes were identified. Deletions, duplications and/or gene silencing seem to have mediated the evolution of these genes in the allotetraploid species. In defensin genes, the IIJJ allopolyploids retained the I subgenome defensin copies in some of the identified groups supporting the closeness of their nuclear genome with the I subgenome species. In both AMPs families, orthologous genes in tetraploids exhibit higher similarity to each other than with diploids. This data supports the theory of a single origin for the allotetraploids. Several copies of both defensin and Snakin/GASA genes were detected in the five polyploids which could have arisen due to duplication events occurring independently during the diploidization processes in the allotetraploid taxa.
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Affiliation(s)
- Susana Rodríguez-Decuadro
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo, 12900, Uruguay.
| | - Stefani Ramos
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo, 12900, Uruguay
| | - María José Rodríguez-Ustra
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo, 12900, Uruguay
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo, 11600, Uruguay
| | - Magdalena Vaio
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo, 12900, Uruguay.
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9
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Aufiero G, Fruggiero C, D’Angelo D, D’Agostino N. Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge-A Transcriptomics Perspective. Genes (Basel) 2024; 15:977. [PMID: 39202338 PMCID: PMC11353593 DOI: 10.3390/genes15080977] [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: 07/02/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.
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Affiliation(s)
| | | | | | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (G.A.); (C.F.); (D.D.)
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10
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Ning W, Meudt HM, Tate JA. A roadmap of phylogenomic methods for studying polyploid plant genera. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11580. [PMID: 39184196 PMCID: PMC11342234 DOI: 10.1002/aps3.11580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/10/2023] [Accepted: 01/13/2024] [Indexed: 08/27/2024]
Abstract
Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole-genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid-rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long-read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.
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Affiliation(s)
- Weixuan Ning
- School of Natural SciencesMassey UniversityPalmerston North4442New Zealand
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa TongarewaWellington6011New Zealand
| | - Jennifer A. Tate
- School of Natural SciencesMassey UniversityPalmerston North4442New Zealand
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11
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Almeida-Silva F, Prost-Boxoen L, Van de Peer Y. hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors. THE NEW PHYTOLOGIST 2024; 243:811-819. [PMID: 38798271 PMCID: PMC7616114 DOI: 10.1111/nph.19862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).
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Affiliation(s)
- Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Lucas Prost-Boxoen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biology, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
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12
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Choi SS, Mc Cartney A, Park D, Roberts H, Brav-Cubitt T, Mitchell C, Buckley TR. Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects. Mol Ecol 2024:e17422. [PMID: 38842022 DOI: 10.1111/mec.17422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/03/2024] [Accepted: 04/17/2024] [Indexed: 06/07/2024]
Abstract
During hybrid speciation, homoeologues combine in a single genome. Homoeologue expression bias (HEB) occurs when one homoeologue has higher gene expression than another. HEB has been well characterized in plants but rarely investigated in animals, especially invertebrates. Consequently, we have little idea as to the role that HEB plays in allopolyploid invertebrate genomes. If HEB is constrained by features of the parental genomes, then we predict repeated evolution of similar HEB patterns among hybrid genomes formed from the same parental lineages. To address this, we reconstructed the history of hybridization between the New Zealand stick insect genera Acanthoxyla and Clitarchus using a high-quality genome assembly from Clitarchus hookeri to call variants and phase alleles. These analyses revealed the formation of three independent diploid and triploid hybrid lineages between these genera. RNA sequencing revealed a similar magnitude and direction of HEB among these hybrid lineages, and we observed that many enriched functions and pathways were also shared among lineages, consistent with repeated evolution due to parental genome constraints. In most hybrid lineages, a slight majority of the genes involved in mitochondrial function showed HEB towards the maternal homoeologues, consistent with only weak effects of mitonuclear incompatibility. We also observed a proteasome functional enrichment in most lineages and hypothesize this may result from the need to maintain proteostasis in hybrid genomes. Reference bias was a pervasive problem, and we caution against relying on HEB estimates from a single parental reference genome.
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Affiliation(s)
- Seung-Sub Choi
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Ann Mc Cartney
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Duckchul Park
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Hester Roberts
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
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13
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Hu G, Grover CE, Vera DL, Lung PY, Girimurugan SB, Miller ER, Conover JL, Ou S, Xiong X, Zhu D, Li D, Gallagher JP, Udall JA, Sui X, Zhang J, Bass HW, Wendel JF. Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton. Mol Biol Evol 2024; 41:msae095. [PMID: 38758089 PMCID: PMC11140268 DOI: 10.1093/molbev/msae095] [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: 11/02/2023] [Revised: 04/10/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.
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Affiliation(s)
- Guanjing Hu
- State Key Laboratory of Cotton Bio-breeding and Integrated, Chinese Academy of Agricultural Sciences, Institute of Cotton Research, Anyang 455000, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Daniel L Vera
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | | | - Emma R Miller
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Justin L Conover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Shujun Ou
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Xianpeng Xiong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - De Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
| | - Dongming Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Joseph P Gallagher
- Forage Seed and Cereal Research Unit, USDA/Agricultural Research Service, Corvallis, OR 97331, USA
| | - Joshua A Udall
- Crop Germplasm Research Unit, USDA/Agricultural Research Service, College Station, TX 77845, USA
| | - Xin Sui
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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14
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Paterson AH, Queitsch C. Genome organization and botanical diversity. THE PLANT CELL 2024; 36:1186-1204. [PMID: 38382084 PMCID: PMC11062460 DOI: 10.1093/plcell/koae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes-both in content and in dynamics-has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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15
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Sun P, Lu Z, Wang Z, Wang S, Zhao K, Mei D, Yang J, Yang Y, Renner SS, Liu J. Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family. Proc Natl Acad Sci U S A 2024; 121:e2313921121. [PMID: 38568968 PMCID: PMC11009661 DOI: 10.1073/pnas.2313921121] [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: 08/12/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
Malvaceae comprise some 4,225 species in 243 genera and nine subfamilies and include economically important species, such as cacao, cotton, durian, and jute, with cotton an important model system for studying the domestication of polyploids. Here, we use chromosome-level genome assemblies from representatives of five or six subfamilies (depending on the placement of Ochroma) to differentiate coexisting subgenomes and their evolution during the family's deep history. The results reveal that the allohexaploid Helicteroideae partially derive from an allotetraploid Sterculioideae and also form a component of the allodecaploid Bombacoideae and Malvoideae. The ancestral Malvaceae karyotype consists of 11 protochromosomes. Four subfamilies share a unique reciprocal chromosome translocation, and two other subfamilies share a chromosome fusion. DNA alignments of single-copy nuclear genes do not yield the same relationships as inferred from chromosome structural traits, probably because of genes originating from different ancestral subgenomes. These results illustrate how chromosome-structural data can unravel the evolutionary history of groups with ancient hybrid genomes.
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Affiliation(s)
- Pengchuan Sun
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Zhiqiang Lu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan666303, China
| | - Zhenyue Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Shang Wang
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Kexin Zhao
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Dong Mei
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
| | - Jiao Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yongzhi Yang
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | | | - Jianquan Liu
- Key Laboratory for Bio-Resources and Eco-Environment, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
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16
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Lopes JML, Nascimento LSDQ, Souza VC, de Matos EM, Fortini EA, Grazul RM, Santos MO, Soltis DE, Soltis PS, Otoni WC, Viccini LF. Water stress modulates terpene biosynthesis and morphophysiology at different ploidal levels in Lippia alba (Mill.) N. E. Brown (Verbenaceae). PROTOPLASMA 2024; 261:227-243. [PMID: 37665420 DOI: 10.1007/s00709-023-01890-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Monoterpenes are the main component in essential oils of Lippia alba. In this species, the chemical composition of essential oils varies with genome size: citral (geraniol and neral) is dominant in diploids and tetraploids, and linalool in triploids. Because environmental stress impacts various metabolic pathways, we hypothesized that stress responses in L. alba could alter the relationship between genome size and essential oil composition. Water stress affects the flowering, production, and reproduction of plants. Here, we evaluated the effect of water stress on morphophysiology, essential oil production, and the expression of genes related to monoterpene synthesis in diploid, triploid, and tetraploid accessions of L. alba cultivated in vitro for 40 days. First, using transcriptome data, we performed de novo gene assembly and identified orthologous genes using phylogenetic and clustering-based approaches. The expression of candidate genes related to terpene biosynthesis was estimated by real-time quantitative PCR. Next, we assessed the expression of these genes under water stress conditions, whereby 1% PEG-4000 was added to MS medium. Water stress modulated L. alba morphophysiology at all ploidal levels. Gene expression and essential oil production were affected in triploid accessions. Polyploid accessions showed greater growth and metabolic tolerance under stress compared to diploids. These results confirm the complex regulation of metabolic pathways such as the production of essential oils in polyploid genomes. In addition, they highlight aspects of genotype and environment interactions, which may be important for the conservation of tropical biodiversity.
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Affiliation(s)
- Juliana Mainenti Leal Lopes
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
- School of Life Science and Environment, Department of Genetic and Biotechnology, University of Trás-Os-Montes and Alto Douro, 5001-801, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1649-004, Lisbon, Portugal
| | | | - Vinicius Carius Souza
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Elyabe Monteiro de Matos
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Evandro Alexandre Fortini
- Laboratory of Plant Tissue Culture (LCTII), Department of Plant Biology/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs S/N, Campus Universitário, Viçosa, MG, 36570-000, Brazil
| | | | - Marcelo Oliveira Santos
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Wagner Campos Otoni
- Laboratory of Plant Tissue Culture (LCTII), Department of Plant Biology/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs S/N, Campus Universitário, Viçosa, MG, 36570-000, Brazil
| | - Lyderson Facio Viccini
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil.
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17
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Wu Y, Sun R, Huan T, Zhao Y, Yu D, Sun Y. An insight into the gene expression evolution in Gossypium species based on the leaf transcriptomes. BMC Genomics 2024; 25:179. [PMID: 38355396 PMCID: PMC10868065 DOI: 10.1186/s12864-024-10091-x] [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: 08/16/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Gene expression pattern is associated with biological phenotype and is widely used in exploring gene functions. Its evolution is also crucial in understanding species speciation and divergence. The genus Gossypium is a bona fide model for studying plant evolution and polyploidization. However, the evolution of gene expression during cotton species divergence has yet to be extensively discussed. RESULTS Based on the seedling leaf transcriptomes, this work analyzed the transcriptomic content and expression patterns across eight cotton species, including six diploids and two natural tetraploids. Our findings indicate that, while the biological function of these cotton transcriptomes remains largely conserved, there has been significant variation in transcriptomic content during species divergence. Furthermore, we conducted a comprehensive analysis of expression distances across cotton species. This analysis lends further support to the use of G. arboreum as a substitute for the A-genome donor of natural cotton polyploids. Moreover, our research highlights the evolution of stress-responsive pathways, including hormone signaling, fatty acid degradation, and flavonoid biosynthesis. These processes appear to have evolved under lower selection pressures, presumably reflecting their critical role in the adaptations of the studied cotton species to diverse environments. CONCLUSIONS In summary, this study provided insights into the gene expression variation within the genus Gossypium and identified essential genes/pathways whose expression evolution was closely associated with the evolution of cotton species. Furthermore, the method of characterizing genes and pathways under unexpected high or slow selection pressure can also serve as a new strategy for gene function exploration.
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Affiliation(s)
- Yuqing Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Rongnan Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Tong Huan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yanyan Zhao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Dongliang Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Yuqiang Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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18
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Li X, Zhang L, Wei X, Datta T, Wei F, Xie Z. Polyploidization: A Biological Force That Enhances Stress Resistance. Int J Mol Sci 2024; 25:1957. [PMID: 38396636 PMCID: PMC10888447 DOI: 10.3390/ijms25041957] [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: 12/24/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.
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Affiliation(s)
- Xiaoying Li
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Luyue Zhang
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T & R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Tanusree Datta
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Fang Wei
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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19
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Liu H, Zhu J, Zhang B, Li Q, Liu C, Huang Q, Cui P. The functional divergence of homologous GPAT9 genes contributes to the erucic acid content of Brassica napus seeds. BMC PLANT BIOLOGY 2024; 24:69. [PMID: 38262947 PMCID: PMC10807112 DOI: 10.1186/s12870-024-04734-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND The early allopolyploid Brassica napus was a hybrid of two Brassica species, that had undergone a whole genome duplication event followed by genome restructuring, including deletions and small scale duplications. A large number of homologous genes appeared functional divergence during species domestication. Due to the high conservation of de novo glycerolipid biosynthesis, multiple homologues of glycerol-3-phosphate acyltransferases (GPATs) have been found in B. napus. Moreover, the functional variances among these homologous GPAT-encoding genes are unclear. RESULTS In this study, four B. napus homologous genes encoding glycerol-3-phosphate acyltransferase 9 (BnaGPAT9) were characterized. Although a bioinformatics analysis indicated high protein sequence similarity, the homologues demonstrated tissue-specific expression patterns and functional divergence. Yeast genetic complementation assays revealed that BnaGPAT9-A1/C1 homologues but not BnaGPAT9-A10/C9 homologues encoded functional GPAT enzymes. Furthermore, a single nucleotide polymorphism of BnaGPAT9-C1 that occurred during the domestication process was associated with enzyme activity and contributed to the fatty acid composition. The seed-specific expression of BnGPAT9-C11124A increased the erucic acid content in the transformant seeds. CONCLUSIONS This study revealed that BnaGPAT9 gene homologues evolved into functionally divergent forms with important roles in erucic acid biosynthesis.
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Affiliation(s)
- Hongbo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| | - Jinbo Zhu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| | - Bingxin Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| | - Qingyang Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| | - Cui Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| | - Qian Huang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China.
| | - Peng Cui
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, China.
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20
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Katayama N, Yamamoto T, Aiuchi S, Watano Y, Fujiwara T. Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales). FRONTIERS IN PLANT SCIENCE 2024; 14:1286320. [PMID: 38264021 PMCID: PMC10803465 DOI: 10.3389/fpls.2023.1286320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern-Phegopteris decursivepinnata-and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.
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Affiliation(s)
- Natsu Katayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Takuya Yamamoto
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Sakura Aiuchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yasuyuki Watano
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Tao Fujiwara
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
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21
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An H, Pires JC, Conant GC. Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. PLoS Comput Biol 2024; 20:e1011803. [PMID: 38227592 PMCID: PMC10817154 DOI: 10.1371/journal.pcbi.1011803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/26/2024] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
Hybridization coupled to polyploidy, or allopolyploidy, has dramatically shaped the evolution of flowering plants, teleost fishes, and other lineages. Studies of recently formed allopolyploid plants have shown that the two subgenomes that merged to form that new allopolyploid do not generally express their genes equally. Instead, one of the two subgenomes expresses its paralogs more highly on average. Meanwhile, older allopolyploidy events tend to show biases in duplicate losses, with one of the two subgenomes retaining more genes than the other. Since reduced expression is a pathway to duplicate loss, understanding the origins of expression biases may help explain the origins of biased losses. Because we expect gene expression levels to experience stabilizing selection, our conceptual frameworks for how allopolyploid organisms form tend to assume that the new allopolyploid will show balanced expression between its subgenomes. It is then necessary to invoke phenomena such as differences in the suppression of repetitive elements to explain the observed expression imbalances. Here we show that, even for phenotypically identical diploid progenitors, the inherent kinetics of gene expression give rise to biases between the expression levels of the progenitor genes in the hybrid. Some of these biases are expected to be gene-specific and not give rise to global differences in progenitor gene expression. However, particularly in the case of allopolyploids formed from progenitors with different genome sizes, global expression biases favoring one subgenome are expected immediately on formation. Hence, expression biases are arguably the expectation upon allopolyploid formation rather than a phenomenon needing explanation. In the future, a deeper understanding of the kinetics of allopolyploidy may allow us to better understand both biases in duplicate losses and hybrid vigor.
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Affiliation(s)
- Hong An
- MU Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - J. Chris Pires
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gavin C. Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
- Program in Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
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22
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Kenchanmane Raju SK, Lensink M, Kliebenstein DJ, Niederhuth C, Monroe G. Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs. THE NEW PHYTOLOGIST 2023; 240:1292-1304. [PMID: 37614211 DOI: 10.1111/nph.19227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023]
Abstract
Processes affecting rates of sequence polymorphism are fundamental to the evolution of gene duplicates. The relationship between gene activity and sequence polymorphism can influence the likelihood that functionally redundant gene copies are co-maintained in stable evolutionary equilibria vs other outcomes such as neofunctionalization. Here, we investigate genic variation in epigenome-associated polymorphism rates in Arabidopsis thaliana and consider whether these affect the evolution of gene duplicates. We compared the frequency of sequence polymorphism and patterns of genetic differentiation between genes classified by exon methylation patterns: unmethylated (unM), gene-body methylated (gbM), and transposon-like methylated (teM) states, which reflect divergence in gene expression. We found that the frequency of polymorphism was higher in teM (transcriptionally repressed, tissue-specific) genes and lower in gbM (active, constitutively expressed) genes. Comparisons of gene duplicates were largely consistent with genome-wide patterns - gene copies that exhibit teM accumulate more variation, evolve faster, and are in chromatin states associated with reduced DNA repair. This relationship between expression, the epigenome, and polymorphism may lead to the breakdown of equilibrium states that would otherwise maintain genetic redundancies. Epigenome-mediated polymorphism rate variation may facilitate the evolution of novel gene functions in duplicate paralogs maintained over evolutionary time.
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Affiliation(s)
| | - Mariele Lensink
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
| | - Grey Monroe
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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23
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Bourret J, Borvető F, Bravo IG. Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: The showcase of polypyrimidine tract binding proteins. J Evol Biol 2023; 36:1375-1392. [PMID: 37667674 DOI: 10.1111/jeb.14212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 09/06/2023]
Abstract
Gene paralogs are copies of an ancestral gene that appear after gene or full genome duplication. When two sister gene copies are maintained in the genome, redundancy may release certain evolutionary pressures, allowing one of them to access novel functions. Here, we focused our study on gene paralogs on the evolutionary history of the three polypyrimidine tract binding protein genes (PTBP) and their concurrent evolution of differential codon usage preferences (CUPrefs) in vertebrate species. PTBP1-3 show high identity at the amino acid level (up to 80%) but display strongly different nucleotide composition, divergent CUPrefs and, in humans and in many other vertebrates, distinct tissue-specific expression levels. Our phylogenetic inference results show that the duplication events leading to the three extant PTBP1-3 lineages predate the basal diversification within vertebrates, and genomic context analysis illustrates that local synteny has been well preserved over time for the three paralogs. We identify a distinct evolutionary pattern towards GC3-enriching substitutions in PTBP1, concurrent with enrichment in frequently used codons and with a tissue-wide expression. In contrast, PTBP2s are enriched in AT-ending, rare codons, and display tissue-restricted expression. As a result of this substitution trend, CUPrefs sharply differ between mammalian PTBP1s and the rest of PTBPs. Genomic context analysis suggests that GC3-rich nucleotide composition in PTBP1s is driven by local substitution processes, while the evidence in this direction is thinner for PTBP2-3. An actual lack of co-variation between the observed GC composition of PTBP2-3 and that of the surrounding non-coding genomic environment would raise an interrogation on the origin of CUPrefs, warranting further research on a putative tissue-specific translational selection. Finally, we communicate an intriguing trend for the use of the UUG-Leu codon, which matches the trends of AT-ending codons. Our results are compatible with a scenario in which a combination of directional mutation-selection processes would have differentially shaped CUPrefs of PTBPs in vertebrates: the observed GC-enrichment of PTBP1 in placental mammals may be linked to genomic location and to the strong and broad tissue-expression, while AT-enrichment of PTBP2 and PTBP3 would be associated with rare CUPrefs and thus, possibly to specialized spatio-temporal expression. Our interpretation is coherent with a gene subfunctionalisation process by differential expression regulation associated with the evolution of specific CUPrefs.
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Affiliation(s)
- Jérôme Bourret
- Laboratoire MIVEGEC (CNRS IRD Univ Montpellier), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Fanni Borvető
- Laboratoire MIVEGEC (CNRS IRD Univ Montpellier), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Ignacio G Bravo
- Laboratoire MIVEGEC (CNRS IRD Univ Montpellier), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
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24
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June V, Xu D, Papoulas O, Boutz D, Marcotte EM, Chen ZJ. Protein nonadditive expression and solubility contribute to heterosis in Arabidopsis hybrids and allotetraploids. FRONTIERS IN PLANT SCIENCE 2023; 14:1252564. [PMID: 37780492 PMCID: PMC10538547 DOI: 10.3389/fpls.2023.1252564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Hybrid vigor or heterosis has been widely applied in agriculture and extensively studied using genetic and gene expression approaches. However, the biochemical mechanism underlying heterosis remains elusive. One theory suggests that a decrease in protein aggregation may occur in hybrids due to the presence of protein variants between parental alleles, but it has not been experimentally tested. Here, we report comparative analysis of soluble and insoluble proteomes in Arabidopsis intraspecific and interspecific hybrids or allotetraploids formed between A. thaliana and A. arenosa. Both allotetraploids and intraspecific hybrids displayed nonadditive expression (unequal to the sum of the two parents) of the proteins, most of which were involved in biotic and abiotic stress responses. In the allotetraploids, homoeolog-expression bias was not observed among all proteins examined but accounted for 17-20% of the nonadditively expressed proteins, consistent with the transcriptome results. Among expression-biased homoeologs, there were more A. thaliana-biased than A. arenosa-biased homoeologs. Analysis of the insoluble and soluble proteomes revealed more soluble proteins in the hybrids than their parents but not in the allotetraploids. Most proteins in ribosomal biosynthesis and in the thylakoid lumen, membrane, and stroma were in the soluble fractions, indicating a role of protein stability in photosynthetic activities for promoting growth. Thus, nonadditive expression of stress-responsive proteins and increased solubility of photosynthetic proteins may contribute to heterosis in Arabidopsis hybrids and allotetraploids and possibly hybrid crops.
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Affiliation(s)
- Viviana June
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Dongqing Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ophelia Papoulas
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Daniel Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Edward M. Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Z. Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
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25
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Shen F, Xu S, Shen Q, Bi C, Lysak MA. The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits. Nat Commun 2023; 14:4102. [PMID: 37491530 PMCID: PMC10368706 DOI: 10.1038/s41467-023-39800-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/29/2023] [Indexed: 07/27/2023] Open
Abstract
Polyploidization can provide a wealth of genetic variation for adaptive evolution and speciation, but understanding the mechanisms of subgenome evolution as well as its dynamics and ultimate consequences remains elusive. Here, we report the telomere-to-telomere (T2T) gap-free reference genome of allotetraploid horseradish (Armoracia rusticana) sequenced using a comprehensive strategy. The (epi)genomic architecture and 3D chromatin structure of the A and B subgenomes differ significantly, suggesting that both the dynamics of the dominant long terminal repeat retrotransposons and DNA methylation have played critical roles in subgenome diversification. Investigation of the genetic basis of biosynthesis of glucosinolates (GSLs) and horseradish peroxidases reveals both the important role of polyploidization and subgenome differentiation in shaping the key traits. Continuous duplication and divergence of essential genes of GSL biosynthesis (e.g., FMOGS-OX, IGMT, and GH1 gene family) contribute to the broad GSL profile in horseradish. Overall, the T2T assembly of the allotetraploid horseradish genome expands our understanding of polyploid genome evolution and provides a fundamental genetic resource for breeding and genetic improvement of horseradish.
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Affiliation(s)
- Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Shixiao Xu
- Tobacco College, Henan Agricultural University, Zhengzhou, Henan, China
| | - Qi Shen
- Genome Research Center, Leeuwenhoek Biotechnology Inc., Hong Kong, China
- Shangji Biotechnology Inc., Tianjin, China
- PheniX, Plant Phenomics Research Centre, Nanjing Agricultural University, Nanjing, China
| | - Changwei Bi
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Martin A Lysak
- Central European Institute of Technology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
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26
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Hajieghrari B, Niazi A. Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family. J Mol Evol 2023:10.1007/s00239-023-10109-0. [PMID: 37191719 DOI: 10.1007/s00239-023-10109-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 04/05/2023] [Indexed: 05/17/2023]
Abstract
HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3'-end uridylation and 3' to 5' exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.
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Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, P.O. Box 74135-111, Jahrom, Islamic Republic of Iran.
| | - Ali Niazi
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Islamic Republic of Iran
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27
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Kenchanmane Raju SK, Ledford M, Niederhuth CE. DNA methylation signatures of duplicate gene evolution in angiosperms. PLANT PHYSIOLOGY 2023:kiad220. [PMID: 37061825 PMCID: PMC10400039 DOI: 10.1093/plphys/kiad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
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28
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Coate JE. Beyond Transcript Concentrations: Quantifying Polyploid Expression Responses per Biomass, per Genome, and per Cell with RNA-Seq. Methods Mol Biol 2023; 2545:227-250. [PMID: 36720816 DOI: 10.1007/978-1-0716-2561-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
RNA-seq has been used extensively to study expression responses to polyploidy. Most current methods for normalizing RNA-seq data yield estimates of transcript concentrations (transcripts per transcriptome). The implicit assumption of these normalization methods is that transcriptome size is equivalent between the samples being compared such that transcript concentrations are equivalent to transcripts per cell. In recent years, however, evidence has mounted that transcriptome size can vary dramatically in response to a range of factors including polyploidy and that such variation is ubiquitous. Where such variation exists, transcript concentration is often a poor or even misleading proxy for expression responses at other biologically relevant scales (e.g., expression per cell). Thus, it is important that transcriptomic studies of polyploids move beyond simply comparing transcript concentrations if we are to gain a complete understanding of how genome multiplication affects gene expression. I discuss this issue in more detail and summarize a suite of approaches that can leverage RNA-seq to quantify expression responses per genome, per cell, and per unit of biomass.
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29
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Ebeed HT. Genome-wide analysis of polyamine biosynthesis genes in wheat reveals gene expression specificity and involvement of STRE and MYB-elements in regulating polyamines under drought. BMC Genomics 2022; 23:734. [PMID: 36309637 PMCID: PMC9618216 DOI: 10.1186/s12864-022-08946-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Polyamines (PAs) are considered promising biostimulants that have diverse key roles during growth and stress responses in plants. Nevertheless, the molecular basis of these roles by PAs has not been completely realized even now, and unfortunately, the transcriptional analyses of the biosynthesis pathway in various wheat tissues have not been investigated under normal or stress conditions. In this research, the findings of genome-wide analyses of genes implicated in the PAs biosynthesis in wheat (ADC, Arginine decarboxylase; ODC, ornithine decarboxylase; AIH, agmatine iminohydrolase; NPL1, Nitrlase like protein 1; SAMDC, S-adenosylmethionine decarboxylase; SPDS, spermidine synthase; SPMS, spermine synthase and ACL5, thermospermine synthase) are shown. RESULTS In total, thirty PAs biosynthesis genes were identified. Analysis of gene structure, subcellular compartmentation and promoters were discussed. Furthermore, experimental gene expression analyses in roots, shoot axis, leaves, and spike tissues were investigated in adult wheat plants under control and drought conditions. Results revealed structural similarity within each gene family and revealed the identity of two new motifs that were conserved in SPDS, SPMS and ACL5. Analysis of the promoter elements revealed the incidence of conserved elements (STRE, CAAT-box, TATA-box, and MYB TF) in all promoters and highly conserved CREs in >80% of promoters (G-Box, ABRE, TGACG-motif, CGTCA-motif, as1, and MYC). The results of the quantification of PAs revealed higher levels of putrescine (Put) in the leaves and higher spermidine (Spd) in the other tissues. However, no spermine (Spm) was detected in the roots. Drought stress elevated Put level in the roots and the Spm in the leaves, shoots and roots, while decreased Put in spikes and elevated the total PAs levels in all tissues. Interestingly, PA biosynthesis genes showed tissue-specificity and some homoeologs of the same gene family showed differential gene expression during wheat development. Additionally, gene expression analysis showed that ODC is the Put biosynthesis path under drought stress in roots. CONCLUSION The information gained by this research offers important insights into the transcriptional regulation of PA biosynthesis in wheat that would result in more successful and consistent plant production.
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Affiliation(s)
- Heba Talat Ebeed
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, 34517, Egypt.
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30
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McRae L, Beric A, Conant GC. Hybridization order is not the driving factor behind biases in duplicate gene losses among the hexaploid Solanaceae. Proc Biol Sci 2022; 289:20221810. [PMID: 36285500 PMCID: PMC9597411 DOI: 10.1098/rspb.2022.1810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We model the post-hexaploidy evolution of four genomes from the Solanaceae, a group of flowering plants comprising tomatoes, potatoes and their relatives. The hexaploidy that these genomes descend from occurred through two sequential allopolyploidy events and was marked by the unequal losses of duplicated genes from the different progenitor subgenomes. In contrast with the hexaploid Brassiceae (broccoli and its relatives), where the subgenome with the most surviving genes arrived last in the hexaploidy, among the Solanaceae the most preserved subgenome descends from one of the original two tetraploid progenitors. In fact, the last-arriving subgenome in these plants actually has the fewest surviving genes in the modern genomes. We explore whether the distribution of repetitive elements (REs) in these genomes can explain the biases in gene losses, but while the signals we find are broadly consistent with a role for high RE density in driving gene losses, the REs turn over so quickly that little signal of the RE condition at the time of paleopolyploidy is extant in the modern genomes.
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Affiliation(s)
- Logan McRae
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Gavin C. Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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31
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Akagi T, Jung K, Masuda K, Shimizu KK. Polyploidy before and after domestication of crop species. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102255. [PMID: 35870416 DOI: 10.1016/j.pbi.2022.102255] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/01/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Katharina Jung
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland
| | - Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan.
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32
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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] [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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Shahzad K, Zhang X, Zhang M, Guo L, Qi T, Tang H, Wang H, Mubeen I, Qiao X, Peng R, Wu J, Xing C. Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization. Funct Integr Genomics 2022; 22:757-768. [PMID: 35771309 DOI: 10.1007/s10142-022-00877-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hybridization is useful to enhance the yield potential of agronomic crops in the world. Cotton has genome doubling due to the allotetraploid process and hybridization in coordination with duplicated genome can produce more yield and adaptability. Therefore, the expression of homoeologous gene pairs between hybrids and inbred parents is vital to characterize the genetic source of heterosis in cotton. Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identified 36853 homoeolog genes in hybrids. It was observed both high and low hybrids had similar trends in homoeolog gene expression patterns in each tissue under study. An average of 96% of homoeolog genes had no biased expression and their expressions were derived from the equal contribution of both parents. Besides, very few homoeolog genes (an average of 1%) showed no biased or novel expression in both hybrids. The functional analysis described secondary metabolic pathways had a majority of novel biased homoeolog genes in hybrids. These results contribute preliminary knowledge about how hybridization affects expression patterns of homoeolog gene pairs in upland cotton hybrids. Our study also highlights the functional genomics of metabolic genes to explore the genetic mechanism of heterosis in cotton.
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Affiliation(s)
- Kashif Shahzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Huini Tang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Iqra Mubeen
- Department of Biochemistry, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Renhai Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China. .,College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China.
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China. .,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China. .,Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
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34
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Wu H, Song X, Lyu S, Ren Y, Liu T, Hou X, Li Y, Zhang C. Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi ( Brassica rapa ssp. chinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:905202. [PMID: 35812944 PMCID: PMC9263584 DOI: 10.3389/fpls.2022.905202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Polyploids generated by the replication of a single genome (autopolyploid) or synthesis of two or more distinct genomes (allopolyploid) usually show significant advantages over their diploid progenitors in biological characteristics, including growth and development, nutrient accumulation, and plant resistance. Whereas, the impacts of genomic replication on transcription regulation and chromatin structure in pak choi have not been explored fully. In this study, we observed the transcriptional and genomic structural alterations between diploid B. rapa (AA) and artificial autotetraploid B. rapa (AAAA) using RNA-seq and Hi-C. RNA-seq revealed 1,786 differentially expressed genes (DEGs) between the diploids and autotetraploids, including 717 down-regulated and 1,069 up-regulated genes in autotetraploids. Of all the 1,786 DEGs, 23 DEGs (10 down-regulated DEGs in autotetraploids) were involved in Compartment A-B shifts, while 28 DEGs (20 up-regulated DEGs in autotetraploids) participated in Compartment B-A shifts. Moreover, there were 15 DEGs in activated topologically associating domains (TADs) (9 up-regulated DEGs in diploids) and 80 DEGs in repressed TADs (49 down-regulated DEGs in diploids). Subsequently, eight DEGs with genomic structural variants were selected as potential candidate genes, including four DEGs involved in photosynthesis (BraA01003143, BraA09002798, BraA04002224, and BraA08000594), three DEGs related to chloroplast (BraA05002974, BraA05001662, and BraA04001148), and one DEG associated with disease resistance (BraA09004451), which all showed high expression in autotetraploids. Overall, our results demonstrated that integrative RNA-seq and Hi-C analysis can identify related genes to phenotypic traits and also provided new insights into the molecular mechanism of the growth advantage of polyploids.
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Affiliation(s)
- Huiyuan Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Xiaoming Song
- Center for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shanwu Lyu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yiming Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
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35
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Shearman JR, Naktang C, Sonthirod C, Kongkachana W, U-Thoomporn S, Jomchai N, Maknual C, Yamprasai S, Promchoo W, Ruang-Areerate P, Pootakham W, Tangphatsornruang S. Assembly of a hybrid mangrove, Bruguiera hainesii, and its two ancestral contributors, Bruguiera cylindrica and Bruguiera gymnorhiza. Genomics 2022; 114:110382. [PMID: 35526741 DOI: 10.1016/j.ygeno.2022.110382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/19/2022] [Accepted: 05/02/2022] [Indexed: 01/14/2023]
Abstract
Mangroves are plants that live in tropical and subtropical coastal regions of the world, they are adapted to high salt environments and cyclic tidal flooding. Mangroves play important ecological roles, including acting as breeding grounds for many fish species and to prevent coastal erosion. The genomes of three mangrove species, Bruguiera gymnorhiza, Bruguiera cylindrica, and a hybrid of the two, Bruguiera hainesii were sequenced, assembled and annotated. The two progenitor species, B. gymnorhiza and B. cylindrica, were found to be highly similar to each other and sufficiently similar to B. parviflora to allow it to be used for reference based scaffolding to generate chromosome level scaffolds. The two subgenomes of B. hainesii were independently assembled and scaffolded. Analysis of B. hainesii confirms that it is a hybrid and the hybridisation event was estimated at 2.4 to 3.5 million years ago using a Bayesian Relaxed Molecular Clock approach.
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Affiliation(s)
- Jeremy R Shearman
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Suchart Yamprasai
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Waratthaya Promchoo
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Panthita Ruang-Areerate
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani 12120, Thailand.
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36
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Xie T, Yang W, Chen X, Rong H, Wang Y, Jiang J. Genome-Wide Identification and Expressional Profiling of the Metal Tolerance Protein Gene Family in Brassica napus. Genes (Basel) 2022; 13:genes13050761. [PMID: 35627146 PMCID: PMC9141485 DOI: 10.3390/genes13050761] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/04/2023] Open
Abstract
The Cation Diffusion Facilitator (CDF) family, also named Metal Tolerance Protein (MTP), is one of the gene families involved in heavy metal transport in plants. However, a comprehensive study of MTPs in Brassica napus has not been reported yet. In the present study, we identified 33 BnMTP genes from the rapeseed genome using bioinformatic analyses. Subsequently, we analyzed the phylogenetic relationship, gene structure, chromosome distribution, conserved domains, and motifs of the BnMTP gene family. The 33 BnMTPs were phylogenetically divided into three major clusters (Zn-CDFs, Fe/Zn-CDFs, and Mn-CDFs) and seven groups (group 1, 5, 6, 7, 8, 9, and 12). The structural characteristics of the BnMTP members were similar in the same group, but different among groups. Evolutionary analysis indicated that the BnMTP gene family mainly expanded through whole-genome duplication (WGD) and segmental duplication events. Moreover, the prediction of cis-acting elements and microRNA target sites suggested that BnMTPs might be involved in plant growth, development, and stress responses. In addition, we found the expression of 24 BnMTPs in rapeseed leaves or roots could respond to heavy metal ion treatments. These results provided an important basis for clarifying the biological functions of BnMTPs, especially in heavy metal detoxification, and will be helpful in the phytoremediation of heavy metal pollution in soil.
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Affiliation(s)
- Tao Xie
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (W.Y.); (X.C.); (Y.W.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou 225009, China
| | - Wenjing Yang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (W.Y.); (X.C.); (Y.W.)
| | - Xin Chen
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (W.Y.); (X.C.); (Y.W.)
| | - Hao Rong
- School of Biological and Food Engineering, Suzhou University, Suzhou 234000, China;
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (W.Y.); (X.C.); (Y.W.)
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (T.X.); (W.Y.); (X.C.); (Y.W.)
- Correspondence: ; Tel.: +86-514-87997303
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37
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Lyu Z, Hao Y, Chen L, Xu S, Wang H, Li M, Ge W, Hou B, Cheng X, Li X, Che N, Zhen T, Sun S, Bao Y, Yang Z, Jia J, Kong L, Wang H. Wheat- Thinopyrum Substitution Lines Imprint Compensation Both From Recipients and Donors. FRONTIERS IN PLANT SCIENCE 2022; 13:837410. [PMID: 35498638 PMCID: PMC9051513 DOI: 10.3389/fpls.2022.837410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Even frequently used in wheat breeding, we still have an insufficient understanding of the biology of the products via distant hybridization. In this study, a transcriptomic analysis was performed for six Triticum aestivum-Thinopyrum elongatum substitution lines in comparison with the host plants. All the six disomic substitution lines showed much stronger "transcriptomic-shock" occurred on alien genomes with 57.43-69.22% genes changed expression level but less on the recipient genome (2.19-8.97%). Genome-wide suppression of alien genes along chromosomes was observed with a high proportion of downregulated genes (39.69-48.21%). Oppositely, the wheat recipient showed genome-wide compensation with more upregulated genes, occurring on all chromosomes but not limited to the homeologous groups. Moreover, strong co-upregulation of the orthologs between wheat and Thinopyrum sub-genomes was enriched in photosynthesis with predicted chloroplastic localization, which indicates that the compensation happened not only on wheat host genomes but also on alien genomes.
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Affiliation(s)
- Zhongfan Lyu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Yongchao Hao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin, China
| | - Shoushen Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Hongjin Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Mengyao Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Wenyang Ge
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Bingqian Hou
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Xinxin Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Xuefeng Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Naixiu Che
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Tianyue Zhen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Silong Sun
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Yinguang Bao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Hongwei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
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38
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Sharbrough J, Conover JL, Fernandes Gyorfy M, Grover CE, Miller ER, Wendel JF, Sloan DB. Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms. Mol Biol Evol 2022; 39:msac074. [PMID: 35383845 PMCID: PMC9040051 DOI: 10.1093/molbev/msac074] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
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Affiliation(s)
- Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Justin L. Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Emma R. Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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Ullah I, Ansari HA, Verry IM, Hussain SW, Ellison NW, McManus MT, Williams WM. Introgression of Trifolium ambiguum Into Allotetraploid White Clover ( Trifolium repens) Using the Ancestral Parent Trifolium occidentale as a Bridging Species. FRONTIERS IN PLANT SCIENCE 2022; 13:858714. [PMID: 35371143 PMCID: PMC8971954 DOI: 10.3389/fpls.2022.858714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
White clover (Trifolium repens) is an allotetraploid pasture legume widely used in moist temperate climates, but its vulnerability to drought, grazing pressure and pests has restricted its wider use. A related species, Caucasian clover (Trifolium ambiguum), is a potential source of resistances to drought, cold, grazing pressure and pests that could potentially be transferred to white clover by interspecific hybridization. Although direct hybridization has been achieved with difficulty, the hybrids have not been easy to backcross for introgression breeding and no interspecific chromosome recombination has been demonstrated. The present work shows that interspecific recombination can be achieved by using Trifolium occidentale, one of the ancestral parents of T. repens, as a bridging species and that large white clover breeding populations carrying recombinant chromosomes can be generated. A 4x hybrid between T. ambiguum and T. occidentale was crossed with T. repens and then backcrossed for two generations. Five backcross hybrid plants with phenotypes appearing to combine traits from the parent species were selected for FISH-GISH analyses. Recombinant chromosome segments from T. ambiguum were found in all five plants, suggesting that recombination frequencies were significant and sufficient for introgression breeding. Despite early chromosome imbalances, the backcross populations were fertile and produced large numbers of seeds. These hybrids represent a major new resource for the breeding of novel resilient forms of white clover.
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Affiliation(s)
- Ihsan Ullah
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
- College of Sciences, Massey University, Palmerston North, New Zealand
| | - Helal A. Ansari
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
| | - Isabelle M. Verry
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
| | | | - Nick W. Ellison
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
| | | | - Warren M. Williams
- AgResearch (Grasslands Research Centre), Palmerston North, New Zealand
- College of Sciences, Massey University, Palmerston North, New Zealand
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GC content of plant genes is linked to past gene duplications. PLoS One 2022; 17:e0261748. [PMID: 35025913 PMCID: PMC8758071 DOI: 10.1371/journal.pone.0261748] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022] Open
Abstract
The frequency of G and C nucleotides in genomes varies from species to species, and sometimes even between different genes in the same genome. The monocot grasses have a bimodal distribution of genic GC content absent in dicots. We categorized plant genes from 5 dicots and 4 monocot grasses by synteny to related species and determined that syntenic genes have significantly higher GC content than non-syntenic genes at their 5`-end in the third position within codons for all 9 species. Lower GC content is correlated with gene duplication, as lack of synteny to distantly related genomes is associated with past interspersed gene duplications. Two mutation types can account for biased GC content, mutation of methylated C to T and gene conversion from A to G. Gene conversion involves non-reciprocal exchanges between homologous alleles and is not detectable when the alleles are identical or heterozygous for presence-absence variation, both likely situations for genes duplicated to new loci. Gene duplication can cause production of siRNA which can induce targeted methylation, elevating mC→T mutations. Recently duplicated plant genes are more frequently methylated and less likely to undergo gene conversion, each of these factors synergistically creating a mutational environment favoring AT nucleotides. The syntenic genes with high GC content in the grasses compose a subset that have undergone few duplications, or for which duplicate copies were purged by selection. We propose a “biased gene duplication / biased mutation” (BDBM) model that may explain the origin and trajectory of the observed link between duplication and genic GC bias. The BDBM model is supported by empirical data based on joint analyses of 9 angiosperm species with their genes categorized by duplication status, GC content, methylation levels and functional classes.
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A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population. PLoS Genet 2022; 18:e1010017. [PMID: 35108269 PMCID: PMC8843129 DOI: 10.1371/journal.pgen.1010017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 02/14/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program. Slash pine is an important source of original timber and resin production on commercial forest plantations. It is necessary to implement precise breeding strategies to improve timber quality and resin yield. However, little is known about the species’ molecular genetic basis. Using a transcriptome dataset with sequencing from 240 individuals in the slash pine population, we combined multiple approaches (based on gene variation, expression variation and co-expression network) to dissect the genetic structure for slash pine major breeding traits. We found that the research population could be divided into three genetic groups with a mean heterozygosity of 0.2246. We also found that six genes with important functions in slash pine resin synthesis and timber formation through association studies. Four new SNPs associatation with the average ring width were also discovered. Our results provide new insights into the molecular genetic basis of important traits in slash pine and provide a comprehensive method for association analyses of conifer tree species with large genome.
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Wong ELY, Hiscock SJ, Filatov DA. The Role of Interspecific Hybridisation in Adaptation and Speciation: Insights From Studies in Senecio. FRONTIERS IN PLANT SCIENCE 2022; 13:907363. [PMID: 35812981 PMCID: PMC9260247 DOI: 10.3389/fpls.2022.907363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/03/2022] [Indexed: 05/08/2023]
Abstract
Hybridisation is well documented in many species, especially plants. Although hybrid populations might be short-lived and do not evolve into new lineages, hybridisaiton could lead to evolutionary novelty, promoting adaptation and speciation. The genus Senecio (Asteraceae) has been actively used to unravel the role of hybridisation in adaptation and speciation. In this article, we first briefly describe the process of hybridisation and the state of hybridisation research over the years. We then discuss various roles of hybridisation in plant adaptation and speciation illustrated with examples from different Senecio species, but also mention other groups of organisms whenever necessary. In particular, we focus on the genomic and transcriptomic consequences of hybridisation, as well as the ecological and physiological aspects from the hybrids' point of view. Overall, this article aims to showcase the roles of hybridisation in speciation and adaptation, and the research potential of Senecio, which is part of the ecologically and economically important family, Asteraceae.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- *Correspondence: Edgar L. Y. Wong,
| | - Simon J. Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Oxford Botanic Garden and Arboretum, Oxford, United Kingdom
| | - Dmitry A. Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Bayer PE, Scheben A, Golicz AA, Yuan Y, Faure S, Lee H, Chawla HS, Anderson R, Bancroft I, Raman H, Lim YP, Robbens S, Jiang L, Liu S, Barker MS, Schranz ME, Wang X, King GJ, Pires JC, Chalhoub B, Snowdon RJ, Batley J, Edwards D. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2488-2500. [PMID: 34310022 PMCID: PMC8633514 DOI: 10.1111/pbi.13674] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/11/2021] [Accepted: 07/20/2021] [Indexed: 05/26/2023]
Abstract
Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.
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Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Armin Scheben
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVICAustralia
| | - Yuxuan Yuan
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - HueyTyng Lee
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Harmeet Singh Chawla
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Robyn Anderson
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural Institute, PMBWagga WaggaNSWAustralia
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeonSouth Korea
| | | | - Lixi Jiang
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Shengyi Liu
- Chinese Academy of Agricultural SciencesOil Crops Research InstituteWuhanChina
| | - Michael S. Barker
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - M. Eric Schranz
- Biosystematics GroupWageningen University and Research CenterWageningenThe Netherlands
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences (IVF, CAAS)BeijingChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - J. Chris Pires
- Division of Biological SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
| | - Boulos Chalhoub
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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Menadue DJ, Riboni M, Baumann U, Schilling RK, Plett DC, Roy SJ. Proton-pumping pyrophosphatase homeolog expression is a dynamic trait in bread wheat ( Triticum aestivum). PLANT DIRECT 2021; 5:e354. [PMID: 34646976 PMCID: PMC8496507 DOI: 10.1002/pld3.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/20/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Proton-pumping pyrophosphatases (H+-PPases) have been shown to enhance biomass and yield. However, to date, there has been little work towards identify genes encoding H+-PPases in bread wheat (Triticum aestivum) (TaVPs) and limited knowledge on how the expression of these genes varies across different growth stages and tissue types. In this study, the IWGSC database was used to identify two novel TaVP genes, TaVP4 and TaVP5, and elucidate the complete homeolog sequences of the three known TaVP genes, bringing the total number of bread wheat TaVPs from 9 to 15. Gene expression levels of each TaVP homeolog were assessed using quantitative real-time PCR (qRT-PCR) in four diverse wheat varieties in terms of phenotypic traits related to high vacuolar pyrophosphatase expression. Homeolog expression was analyzed across multiple tissue types and developmental stages. Expression levels of the TaVP homeologs were found to vary significantly between varieties, tissues and plant developmental stages. During early development (Z10 and Z13), expressions of TaVP1 and TaVP2 homeologs were higher in shoot tissue than root tissue, with both shoot and root expression increasing in later developmental stages (Z22). TaVP2-D was expressed in all varieties and tissue types and was the most highly expressed homeolog at all developmental stages. Expression of the TaVP3 homeologs was restricted to developing grain (Z75), while TaVP4 homeolog expression was higher at Z22 than earlier developmental stages. Variation in TaVP4B was detected among varieties at Z22 and Z75, with Buck Atlantico (high biomass) and Scout (elite Australian cultivar) having the highest levels of expression. These findings offer a comprehensive overview of the bread wheat H+-PPase family and identify variation in TaVP homeolog expression that will be of use to improve the growth, yield, and abiotic stress tolerance of bread wheat.
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Affiliation(s)
- Daniel Jamie Menadue
- School of Agriculture, Food and WineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Australian Centre for Plant Functional GenomicsThe University of AdelaideUrrbraeSouth AustraliaAustralia
| | - Matteo Riboni
- School of Agriculture, Food and WineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Australian Centre for Plant Functional GenomicsThe University of AdelaideUrrbraeSouth AustraliaAustralia
| | - Ute Baumann
- School of Agriculture, Food and WineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Australian Centre for Plant Functional GenomicsThe University of AdelaideUrrbraeSouth AustraliaAustralia
| | - Rhiannon Kate Schilling
- School of Agriculture, Food and WineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Australian Centre for Plant Functional GenomicsThe University of AdelaideUrrbraeSouth AustraliaAustralia
- Department of Primary Industries and RegionsSouth Australian Research and Development InstituteUrrbraeSouth AustraliaAustralia
| | - Darren Craig Plett
- School of Agriculture, Food and WineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Australian Plant Phenomics Facility, The Plant AcceleratorThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Stuart John Roy
- School of Agriculture, Food and WineUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Australian Centre for Plant Functional GenomicsThe University of AdelaideUrrbraeSouth AustraliaAustralia
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry ClimateUniversity of AdelaideAdelaideSouth AustraliaAustralia
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Zhao Y, Chen Z, Chen J, Chen B, Tang W, Chen X, Lai Z, Guo R. Comparative transcriptomic analyses of glucosinolate metabolic genes during the formation of Chinese kale seeds. BMC PLANT BIOLOGY 2021; 21:394. [PMID: 34418959 PMCID: PMC8380351 DOI: 10.1186/s12870-021-03168-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/10/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND To understand the mechanism of glucosinolates (GSs) accumulation in the specific organs, combined analysis of physiological change and transcriptome sequencing were applied in the current study. Taking Chinese kale as material, seeds and silique walls were divided into different stages based on the development of the embryo in seeds and then subjected to GS analysis and transcriptome sequencing. RESULTS The main GS in seeds of Chinese kale were glucoiberin and gluconapin and their content changed with the development of the seed. During the transition of the embryo from torpedo- to the early cotyledonary-embryo stage, the accumulation of GS in the seed was accompanied by the salient decline of GS in the corresponding silique wall. Thus, the seed and corresponding silique wall at these two stages were subjected to transcriptomic sequencing analysis. 135 genes related to GS metabolism were identified, of which 24 genes were transcription factors, 81 genes were related to biosynthetic pathway, 25 genes encoded catabolic enzymes, and 5 genes matched with transporters. The expression of GS biosynthetic genes was detected both in seeds and silique walls. The high expression of FMOGS-OX and AOP2, which is related to the production of gluconapin by side modification, was noted in seeds at both stages. Interestingly, the expression of GS biosynthetic genes was higher in the silique wall compared with that in the seed albeit lower content of GS existed in the silique wall than in the seed. Combined with the higher expression of transporter genes GTRs in silique walls than in seeds, it was proposed that the transportation of GS from the silique wall to the seed is an important source for seed GS accumulation. In addition, genes related to GS degradation expressed abundantly in the seed at the early cotyledonary-embryo stage indicating its potential role in balancing seed GS content. CONCLUSIONS Two stages including the torpedo-embryo and the early cotyledonary-embryo stage were identified as crucial in GS accumulation during seed development. Moreover, we confirmed the transportation of GS from the silique wall to the seed and proposed possible sidechain modification of GS biosynthesis may exist during seed formation.
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Affiliation(s)
- Yijiao Zhao
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zeyuan Chen
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jiaxuan Chen
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Bingxing Chen
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weiling Tang
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaodong Chen
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhongxiong Lai
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Rongfang Guo
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Glombik M, Copetti D, Bartos J, Stoces S, Zwierzykowski Z, Ruttink T, Wendel JF, Duchoslav M, Dolezel J, Studer B, Kopecky D. Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1166-1182. [PMID: 34152039 PMCID: PMC8518873 DOI: 10.1111/tpj.15375] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/21/2021] [Accepted: 06/11/2021] [Indexed: 05/19/2023]
Abstract
Allopolyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being "dominant." Such "genome dominance" can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k-mer-based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans-acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent-specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.
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Affiliation(s)
- Marek Glombik
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
- National Centre for Biomolecular ResearchFaculty of ScienceMasaryk UniversityKotlářská 261137BrnoCzech Republic
| | - Dario Copetti
- Molecular Plant BreedingInstitute of Agricultural SciencesETH ZurichUniversitaetstrasse 28092ZurichSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Jan Bartos
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
| | - Stepan Stoces
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
| | - Zbigniew Zwierzykowski
- Department of Environmental Stress BiologyInstitute of Plant GeneticsPolish Academy of SciencesStrzeszyńska 3460‐479PoznańPoland
| | - Tom Ruttink
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)Caritasstraat 399090MelleBelgium
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Martin Duchoslav
- Department of BotanyFaculty of SciencePalacký University in OlomoucŠlechtitelů 2778371OlomoucCzech Republic
| | - Jaroslav Dolezel
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
| | - Bruno Studer
- Molecular Plant BreedingInstitute of Agricultural SciencesETH ZurichUniversitaetstrasse 28092ZurichSwitzerland
| | - David Kopecky
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesŠlechtitelů 3177900OlomoucCzech Republic
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Zhang J, Shi SZ, Jiang Y, Zhong F, Liu G, Yu C, Lian B, Chen Y. Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow ( Salix matsudana). PeerJ 2021; 9:e11076. [PMID: 33954030 PMCID: PMC8051338 DOI: 10.7717/peerj.11076] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/17/2021] [Indexed: 12/15/2022] Open
Abstract
AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species. However, little is known about the AP2/ERF gene family of Chinese willow (Salix matsudana), which is a tetraploid ornamental tree species that is widely planted and is also considered as a species that can improve the soil salinity of coastal beaches. In this study, 364 AP2/ERF genes of Salix matsudana (SmAP2/ERF) were identified depending on the recently produced whole genome sequencing data of Salix matsudana. These genes were renamed according to the chromosomal location of the SmAP2/ERF genes. The SmAP2/ERF genes included three major subfamilies: AP2 (55 members), ERF (301 members), and RAV (six members) and two Soloist genes. Genes’ structure and conserved motifs were analyzed in SmAP2/ERF family members, and introns were not found in most genes of the ERF subfamily, some unique motifs were found to be important for the function of SmAP2/ERF genes. Syntenic relationships between the SmAP2/ERF genes and AP2/ERF genes from Populus trichocarpa and Salix purpurea showed that Salix matsudana is genetically more closely related to Populus trichocarpa than to Salix purpurea. Evolution analysis on paralog gene pairs suggested that progenitor of S. matsudana originated from hybridization between two different diploid salix germplasms and underwent genome duplication not more than 10 Mya. RNA sequencing results demonstrated the differential expression patterns of some SmAP2/ERF genes under salt stress and this information can help reveal the mechanism of salt tolerance regulation in Salix matsudana.
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Affiliation(s)
- Jian Zhang
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, Jiangsu, China
| | - Shi Zheng Shi
- Jiangsu Academy of Forestry, Nanjing, Jiangsu, China
| | - Yuna Jiang
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, Jiangsu, China
| | - Fei Zhong
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, Jiangsu, China
| | - Guoyuan Liu
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, Jiangsu, China
| | - Chunmei Yu
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, Jiangsu, China
| | - Bolin Lian
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, Jiangsu, China
| | - Yanhong Chen
- Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, Jiangsu, China
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Xiong W, Zhang J, Lan T, Kong W, Wang X, Liu L, Chen X, Mo B. High resolution RNA-seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in Arabidopsis thaliana. PLANT DIRECT 2021; 5:e00320. [PMID: 34095740 PMCID: PMC8156134 DOI: 10.1002/pld3.320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 05/12/2023]
Abstract
In Arabidopsis thaliana, each ribosomal protein (RP) is encoded by a small gene family consisting of two or more highly homologous paralogues, which results in ribosome heterogeneity. It is largely unknown that how genes from multiple member containing RP families are regulated at transcriptional level to accommodate the needs of different plant organs and developmental stages. In this study, we investigated the transcript accumulation profiles of RP genes and found that the expression levels of RP genes are varied dramatically in different organs and developmental stages. Although most RP genes are found to be ubiquitously transcribed, some are obviously transcribed with spatiotemporal specificity. The hierarchical clustering trees of transcript accumulation intensity of RP genes revealed that different organs and developmental stages have different population of RP gene transcripts. By interrogating of the expression fluctuation trend of RP genes, we found that in spite of the fact that most groups of paralogous RP genes are transcribed in concerted manners, some RPs gene have contrasting expression patterns. When transcripts of paralogous RP genes from the same family are considered together, the expression level of most RP genes are well-matched but some are obviously higher or lower, therefore we speculate that some superfluous RPs may act outside the ribosome and a portion of ribosomes may lack one or even more RP(s). Altogether, our analysis results suggested that functional divergence may exist among heterogeneous ribosomes that resulted from different combination of RP paralogues, and substoichiometry of several RP gene families may lead to another layer of heterogeneous ribosomes which also have divergent functions in plants.
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Affiliation(s)
- Wei Xiong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Jiancong Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Wenwen Kong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Xiaoyan Wang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Xuemei Chen
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCAUSA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
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49
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Peng Z, Chen H, Tan L, Shu H, Varshney RK, Zhou Z, Zhao Z, Luo Z, Chitikineni A, Wang L, Maku J, López Y, Gallo M, Zhou H, Wang J. Natural polymorphisms in a pair of NSP2 homoeologs can cause loss of nodulation in peanut. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1104-1118. [PMID: 33130897 DOI: 10.1093/jxb/eraa505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, and these are important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3~1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings reveal the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results have implications for and provide insights into the evolution of homoeologous genes in allopolyploid species.
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Affiliation(s)
- Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Huiqiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Lubin Tan
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Hongmei Shu
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Zhekai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - James Maku
- Sciences and Mathematics Department, Glenville State College, Glenville, WV, USA
| | - Yolanda López
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Maria Gallo
- Delaware Valley University, Doylestown, PA, USA
| | - Hai Zhou
- Agronomy Department, University of Florida, Gainesville, FL, USA
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
- Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
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50
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Huang KM, Chain FJJ. Copy number variations and young duplicate genes have high methylation levels in sticklebacks. Evolution 2021; 75:706-718. [PMID: 33527399 DOI: 10.1111/evo.14184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/11/2022]
Abstract
Gene duplication is an important driver of genomic diversity that can promote adaptive evolution. However, like most mutations, a newly duplicated gene is often deleterious and removed from the genome by drift or natural selection. The early molecular changes that occur soon after duplication therefore may influence the long-term survival of gene duplicates, but relatively little empirical data exist on the events near the onset of duplication before mutations have time to accumulate. In this study, we contrast gene expression and DNA methylation levels of duplicate genes in the threespine stickleback, Gasterosteus aculeatus, including recently emerged duplications that segregate as copy number variations (CNVs). We find that younger duplicate genes have higher levels of promoter methylation than older genes, and that gene CNVs have higher promoter methylation than non-CNVs. These results suggest preferential duplication of highly methylated genes or rapid methylation changes soon after duplication. We also find a negative association between methylation and expression, providing a putative role for methylation in suppressing transcription that compensates for increases in gene copy numbers and promoting paralog retention. We propose that methylation contributes to the longevity of young duplicate genes, extending the window of opportunity for functional divergence via mutation.
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Affiliation(s)
- Katherine M Huang
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, 01854.,Comparative Media Studies/Writing, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, 01854
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