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Kang JS, Yu JG, Xiang QP, Zhang XC. The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae. Mol Biol Evol 2024; 41:msae153. [PMID: 39101470 PMCID: PMC11299036 DOI: 10.1093/molbev/msae153] [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: 09/26/2023] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024] Open
Abstract
Selaginellaceae, originated in the Carboniferous and survived the Permian-Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.
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Affiliation(s)
- Jong-Soo Kang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ji-Gao Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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Wang Y, Tang H, Wang X, Sun Y, Joseph PV, Paterson AH. Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX. Nat Protoc 2024; 19:2206-2229. [PMID: 38491145 DOI: 10.1038/s41596-024-00968-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 12/20/2023] [Indexed: 03/18/2024]
Abstract
As different taxa evolve, gene order often changes slowly enough that chromosomal 'blocks' with conserved gene orders (synteny) are discernible. The MCScanX toolkit ( https://github.com/wyp1125/MCScanX ) was published in 2012 as freely available software for the detection of such 'colinear blocks' and subsequent synteny and evolutionary analyses based on genome-wide gene location and protein sequence information. Owing to its simplicity and high efficiency for colinear block detection, MCScanX provides a powerful tool for conducting diverse synteny and evolutionary analyses. Moreover, the detection of colinear blocks has been embraced as an integral step for pangenome graph construction. Here, new application trends of MCScanX are explored, striving to better connect this increasingly used tool to other tools and accelerate insight generation from exponentially growing sequence data. We provide a detailed protocol that covers how to install MCScanX on diverse platforms, tune parameters, prepare input files from data from the National Center for Biotechnology Information, run MCScanX and its visualization and evolutionary analysis tools, and connect MCScanX with external tools, including MCScanX-transposed, Circos and SynVisio. This protocol is easily implemented by users with minimal computational background and is adaptable to new data of interest to them. The data and utility programs for this protocol can be obtained from http://bdx-consulting.com/mcscanx-protocol .
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Affiliation(s)
- Yupeng Wang
- BDX Research & Consulting LLC, Herndon, VA, USA
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
| | - Haibao Tang
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
- Center for Genomics, College of Science, North China University of Science and Technology, Tangshan, China
| | - Ying Sun
- BDX Research & Consulting LLC, Herndon, VA, USA
| | - Paule V Joseph
- Section of Sensory Science and Metabolism, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, USA.
- National Institute of Nursing Research, Bethesda, MD, USA.
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA.
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3
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Vinay ND, Singh K, Ellur RK, Chinnusamy V, Jaiswal S, Iquebal MA, Munshi AD, Matsumura H, Boopalakrishnan G, Jat GS, Kole C, Gaikwad AB, Kumar D, Dey SS, Behera TK. High-quality Momordica balsamina genome elucidates its potential use in improving stress resilience and therapeutic properties of bitter gourd. FRONTIERS IN PLANT SCIENCE 2024; 14:1258042. [PMID: 38333042 PMCID: PMC10851156 DOI: 10.3389/fpls.2023.1258042] [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: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 02/10/2024]
Abstract
Introduction Momordica balsamina is the closest wild species that can be crossed with an important fruit vegetable crop, Momordica charantia, has immense medicinal value, and placed under II subclass of primary gene pool of bitter gourd. M. balsamina is tolerant to major biotic and abiotic stresses. Genome characterization of Momordica balsamina as a wild relative of bitter gourd will contribute to the knowledge of the gene pool available for improvement in bitter gourd. There is potential to transfer gene/s related to biotic resistance and medicinal importance from M. balsamina to M. charantia to produce high-quality, better yielding and stress tolerant bitter gourd genotypes. Methods The present study provides the first and high-quality chromosome-level genome assembly of M. balsamina with size 384.90 Mb and N50 30.96 Mb using sequence data from 10x Genomics, Nanopore, and Hi-C platforms. Results A total of 6,32,098 transposons elements; 2,15,379 simple sequence repeats; 5,67,483 transcription factor binding sites; 3,376 noncoding RNA genes; and 41,652 protein-coding genes were identified, and 4,347 disease resistance, 67 heat stress-related, 05 carotenoid-related, 15 salt stress-related, 229 cucurbitacin-related, 19 terpenes-related, 37 antioxidant activity, and 06 sex determination-related genes were characterized. Conclusion Genome sequencing of M. balsamina will facilitate interspecific introgression of desirable traits. This information is cataloged in the form of webgenomic resource available at http://webtom.cabgrid.res.in/mbger/. Our finding of comparative genome analysis will be useful to get insights into the patterns and processes associated with genome evolution and to uncover functional regions of cucurbit genomes.
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Affiliation(s)
- N. D. Vinay
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Kalpana Singh
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ranjith Kumar Ellur
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anilabha Das Munshi
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | | | - G. Boopalakrishnan
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gograj Singh Jat
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | | | - Ambika Baladev Gaikwad
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shyam Sundar Dey
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Tusar Kanti Behera
- Division of Vegetable Science, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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Wang J, Yuan M, Feng Y, Zhang Y, Bao S, Hao Y, Ding Y, Gao X, Yu Z, Xu Q, Zhao J, Zhu Q, Wang P, Wu C, Wang J, Li Y, Xu C, Wang J. A common whole-genome paleotetraploidization in Cucurbitales. PLANT PHYSIOLOGY 2022; 190:2430-2448. [PMID: 36053177 PMCID: PMC9706448 DOI: 10.1093/plphys/kiac410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/10/2022] [Indexed: 06/01/2023]
Abstract
Cucurbitales are an important order of flowering plants known for encompassing edible plants of economic and medicinal value and numerous ornamental plants of horticultural value. By reanalyzing the genomes of two representative families (Cucurbitaceae and Begoniaceae) in Cucurbitales, we found that the previously identified Cucurbitaceae common paleotetraploidization that occurred shortly after the core-eudicot-common hexaploidization event is shared by Cucurbitales, including Begoniaceae. We built a multigenome alignment framework for Cucurbitales by identifying orthologs and paralogs and systematically redating key evolutionary events in Cucurbitales. Notably, characterizing the gene retention levels and genomic fractionation patterns between subgenomes generated from different polyploidizations in Cucurbitales suggested the autopolyploid nature of the Begoniaceae common tetraploidization and the allopolyploid nature of the Cucurbitales common tetraploidization and the Cucurbita-specific tetraploidization. Moreover, we constructed the ancestral Cucurbitales karyotype comprising 17 proto-chromosomes, confirming that the most recent common ancestor of Cucurbitaceae contained 15 proto-chromosomes and rejecting the previous hypothesis for an ancestral Cucurbitaceae karyotype with 12 proto-chromosomes. In addition, we found that the polyploidization and tandem duplication events promoted the expansion of gene families involved in the cucurbitacin biosynthesis pathway; however, gene loss and chromosomal rearrangements likely limited the expansion of these gene families.
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Affiliation(s)
- Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Min Yuan
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yan Zhang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Shoutong Bao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qiang Xu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Junxin Zhao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qianwen Zhu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Ping Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Chunyang Wu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
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Wang J, Zhang L, Wang J, Hao Y, Xiao Q, Teng J, Shen S, Zhang Y, Feng Y, Bao S, Li Y, Yan Z, Wei C, Wang L, Wang J. Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow. BMC PLANT BIOLOGY 2022; 22:298. [PMID: 35710333 PMCID: PMC9205023 DOI: 10.1186/s12870-022-03684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remains poorly understood. RESULTS Here, through genomic synteny analyses, we identified duplicate genes generated by the Salicaceae common tetraploidization (SCT) in the poplar and willow genomes. We estimated that at least 0.58% and 0.25% of poplar and willow duplicates were affected by whole-gene conversion after the poplar-willow divergence, with more (5.73% and 2.66%) affected by partial-gene conversion. Moreover, we found that the converted duplicated genes were unevenly distributed on each chromosome in the two genomes, and the well-preserved homoeologous chromosome regions may facilitate the conversion of duplicates. Notably, we found that conversion maintained the similarity of duplicates, likely contributing to the conservation of certain sequences, but is essentially accelerated the rate of evolution and increased species divergence. In addition, we found that converted duplicates tended to have more similar expression patterns than nonconverted duplicates. We found that genes associated with multigene families were preferentially converted. We also found that the genes encoding conserved structural domains associated with specific traits exhibited a high frequency of conversion. CONCLUSIONS Extensive conversion between duplicate genes generated from the SCT contributes to the diversification of the family Salicaceae and has had long-lasting effects on those genes with important biological functions.
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Affiliation(s)
- Jianyu Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Lan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jiaqi Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yanan Hao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Qimeng Xiao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jia Teng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shaoqi Shen
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yishan Feng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shoutong Bao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yu Li
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Zimo Yan
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Chendan Wei
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Li Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
| | - Jinpeng Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
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Ren G, Jiang Y, Li A, Yin M, Li M, Mu W, Wu Y, Liu J. The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:116-128. [PMID: 34487631 PMCID: PMC8710827 DOI: 10.1111/pbi.13699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/18/2021] [Accepted: 09/01/2021] [Indexed: 05/02/2023]
Abstract
Achnatherum splendens Trin. (Gramineae) is a constructive species of the arid grassland ecosystem in Northwest China and is a major forage grass. It has good tolerance of salt and drought stress in alkaline habitats. Here, we report its chromosome-level genome, determined through a combination of Illumina HiSeq sequencing, PacBio sequencing and Hi-C technology. The final assembly of the ~1.17 Gb genome sequence had a super-scaffold N50 of 40.3 Mb. A total of 57 374 protein-coding genes were annotated, of which 54 426 (94.5%) genes have functional protein annotations. Approximately 735 Mb (62.37%) of the assembly were identified as repetitive elements, and among these, LTRs (40.53%) constitute the highest proportion, having made a major contribution to the expansion of genome size in A. splendens. Phylogenetic analysis revealed that A. splendens diverged from the Brachypodium distachyon-Hordeum vulgare-Aegilops tauschii subclade around 37 million years ago (Ma) and that a clade comprising these four species diverged from the Phyllostachys edulis clade ~47 Ma. Genomic synteny indicates that A. splendens underwent an additional species-specific whole-genome duplication (WGD) 18-20 Ma, which further promoted an increase in copies of numerous saline-alkali-related gene families in the A. splendens genome. By transcriptomic analysis, we further found that many of these duplicated genes from this extra WGD exhibited distinct functional divergence in response to salt stress. This WGD, therefore, contributed to the strong resistance to salt stress and widespread arid adaptation of A. splendens.
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Affiliation(s)
- Guangpeng Ren
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Yanyou Jiang
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ao Li
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Mou Yin
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Minjie Li
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Wenjie Mu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ying Wu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
- Key Laboratory of Bio‐Resources and Eco‐Environment of the Ministry of Education & State Key Lab of Hydraulics & Mountain River EngineeringCollege of Life SciencesSichuan UniversityChengduChina
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7
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Shen S, Li Y, Wang J, Wei C, Wang Z, Ge W, Yuan M, Zhang L, Wang L, Sun S, Teng J, Xiao Q, Bao S, Feng Y, Zhang Y, Wang J, Hao Y, Lei T, Wang J. Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis. Genes (Basel) 2021; 12:genes12121944. [PMID: 34946893 PMCID: PMC8701993 DOI: 10.3390/genes12121944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/11/2023] Open
Abstract
The peanut (Arachis hypogaea L.) is the leading oil and food crop among the legume family. Extensive duplicate gene pairs generated from recursive polyploidizations with high sequence similarity could result from gene conversion, caused by illegitimate DNA recombination. Here, through synteny-based comparisons of two diploid and three tetraploid peanut genomes, we identified the duplicated genes generated from legume common tetraploidy (LCT) and peanut recent allo-tetraploidy (PRT) within genomes. In each peanut genome (or subgenomes), we inferred that 6.8–13.1% of LCT-related and 11.3–16.5% of PRT-related duplicates were affected by gene conversion, in which the LCT-related duplicates were the most affected by partial gene conversion, whereas the PRT-related duplicates were the most affected by whole gene conversion. Notably, we observed the conversion between duplicates as the long-lasting contribution of polyploidizations accelerated the divergence of different Arachis genomes. Moreover, we found that the converted duplicates are unevenly distributed across the chromosomes and are more often near the ends of the chromosomes in each genome. We also confirmed that well-preserved homoeologous chromosome regions may facilitate duplicates’ conversion. In addition, we found that these biological functions contain a higher number of preferentially converted genes, such as catalytic activity-related genes. We identified specific domains that are involved in converted genes, implying that conversions are associated with important traits of peanut growth and development.
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Affiliation(s)
- Shaoqi Shen
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Yuxian Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Jianyu Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Chendan Wei
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Zhenyi Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Weina Ge
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Min Yuan
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Lan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Li Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Sangrong Sun
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Jia Teng
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Qimeng Xiao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Shoutong Bao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Yishan Feng
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Yan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Jiaqi Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Yanan Hao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Tianyu Lei
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
- Correspondence: (T.L.); (J.W.)
| | - Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Correspondence: (T.L.); (J.W.)
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Wei C, Wang Z, Wang J, Teng J, Shen S, Xiao Q, Bao S, Feng Y, Zhang Y, Li Y, Sun S, Yue Y, Wu C, Wang Y, Zhou T, Xu W, Yu J, Wang L, Wang J. Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence. BMC Genomics 2021; 22:460. [PMID: 34147070 PMCID: PMC8214281 DOI: 10.1186/s12864-021-07776-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. indica (XI) and Oryza sativa ssp. japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing gene conversion events and their impact on genome evolution. RESULTS Using comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19-5.77% of genes duplicated across the three rice genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~ 0.4 mya, with more (7.77-9.53%) showing conversion of only portions of genes. Independently converted duplicates surviving in the genomes of different subspecies often use the same donor genes. The ongoing gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes, 11 and 12, in each rice genome being most affected. Notably, ongoing gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. Chromosome rearrangements after polyploidization are associated with ongoing gene conversion events, and they directly restrict recombination and inhibit duplicated gene conversion between homeologous regions. Furthermore, we found that the converted genes tended to have more similar expression patterns than nonconverted duplicates. Gene conversion affects biological functions associated with multiple genes, such as catalytic activity, implying opportunities for interaction among members of large gene families, such as NBS-LRR disease-resistance genes, contributing to the occurrence of the gene conversion. CONCLUSION Duplicated genes in rice subspecies generated by grass polyploidization ~ 100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies.
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Affiliation(s)
- Chendan Wei
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Zhenyi Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jianyu Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jia Teng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shaoqi Shen
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Qimeng Xiao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shoutong Bao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yishan Feng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yuxian Li
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Sangrong Sun
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yuanshuai Yue
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Chunyang Wu
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yanli Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Tianning Zhou
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Wenbo Xu
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jigao Yu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Li Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
| | - Jinpeng Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
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Wang C, Chen S, Feng A, Su J, Wang W, Feng J, Chen B, Zhang M, Yang J, Zeng L, Zhu X. Xa7, a Small Orphan Gene Harboring Promoter Trap for AvrXa7, Leads to the Durable Resistance to Xanthomonas oryzae Pv. oryzae. RICE (NEW YORK, N.Y.) 2021; 14:48. [PMID: 34056673 PMCID: PMC8165051 DOI: 10.1186/s12284-021-00490-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/10/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND The rice (Oryza sativa) gene Xa7 has been hypothesized to be a typical executor resistance gene against Xanthomonas oryzae pv. oryzae (Xoo), and has conferred durable resistance in the field for decades. Its identity and the molecular mechanisms underlying this resistance remain elusive. RESULTS Here, we filled in gaps of genome in Xa7 mapping locus via BAC library construction, revealing the presence of a 100-kb non-collinear sequence in the line IRBB7 compared with Nipponbare reference genomes. Complementary transformation with sequentially overlapping subclones of the BACs demonstrated that Xa7 is an orphan gene, encoding a small novel protein distinct from any other resistance proteins reported. A 27-bp effector binding element (EBE) in the Xa7 promoter is essential for AvrXa7-inducing expression model. XA7 is anchored in the endoplasmic reticulum membrane and triggers programmed cell death in rice and tobacco (Nicotiana benthamiana). The Xa7 gene is absent in most cultivars, landraces, and wild rice accessions, but highly homologs of XA7 were identified in Leersia perrieri, the nearest outgroup of the genus Oryza. CONCLUSIONS Xa7 acts as a trap to perceive AvrXa7 via EBEAvrXa7 in its promoter, leading to the initiation of resistant reaction. Since EBEAvrXa7 is ubiquitous in promoter of rice susceptible gene SWEET14, the elevated expression of which is conducive to the proliferation of Xoo, that lends a great benefit for the Xoo strains retaining AvrXa7. As a result, varieties harboring Xa7 would show more durable resistance in the field. Xa7 alleles analysis suggests that the discovery of new resistance genes could be extended beyond wild rice, to include wild grasses such as Leersia species.
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Affiliation(s)
- Congying Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shen Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Aiqing Feng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jing Su
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wenjuan Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jinqi Feng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bing Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Meiying Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jianyuan Yang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Liexian Zeng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiaoyuan Zhu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Kong W, Nabukalu P, Cox TS, Goff VH, Pierce GJ, Lemke C, Robertson JS, Compton R, Tang H, Paterson AH. Transmission Genetics of a Sorghum bicolor × S. halepense Backcross Populations. FRONTIERS IN PLANT SCIENCE 2020; 11:467. [PMID: 32425964 PMCID: PMC7203413 DOI: 10.3389/fpls.2020.00467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Despite a "ploidy barrier," interspecific crosses to wild and/or cultivated sorghum (Sorghum bicolor, 2n = 2x = 20) may have aided the spread across six continents of Sorghum halepense, also exemplifying risks of "transgene escape" from crops that could make weeds more difficult to control. Genetic maps of two BC1F1 populations derived from crosses of S. bicolor (sorghum) and S. halepense with totals of 722 and 795 single nucleotide polymorphism (SNP) markers span 37 and 35 linkage groups, with 2-6 for each of the 10 basic sorghum chromosomes due to fragments covering different chromosomal portions or independent segregation from different S. halepense homologs. Segregation distortion favored S. halepense alleles on chromosomes 2 (1.06-4.68 Mb, near a fertility restoration gene), 7 (1.20-6.16 Mb), 8 (1.81-5.33 Mb, associated with gene conversion), and 9 (47.5-50.1 Mb); and S. bicolor alleles on chromosome 6 (0-40 Mb), which contains both a large heterochromatin block and the Ma1 gene. Regions of the S. halepense genome that are recalcitrant to gene flow from sorghum might be exploited as part a multi-component system to reduce the likelihood of spread of transgenes or other modified genes. Its SNP profile suggests that chromosome segments from its respective progenitors S. bicolor and Sorghum propinquum have extensively recombined in S. halepense. This study reveals genomic regions that might discourage crop-to-weed gene escape, and provides a foundation for marker-trait association analysis to determine the genetic control of traits contributing to weediness, invasiveness, and perenniality of S. halepense.
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Affiliation(s)
- Wenqian Kong
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | | | - T. Stan Cox
- The Land Institute, Salina, KS, United States
| | - Valorie H. Goff
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Gary J. Pierce
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Jon S. Robertson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Rosana Compton
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
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11
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Diop SI, Subotic O, Giraldo-Fonseca A, Waller M, Kirbis A, Neubauer A, Potente G, Murray-Watson R, Boskovic F, Bont Z, Hock Z, Payton AC, Duijsings D, Pirovano W, Conti E, Grossniklaus U, McDaniel SF, Szövényi P. A pseudomolecule-scale genome assembly of the liverwort Marchantia polymorpha. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1378-1396. [PMID: 31692190 DOI: 10.1111/tpj.14602] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 10/28/2019] [Indexed: 05/07/2023]
Abstract
Marchantia polymorpha has recently become a prime model for cellular, evo-devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule-scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high-density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map-based cloning, feasible.
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Affiliation(s)
- Seydina I Diop
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Oliver Subotic
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Alejandro Giraldo-Fonseca
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Alexander Kirbis
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Rachel Murray-Watson
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Filip Boskovic
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, CB3 0HE, Cambridge, UK
| | - Zoe Bont
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
| | - Zsofia Hock
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Adam C Payton
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL, 32611, USA
| | | | - Walter Pirovano
- BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, the Netherlands
| | - Elena Conti
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Stuart F McDaniel
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL, 32611, USA
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
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Fan K, Mao Z, Zheng J, Chen Y, Li Z, Lin W, Zhang Y, Huang J, Lin W. Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species Gossypium hirsutum and Gossypium barbadense. FRONTIERS IN PLANT SCIENCE 2020; 11:545042. [PMID: 33101325 PMCID: PMC7554350 DOI: 10.3389/fpls.2020.545042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/14/2020] [Indexed: 05/07/2023]
Abstract
The comprehensive analysis of gene family evolution will elucidate the origin and evolution of gene families. The K+ uptake (KUP) gene family plays important roles in K+ uptake and transport, plant growth and development, and abiotic stress responses. However, the current understanding of the KUP family in cotton is limited. In this study, 51 and 53 KUPs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. These KUPs were divided into five KUP subfamilies, with subfamily 2 containing three groups. Different subfamilies had different member numbers, conserved motifs, gene structures, regulatory elements, and gene expansion and loss rates. A paleohexaploidization event caused the expansion of GhKUP and GbKUP in cotton, and duplication events in G. hirsutum and G. barbadense have happened in a common ancestor of Gossypium. Meanwhile, the KUP members of the two allopolyploid subgenomes of G. hirsutum and G. barbadense exhibited unequal gene proportions, gene structural diversity, uneven chromosomal distributions, asymmetric expansion rates, and biased gene loss rates. In addition, the KUP families of G. hirsutum and G. barbadense displayed evolutionary conservation and divergence. Taken together, these results illustrated the molecular evolution and expansion of the KUP family in allopolyploid cotton species.
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Affiliation(s)
- Kai Fan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Zhijun Mao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Jiaxin Zheng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Yunrui Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Zhaowei Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Weiwei Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Yongqiang Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Jinwen Huang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- *Correspondence: Jinwen Huang, ; Wenxiong Lin,
| | - Wenxiong Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- *Correspondence: Jinwen Huang, ; Wenxiong Lin,
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Li ZK, Chen B, Li XX, Wang JP, Zhang Y, Wang XF, Yan YY, Ke HF, Yang J, Wu JH, Wang GN, Zhang GY, Wu LQ, Wang XY, Ma ZY. A newly identified cluster of glutathione S-transferase genes provides Verticillium wilt resistance in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:213-227. [PMID: 30561788 DOI: 10.1111/tpj.14206] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 05/08/2023]
Abstract
As the largest cultivated fiber crop in the world, cotton (Gossypium hirsutum) is often exposed to various biotic stresses during its growth periods. Verticillium wilt caused by Verticillium dahliae is a severe disease in cotton, and the molecular mechanism of cotton resistance for Verticillium wilt needs to be further investigated. Here, we revealed that the cotton genome contains nine types of GST genes. An evolutionary analysis showed that a newly identified cluster (including Gh_A09G1508, Gh_A09G1509 and Gh_A09G1510) located on chromosome 09 of the A-subgenome was under positive selection pressure during the formation of an allotetraploid. Transcriptome analysis showed that this cluster participates in Verticillium wilt resistance. Because the Gh_A09G1509 gene showed the greatest differential expression in the resistant cultivar under V. dahliae stress, we overexpressed this gene in tobacco and found that its overexpression resulted in enhanced Verticillium wilt resistance. Suppression of the gene cluster via virus-induced gene silencing made cotton plants of the resistant cultivar Nongda601 significantly susceptible. These results demonstrated that the GST cluster played an important role in Verticillium wilt resistance. Further investigation showed that the encoded enzymes of the cluster were essential for the delicate equilibrium between the production and scavenging of H2 O2 during V. dahliae stress.
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Affiliation(s)
- Zhi-Kun Li
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Bin Chen
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xiu-Xin Li
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Jin-Peng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, China
| | - Yan Zhang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xing-Fen Wang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Yuan-Yuan Yan
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Hui-Feng Ke
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Jun Yang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Jin-Hua Wu
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Guo-Ning Wang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Gui-Yin Zhang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Li-Qiang Wu
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xi-Yin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, China
| | - Zhi-Ying Ma
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
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14
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Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol 2019; 20:38. [PMID: 30791939 PMCID: PMC6383267 DOI: 10.1186/s13059-019-1650-2] [Citation(s) in RCA: 453] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. RESULTS We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. CONCLUSIONS We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qionghou Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Yin
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaijie Qi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605 USA
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15
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Jia L, Zhao Q, Chen S. Evolution and expression analysis of the sorghum ubiquitin-conjugating enzyme family. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:236-247. [PMID: 32172767 DOI: 10.1071/fp18184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/02/2018] [Indexed: 06/10/2023]
Abstract
Ubiquitin-conjugating enzymes (UBCs), which catalyse the transfer of ubiquitin to substrate or E3 ligases, are key enzymes in ubiquitination modifications of target proteins. Current knowledge regarding the sorghum (Sorghum bicolor (L.) Moench) ubiquitin-conjugating enzyme (SbUBC) family remains very limited. We identified 53 UBC-encoding genes in the sorghum genome and divided these into 18 groups according to their phylogenetic relationship with Arabidopsis thaliana (L.) Heynh., which was further supported by conserved motif and gene structure analyses. Different expression levels under a variety of abiotic stresses suggested that these might participate in distinct signalling pathways and that they underwent functional divergence during evolution. Furthermore, several SbUBC genes responded to single treatments, and individual SbUBC genes responded to multiple treatments, suggesting that sorghum UBCs may mediate crosstalk among different signalling pathways. Overall, the results provide valuable information for better understanding the classification and putative functions of sorghum UBC-encoding genes.
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Affiliation(s)
- Liqiang Jia
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - QiuFang Zhao
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Shu Chen
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
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16
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Cossu RM, Casola C, Giacomello S, Vidalis A, Scofield DG, Zuccolo A. LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes. Genome Biol Evol 2018; 9:3449-3462. [PMID: 29228262 PMCID: PMC5751070 DOI: 10.1093/gbe/evx260] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 12/29/2022] Open
Abstract
The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read-based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.
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Affiliation(s)
- Rosa Maria Cossu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University
| | - Stefania Giacomello
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Amaryllis Vidalis
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Section of Population Epigenetics and Epigenomics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Douglas G Scofield
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Sweden
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Istituto di Genomica Applicata, Udine, Italy
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17
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Qiao X, Yin H, Li L, Wang R, Wu J, Wu J, Zhang S. Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear ( Pyrus bretschneideri). FRONTIERS IN PLANT SCIENCE 2018; 9:161. [PMID: 29487610 PMCID: PMC5816897 DOI: 10.3389/fpls.2018.00161] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/29/2018] [Indexed: 05/21/2023]
Abstract
Pear is an important fruit crop of the Rosaceae family and has experienced two rounds of ancient whole-genome duplications (WGDs). However, whether different types of gene duplications evolved differently after duplication remains unclear in the pear genome. In this study, we identified the different modes of gene duplication in pear. Duplicate genes derived from WGD, tandem, proximal, retrotransposed, DNA-based transposed or dispersed duplications differ in genomic distribution, gene features, selection pressure, expression divergence, regulatory divergence and biological roles. Widespread sequence, expression and regulatory divergence have occurred between duplicate genes over the 30-45 million years of evolution after the recent genome duplication in pear. The retrotransposed genes show relatively higher expression and regulatory divergence than other gene duplication modes. In contrast, WGD genes underwent a slower sequence divergence and may be influenced by abundant gene conversion events. Moreover, the different classes of duplicate genes exhibited biased functional roles. We also investigated the evolution and expansion patterns of the gene families involved in sugar and organic acid metabolism pathways, which are closely related to the fruit quality and taste in pear. Single-gene duplications largely account for the extensive expansion of gene families involved in the sorbitol metabolism pathway in pear. Gene family expansion was also detected in the sucrose metabolism pathway and tricarboxylic acid cycle pathways. Thus, this study provides insights into the evolutionary fates of duplicated genes.
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Affiliation(s)
| | | | | | | | | | | | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
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18
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Wang J, Sun P, Li Y, Liu Y, Yu J, Ma X, Sun S, Yang N, Xia R, Lei T, Liu X, Jiao B, Xing Y, Ge W, Wang L, Wang Z, Song X, Yuan M, Guo D, Zhang L, Zhang J, Jin D, Chen W, Pan Y, Liu T, Jin L, Sun J, Yu J, Cheng R, Duan X, Shen S, Qin J, Zhang MC, Paterson AH, Wang X. Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform. PLANT PHYSIOLOGY 2017; 174:284-300. [PMID: 28325848 PMCID: PMC5411148 DOI: 10.1104/pp.16.01981] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/19/2017] [Indexed: 05/18/2023]
Abstract
Mainly due to their economic importance, genomes of 10 legumes, including soybean (Glycine max), wild peanut (Arachis duranensis and Arachis ipaensis), and barrel medic (Medicago truncatula), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape (Vitis vinifera) and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by widespread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported the likely autopolyploidy nature of its tetraploid ancestor. Moreover, although most gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to the copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes and, by performing synonymous nucleotide substitutions at synonymous sites correction, redated major evolutionary events during their expansion. This effort laid a solid foundation for further genomics exploration in the legume research community and beyond. We describe only a tiny fraction of legume comparative genomics analysis that we performed; more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org).
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Affiliation(s)
- Jinpeng Wang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Pengchuan Sun
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Yuxian Li
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Yinzhe Liu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jigao Yu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xuelian Ma
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Sangrong Sun
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Nanshan Yang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Ruiyan Xia
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Tianyu Lei
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xiaojian Liu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Beibei Jiao
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Yue Xing
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Weina Ge
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Li Wang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Zhenyi Wang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xiaoming Song
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Min Yuan
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Di Guo
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Lan Zhang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jiaqi Zhang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Dianchuan Jin
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Wei Chen
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Yuxin Pan
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Tao Liu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Ling Jin
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jinshuai Sun
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jiaxiang Yu
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Rui Cheng
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xueqian Duan
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Shaoqi Shen
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Jun Qin
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Meng-Chen Zhang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Andrew H Paterson
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
| | - Xiyin Wang
- School of Life Sciences (J.W., Y.Li, Y.Liu, J.Y., X.M., S.Su., N.Y., R.X., T.Le., X.L., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., Y.P., J.S., J.Y., R.C., X.D., S.Sh., X.W.) and Center for Genomics and Computational Biology (J.W., P.S., Y.Li, Y.Liu, J.Y., S.Su., N.Y., T.Le., B.J., Y.X., W.G., L.W., Z.W., X.S., M.Y., D.G., L.Z., J.Z., D.J., W.C., Y.P., T.Li., L.J., J.Y., X.W.), North China University of Science and Technology, Tangshan, Hebei 063000, China
- Cereal and Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China (J.Q., M.Z.); and
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605 (A.P.)
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Yu Y, Xiang Q, Manos PS, Soltis DE, Soltis PS, Song BH, Cheng S, Liu X, Wong G. Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences. PLoS One 2017; 12:e0171361. [PMID: 28225773 PMCID: PMC5321274 DOI: 10.1371/journal.pone.0171361] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/18/2017] [Indexed: 11/18/2022] Open
Abstract
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants.
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Affiliation(s)
- Yan Yu
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China
- Department of Biology, Duke University, 130 Science Drive, Durham, NC, United States of America
- * E-mail: (QX); (YY)
| | - Qiuyun Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
- * E-mail: (QX); (YY)
| | - Paul S. Manos
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, PR China
| | - Douglas E. Soltis
- Florida Natural History Museum, University of Florida, Gainesville, FL, United States of America
- Department of Biology, University of Florida, Gainesville, FL, United States of America
| | - Pamela S. Soltis
- Florida Natural History Museum, University of Florida, Gainesville, FL, United States of America
- Department of Biology, University of Florida, Gainesville, FL, United States of America
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, United States of America
| | | | - Xin Liu
- BGI-Shenzhen, Shenzhen, China
| | - Gane Wong
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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Liu Y, Wang J, Ge W, Wang Z, Li Y, Yang N, Sun S, Zhang L, Wang X. Two Highly Similar Poplar Paleo-subgenomes Suggest an Autotetraploid Ancestor of Salicaceae Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:571. [PMID: 28446920 PMCID: PMC5388744 DOI: 10.3389/fpls.2017.00571] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/29/2017] [Indexed: 05/12/2023]
Abstract
As a model plant to study perennial trees in the Salicaceae family, the poplar (Populus trichocarpa) genome was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment of its genome to a well-selected reference genome would help us better understand poplar's genome structure and gene family evolution. Here, by adopting the relatively simpler grape (Vitis vinifera) genome as reference, and by inferring both intra- and inter-genomic gene collinearity, we produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation. We uncovered homologous blocks in the grape and poplar genomes and also between them. Moreover, we characterized the genes missing and found that poplar had two considerably similar subgenomes (≤0.05 difference in gene deletion) produced by the Salicaceae-common tetraploidization, suggesting its autotetraploid nature. Taken together, this work provides a timely and valuable dataset of orthologous and paralogous genes for further study of the genome structure and functional evolution of poplar and other Salicaceae plants.
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Affiliation(s)
- Yinzhe Liu
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Jinpeng Wang
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Weina Ge
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Zhenyi Wang
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Yuxian Li
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Nanshan Yang
- School of Life Science, North China University of Science and TechnologyTangshan, China
| | - Sangrong Sun
- School of Life Science, North China University of Science and TechnologyTangshan, China
| | - Liwei Zhang
- School of Life Science, North China University of Science and TechnologyTangshan, China
| | - Xiyin Wang
- School of Life Science, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
- *Correspondence: Xiyin Wang,
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21
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Sun S, Wang J, Yu J, Meng F, Xia R, Wang L, Wang Z, Ge W, Liu X, Li Y, Liu Y, Yang N, Wang X. Alignment of Common Wheat and Other Grass Genomes Establishes a Comparative Genomics Research Platform. FRONTIERS IN PLANT SCIENCE 2017; 8:1480. [PMID: 28912789 PMCID: PMC5582351 DOI: 10.3389/fpls.2017.01480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 08/09/2017] [Indexed: 05/06/2023]
Abstract
Grass genomes are complicated structures as they share a common tetraploidization, and particular genomes have been further affected by extra polyploidizations. These events and the following genomic re-patternings have resulted in a complex, interweaving gene homology both within a genome, and between genomes. Accurately deciphering the structure of these complicated plant genomes would help us better understand their compositional and functional evolution at multiple scales. Here, we build on our previous research by performing a hierarchical alignment of the common wheat genome vis-à-vis eight other sequenced grass genomes with most up-to-date assemblies, and annotations. With this data, we constructed a list of the homologous genes, and then, in a layer-by-layer process, separated their orthology, and paralogy that were established by speciations and recursive polyploidizations, respectively. Compared with the other grasses, the far fewer collinear outparalogous genes within each of three subgenomes of common wheat suggest that homoeologous recombination, and genomic fractionation should have occurred after its formation. In sum, this work contributes to the establishment of an important and timely comparative genomics platform for researchers in the grass community and possibly beyond. Homologous gene list can be found in Supplemental material.
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Affiliation(s)
- Sangrong Sun
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Ruiyan Xia
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Li Wang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Zhenyi Wang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Weina Ge
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Xiaojian Liu
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Yuxian Li
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Yinzhe Liu
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Nanshan Yang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and TechnologyTangshan, China
- Center for Genomics and Computational Biology, North China University of Science and TechnologyTangshan, China
- *Correspondence: Xiyin Wang
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22
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Korunes KL, Noor MAF. Gene conversion and linkage: effects on genome evolution and speciation. Mol Ecol 2016; 26:351-364. [DOI: 10.1111/mec.13736] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/07/2016] [Accepted: 06/22/2016] [Indexed: 12/12/2022]
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A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7237053. [PMID: 27195295 PMCID: PMC4852346 DOI: 10.1155/2016/7237053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/24/2016] [Accepted: 03/28/2016] [Indexed: 11/18/2022]
Abstract
Motivation. Clustered regularly interspaced short palindromic repeat (CRISPR) is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas) gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals. Results. This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition is proposed to cover all the CRISPRs. The comprehensive comparison of CRISPR numbers on the taxonomic levels of both domains and genus shows high variations for closely related species even in the same genus. The detailed investigation of how CRISPRs are evolutionarily manipulated in the 8 completely sequenced species in the genus Thermoanaerobacter demonstrates that transposons act as a frequent tool for splitting long CRISPRs into shorter ones along a long evolutionary history.
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24
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Wang X, Guo H, Wang J, Lei T, Liu T, Wang Z, Li Y, Lee TH, Li J, Tang H, Jin D, Paterson AH. Comparative genomic de-convolution of the cotton genome revealed a decaploid ancestor and widespread chromosomal fractionation. THE NEW PHYTOLOGIST 2016; 209:1252-63. [PMID: 26756535 DOI: 10.1111/nph.13689] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 08/28/2015] [Indexed: 05/23/2023]
Abstract
The 'apparently' simple genomes of many angiosperms mask complex evolutionary histories. The reference genome sequence for cotton (Gossypium spp.) revealed a ploidy change of a complexity unprecedented to date, indeed that could not be distinguished as to its exact dosage. Herein, by developing several comparative, computational and statistical approaches, we revealed a 5× multiplication in the cotton lineage of an ancestral genome common to cotton and cacao, and proposed evolutionary models to show how such a decaploid ancestor formed. The c. 70% gene loss necessary to bring the ancestral decaploid to its current gene count appears to fit an approximate geometrical model; that is, although many genes may be lost by single-gene deletion events, some may be lost in groups of consecutive genes. Gene loss following cotton decaploidy has largely just reduced gene copy numbers of some homologous groups. We designed a novel approach to deconvolute layers of chromosome homology, providing definitive information on gene orthology and paralogy across broad evolutionary distances, both of fundamental value and serving as an important platform to support further studies in and beyond cotton and genomics communities.
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Affiliation(s)
- Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Jinpeng Wang
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China
| | - Tianyu Lei
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China
- School of Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China
| | - Tao Liu
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China
- School of Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China
| | - Zhenyi Wang
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China
| | - Yuxian Li
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Jingping Li
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, 85721, USA
- Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, IA, 50011, USA
| | - Dianchuan Jin
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei, 063000, China
- School of Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
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25
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Malviya N, Jaiswal P, Yadav D. Genome- wide characterization of Nuclear Factor Y (NF-Y) gene family of sorghum [Sorghum bicolor (L.) Moench]: a bioinformatics approach. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:33-49. [PMID: 27186017 PMCID: PMC4840140 DOI: 10.1007/s12298-016-0349-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 03/11/2016] [Accepted: 03/28/2016] [Indexed: 05/29/2023]
Abstract
Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor (TF) complex with preferential binding to CCAAT elements of promoters, regulating gene expression in most of the higher eukaryotes. The availability of plant genome sequences have revealed multiple number of genes coding for the three subunits, namely NF-YA, NF-YB and NF-YC in contrast to single NF-Y gene for each subunit reported in yeast and animals. A total of 33 NF-YTF comprising of 8 NF-YA, 11 NF-YB and 14 NF-YC subunits were accessed from the sorghum genome. The bioinformatic characterization of NF-Y gene family of sorghum for gene structure, chromosome location, protein motif, phylogeny, gene duplication and in-silico expression under abiotic stresses have been attempted in the present study. The identified SbNF-Y genes are distributed on all the 10 chromosomes of sorghum with variability in the frequency and 18 out of 33 SbNF-Ys were found to be intronless. Segmental duplication event was found to be predominant feature based on gene duplication pattern study. Several orthologs and paralogs groups were disclosed through the comprehensive phylogenetic analysis of SbNF-Y proteins along with 36 Arabidopsis and 28 rice NF-Y proteins. In-silico expression analysis under abiotic stresses using rice transcriptome data revealed several of the sorghum NF-Y genes to be associated with salt, drought, cold and heat stresses.
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Affiliation(s)
- Neha Malviya
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh 273 009 India
| | - Parul Jaiswal
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh 273 009 India
| | - Dinesh Yadav
- Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur, Uttar Pradesh 273 009 India
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26
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Song X, Wang J, Ma X, Li Y, Lei T, Wang L, Ge W, Guo D, Wang Z, Li C, Zhao J, Wang X. Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1186. [PMID: 27570529 PMCID: PMC4982375 DOI: 10.3389/fpls.2016.01186] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/22/2016] [Indexed: 05/03/2023]
Abstract
The AP2/ERF superfamily, one of the most important transcription factor families, plays crucial roles in response to biotic and abiotic stresses. So far, a comprehensive evolutionary inference of its origination and expansion has not been available. Here, we identified 515 AP2/ERF genes in B. napus, a neo-tetraploid forming ~7500 years ago, and found that 82.14% of them were duplicated in the tetraploidization. A prominent subgenome bias was revealed in gene expression, tissue-specific, and gene conversion. Moreover, a large-scale analysis across plants and alga suggested that this superfamily could have been originated from AP2 family, expanding to form other families (ERF, and RAV). This process was accompanied by duplicating and/or alternative deleting AP2 domain, intragenic domain sequence conversion, and/or by acquiring other domains, resulting in copy number variations, alternatively contributing to functional innovation. We found that significant positive selection occurred at certain critical nodes during the evolution of land plants, possibly responding to changing environment. In conclusion, the present research revealed origination, functional innovation, and evolutionary trajectory of the AP2/ERF superfamily, contributing to understanding their roles in plant stress tolerance.
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Affiliation(s)
- Xiaoming Song
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Jinpeng Wang
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Xiao Ma
- Library, North China University of Science and TechnologyTangshan, China
| | - Yuxian Li
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Tianyu Lei
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Li Wang
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Weina Ge
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Di Guo
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Zhenyi Wang
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Chunjin Li
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
- Jianjun Zhao
| | - Xiyin Wang
- Department of Life Sciences, North China University of Science and TechnologyTangshan, China
- *Correspondence: Xiyin Wang
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27
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Wicker T, Wing RA, Schubert I. Recurrent sequence exchange between homeologous grass chromosomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:747-59. [PMID: 26408412 DOI: 10.1111/tpj.13040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/03/2015] [Accepted: 09/14/2015] [Indexed: 05/10/2023]
Abstract
All grass species evolved from an ancestor that underwent a whole-genome duplication (WGD) approximately 70 million years ago. Interestingly, the short arms of rice chromosomes 11 and 12 (and independently their homologs in sorghum) were found to be much more similar to each other than other homeologous regions within the duplicated genome. Based on detailed analysis of rice chromosomes 11 and 12 and their homologs in seven grass species, we propose a mechanism that explains the apparently 'younger' age of the duplication in this region of the genome, assuming a small number of reciprocal translocations at the chromosome termini. In each case the translocations were followed by unbalanced transmission and subsequent lineage sorting of the involved chromosomes to offspring. Molecular dating of these translocation events also allowed us to date major chromosome 'fusions' in the evolutionary lineages that led to Brachypodium and Triticeae. Furthermore, we provide evidence that rice is exceptional regarding the evolution of chromosomes 11 and 12, inasmuch as in other species the process of sequence exchange between homeologous chromosomes ceased much earlier than in rice. We presume that random events rather than selective forces are responsible for the observed high similarity between the short arm ends of rice chromosomes 11 and 12.
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Affiliation(s)
- Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, D-06466, Germany
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
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28
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Wang X, Wang J, Jin D, Guo H, Lee TH, Liu T, Paterson AH. Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for Key Evolutionary Events. MOLECULAR PLANT 2015; 8:885-98. [PMID: 25896453 DOI: 10.1016/j.molp.2015.04.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 03/13/2015] [Accepted: 04/06/2015] [Indexed: 05/06/2023]
Abstract
Multiple comparisons among genomes can clarify their evolution, speciation, and functional innovations. To date, the genome sequences of eight grasses representing the most economically important Poaceae (grass) clades have been published, and their genomic-level comparison is an essential foundation for evolutionary, functional, and translational research. Using a formal and conservative approach, we aligned these genomes. Direct comparison of paralogous gene pairs all duplicated simultaneously reveal striking variation in evolutionary rates among whole genomes, with nucleotide substitution slowest in rice and up to 48% faster in other grasses, adding a new dimension to the value of rice as a grass model. We reconstructed ancestral genome contents for major evolutionary nodes, potentially contributing to understanding the divergence and speciation of grasses. Recent fossil evidence suggests revisions of the estimated dates of key evolutionary events, implying that the pan-grass polyploidization occurred ∼96 million years ago and could not be related to the Cretaceous-Tertiary mass extinction as previously inferred. Adjusted dating to reflect both updated fossil evidence and lineage-specific evolutionary rates suggested that maize subgenome divergence and maize-sorghum divergence were virtually simultaneous, a coincidence that would be explained if polyploidization directly contributed to speciation. This work lays a solid foundation for Poaceae translational genomics.
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Affiliation(s)
- Xiyin Wang
- Plant Genome Mapping Laboratory, University of Athens, GA 30602, USA; Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China; College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jingpeng Wang
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China; College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Dianchuan Jin
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China; College of Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Athens, GA 30602, USA; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Athens, GA 30602, USA
| | - Tao Liu
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China; College of Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Athens, GA 30602, USA; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA; Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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29
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Tennessen JA, Govindarajulu R, Ashman TL, Liston A. Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. Genome Biol Evol 2014; 6:3295-313. [PMID: 25477420 PMCID: PMC4986458 DOI: 10.1093/gbe/evu261] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes.
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Affiliation(s)
| | | | | | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University
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Murat F, Zhang R, Guizard S, Flores R, Armero A, Pont C, Steinbach D, Quesneville H, Cooke R, Salse J. Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Genome Biol Evol 2014; 6:12-33. [PMID: 24317974 PMCID: PMC3914691 DOI: 10.1093/gbe/evt200] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted, and shuffled, defining dominant (bias toward duplicate retention) and sensitive (bias toward duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in seven protochromosomes containing 16,464 protogenes and following evolutionary rules where 1) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) subgenomes, 2) subgenome dominance is revealed by both gene deletion and shuffling from the S blocks, 3) duplicate deletion/movement may have been mediated by single-/double-stranded illegitimate recombination mechanisms, 4) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, 5) the fusion of two dominant blocks leads to supradominant neochromosomes (D + D = D) with higher ancestral gene retention compared with D + S = D (i.e., fusion of blocks with opposite sensitivity) or even S + S = S (i.e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named "PlantSyntenyViewer," available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data.
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Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC (Génétique, Diversité et Ecophysiologie des Céréales), Clermont Ferrand, France
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Aitken KS, McNeil MD, Berkman PJ, Hermann S, Kilian A, Bundock PC, Li J. Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane. BMC PLANT BIOLOGY 2014; 14:190. [PMID: 25059596 PMCID: PMC4222257 DOI: 10.1186/s12870-014-0190-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/14/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND The understanding of sugarcane genetics has lagged behind that of other members of the Poaceae family such as wheat, rice, barley and sorghum mainly due to the complexity, size and polyploidization of the genome. We have used the genetic map of a sugarcane cultivar to generate a consensus genetic map to increase genome coverage for comparison to the sorghum genome. We have utilized the recently developed sugarcane DArT array to increase the marker density within the genetic map. The sequence of these DArT markers plus SNP and EST-SSR markers was then used to form a bridge to the sorghum genomic sequence by BLAST alignment to start to unravel the complex genomic architecture of sugarcane. RESULTS Comparative mapping revealed that certain sugarcane chromosomes show greater levels of synteny to sorghum than others. On a macrosyntenic level a good collinearity was observed between sugarcane and sorghum for 4 of the 8 homology groups (HGs). These 4 HGs were syntenic to four sorghum chromosomes with from 98% to 100% of these chromosomes covered by these linked markers. Four major chromosome rearrangements were identified between the other four sugarcane HGs and sorghum, two of which were condensations of chromosomes reducing the basic chromosome number of sugarcane from x = 10 to x = 8. This macro level of synteny was transferred to other members within the Poaceae family such as maize to uncover the important evolutionary relationships that exist between sugarcane and these species. CONCLUSIONS Comparative mapping of sugarcane to the sorghum genome has revealed new information on the genome structure of sugarcane which will help guide identification of important genes for use in sugarcane breeding. Furthermore of the four major chromosome rearrangements identified in this study, three were common to maize providing some evidence that chromosome reduction from a common paleo-ancestor of both maize and sugarcane was driven by the same translocation events seen in both species.
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Affiliation(s)
- Karen S Aitken
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia
| | - Meredith D McNeil
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia
| | - Paul J Berkman
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia
| | - Scott Hermann
- BSES Limited, 50 Meiers Road, Indooroopilly, Brisbane 4068, QLD, Australia
| | - Andrzej Kilian
- Diversity Arrays P/L, 1 Wilf Crane Crescent, Yarralumla, Canberra 2600, ACT, Australia
| | - Peter C Bundock
- Southern Cross University, Ctr Plant Conservation Genetics, Lismore 2480, NSW, Australia
| | - Jingchuan Li
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia
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Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton). Genetics 2014; 197:1153-63. [PMID: 24907262 DOI: 10.1534/genetics.114.166124] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Genome duplication is thought to be central to the evolution of morphological complexity, and some polyploids enjoy a variety of capabilities that transgress those of their diploid progenitors. Comparison of genomic sequences from several tetraploid (AtDt) Gossypium species and genotypes with putative diploid A- and D-genome progenitor species revealed that unidirectional DNA exchanges between homeologous chromosomes were the predominant mechanism responsible for allelic differences between the Gossypium tetraploids and their diploid progenitors. Homeologous gene conversion events (HeGCEs) gradually subsided, declining to rates similar to random mutation during radiation of the polyploid into multiple clades and species. Despite occurring in a common nucleus, preservation of HeGCE is asymmetric in the two tetraploid subgenomes. At-to-Dt conversion is far more abundant than the reciprocal, is enriched in heterochromatin, is highly correlated with GC content and transposon distribution, and may silence abundant A-genome-derived retrotransposons. Dt-to-At conversion is abundant in euchromatin and genes, frequently reversing losses of gene function. The long-standing observation that the nonspinnable-fibered D-genome contributes to the superior yield and quality of tetraploid cotton fibers may be explained by accelerated Dt to At conversion during cotton domestication and improvement, increasing dosage of alleles from the spinnable-fibered A-genome. HeGCE may provide an alternative to (rare) reciprocal DNA exchanges between chromosomes in heterochromatin, where genes have approximately five times greater abundance of Dt-to-At conversion than does adjacent intergenic DNA. Spanning exon-to-gene-sized regions, HeGCE is a natural noninvasive means of gene transfer with the precision of transformation, potentially important in genetic improvement of many crop plants.
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Kim C, Wang X, Lee TH, Jakob K, Lee GJ, Paterson AH. Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates. THE PLANT CELL 2014; 26:2420-2429. [PMID: 24963058 PMCID: PMC4114942 DOI: 10.1105/tpc.114.125583] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/28/2014] [Accepted: 06/04/2014] [Indexed: 05/18/2023]
Abstract
Multiple polyploidizations with divergent consequences in the grass subtribe Saccharinae provide a singular opportunity to study in situ adaptation of a genome to the duplicated state, heretofore known primarily from paleogenomics. We show that allopolyploidy in a common Miscanthus-Saccharum ancestor ∼3.8 to 4.6 million years ago closely coincides in time with their divergence from the Sorghum lineage. Subsequent Saccharum-specific autopolyploidy may have created pseudo-paralogous chromosome groups with random pairing within a group but infrequent pairing between groups. High chromosome number may reduce differentiation among Saccharum pseudo-paralogs by increasing opportunities for recombinations, with the lower chromosome numbers of Miscanthus favoring the return to disomic inheritance. The widespread tendency of plant chromosome numbers to recursively return to a narrow range following genome duplication appears to be occurring now in Saccharum spontaneum based on rich polymorphism for chromosome number among genotypes, with past reductions indicated by condensations of two ancestral chromosomes in Miscanthus (now n = 19) and perhaps as many as 10 in the Narenga-Sclerostachya clade (n = 15).
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Affiliation(s)
- Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 Center for Genomics and Computational Biology, College of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | | | - Geung-Joo Lee
- Department of Horticulture, Chungnam National University, Daejeon, 305-764, South Korea
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
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Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing. G3-GENES GENOMES GENETICS 2013; 3:1809-18. [PMID: 23979935 PMCID: PMC3789805 DOI: 10.1534/g3.113.007229] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton.
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Guo H, Lee TH, Wang X, Paterson AH. Function relaxation followed by diversifying selection after whole-genome duplication in flowering plants. PLANT PHYSIOLOGY 2013; 162:769-78. [PMID: 23580595 PMCID: PMC3668069 DOI: 10.1104/pp.112.213447] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 04/09/2013] [Indexed: 05/20/2023]
Abstract
Episodes of whole-genome duplication (WGD) followed by gene loss dominate the evolutionary history of flowering plants. Despite the importance of understanding gene evolution following WGD, little is known about the evolutionary dynamics of this process. In this study, we analyzed duplicated genes from three WGD events in the Arabidopsis (Arabidopsis thaliana) lineage using multiple data types. Most duplicated genes that have survived from the most recent WGD (α) are under purifying selection in modern Arabidopsis populations. Using the number of identified protein-protein interactions as a proxy for functional divergence, approximately 92.7% of α-duplicated genes were diverged in function from one another in modern Arabidopsis populations, indicating that their preservation is no longer explicable by dosage balance. Dosage-balanced retention declines with antiquity of duplication: 24.1% of α-duplicated gene pairs in Arabidopsis remain in dosage balance with interacting partners, versus 12.9% and 9.4% for the earlier β-duplication and γ-triplication. GO-slim (a cut-down version of gene ontologies) terms reinforce evidence from protein-protein interactions, showing that the putatively diverged gene pairs are adapted to different cellular components. We identified a group of α-duplicated genes that show higher than average single-nucleotide polymorphism density, indicating that a period of positive selection, potentially driving functional divergence, may have preceded the current phase of purifying selection. We propose three possible paths for the evolution of duplicated genes following WGD.
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Jacquemin J, Bhatia D, Singh K, Wing RA. The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:147-56. [PMID: 23518283 DOI: 10.1016/j.pbi.2013.02.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 05/03/2023]
Abstract
The wild relatives of rice contain a virtually untapped reservoir of traits that can be used help drive the 21st century green revolution aimed at solving world food security issues by 2050. To better understand and exploit the 23 species of the Oryza genus the rice research community is developing foundational resources composed of: 1) reference genomes and transcriptomes for all 23 species; 2) advanced mapping populations for functional and breeding studies; and 3) in situ conservation sites for ecological, evolutionary and population genomics. To this end, 16 genome sequencing projects are currently underway, and all completed assemblies have been annotated; and several advanced mapping populations have been developed, and more will be generated, mapped, and phenotyped, to uncover useful alleles. As wild Oryza populations are threatened by human activity and climate change, we also discuss the urgent need for sustainable in situ conservation of the genus.
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Affiliation(s)
- Julie Jacquemin
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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Why assembling plant genome sequences is so challenging. BIOLOGY 2012; 1:439-59. [PMID: 24832233 PMCID: PMC4009782 DOI: 10.3390/biology1020439] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/05/2012] [Accepted: 09/06/2012] [Indexed: 12/16/2022]
Abstract
In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. The arrival of next-generation sequencing technologies has allowed the rapid and efficient development of new genomic resources for non-model or orphan plant species. But the sequencing pace of plants is far from that of animals and microorganisms. This review focuses on the typical challenges of plant genomes that can explain why plant genomics is less developed than animal genomics. Explanations about the impact of some confounding factors emerging from the nature of plant genomes are given. As a result of these challenges and confounding factors, the correct assembly and annotation of plant genomes is hindered, genome drafts are produced, and advances in plant genomics are delayed.
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Jung CG, Lim SD, Hwang SG, Jang CS. Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene 2012; 505:9-18. [DOI: 10.1016/j.gene.2012.05.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/15/2012] [Accepted: 05/30/2012] [Indexed: 01/21/2023]
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Casola C, Conant GC, Hahn MW. Very low rate of gene conversion in the yeast genome. Mol Biol Evol 2012; 29:3817-26. [PMID: 22844073 DOI: 10.1093/molbev/mss192] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Gene duplication is a major driver of organismal adaptation and evolution and plays an important role in multiple human diseases. Whole-genome analyses have shown similar and high rates of gene duplication across a variety of eukaryotic species. Most of these studies, however, did not address the possible impact of interlocus gene conversion (IGC) on the evolution of gene duplicates. Because IGC homogenizes pairs of duplicates, widespread conversion would cause gene duplication events that happened long ago to appear more recent, resulting in artificially high estimates of duplication rates. Although the majority of genome-wide studies (including in the budding yeast Saccharomyces cerevisiae [Scer]) point to levels of IGC between paralogs ranging from 2% to 18%, Gao and Innan (Gao LZ, Innan H. 2004. Very low gene duplication rate in the yeast genome. Science 306:1367-1370.) found that gene conversion in yeast affected >80% of paralog pairs. If conversion rates really are this high, it would imply that the rate of gene duplication in eukaryotes is much lower than previously reported. In this work, we apply four different methodologies-including one approach that closely mirrors Gao and Innan's method-to estimate the level of IGC in Scer. Our analyses point to a maximum conversion level of 13% between paralogs in this species, in close agreement with most estimates of IGC in eukaryotes. We also show that the exceedingly high levels of conversion found previously derive from application of an accurate method to an inappropriate data set. In conclusion, our work provides the most striking evidence to date supporting the reduced incidence of IGC among Scer paralogs and sets up a framework for future analyses in other eukaryotes.
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Wang HW, Hwang SG, Karuppanapandian T, Liu A, Kim W, Jang CS. Insight into the molecular evolution of non-specific lipid transfer proteins via comparative analysis between rice and sorghum. DNA Res 2012; 19:179-94. [PMID: 22368182 PMCID: PMC3325081 DOI: 10.1093/dnares/dss003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic analysis was conducted on 9 kDa non-specific lipid transfer protein (nsLTP) genes from nine plant species. Each of the five classified types in angiosperms exhibited eight conserved cysteine patterns. The most abundant nsLTP genes fell into the type I category, which was particularly enriched in a grass-specific lineage of clade I.1. Six pairs of tandem copies of nsLTP genes on the distal region of rice chromosomes 11 and 12 were well-preserved under concerted evolution, which was not observed in sorghum. The transgenic promoter–reporter assay revealed that both rice and sorghum nsLTP genes of type I displayed a relatively conserved expression feature in the epidermis of growing tissue, supporting its functional roles in cutin synthesis or defence against phytopathogens. For type I, the frequent expression in the stigma and seed are indicative of functional involvement in pistil–pollen interactions and seed development. By way of contrast, several type V genes were observed, mainly in the vascular bundle of the rosette as well as the young shoots, which might be related with vascular tissue differentiation or defence signalling. Compared with sorghum, the highly redundant tissue-specific expression pattern among members of rice nsLTP genes in clade I.1 suggests that concerted evolution via gene conversion favours the preservation of crucial expression motifs via the homogenization of proximal promoter sequences under high selection constraints. However, extensive regulatory subfunctionalization might also have occurred under relative low selection constraints, resulting in functional divergence at the expression level.
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Affiliation(s)
- Hong Wei Wang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
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Wang Y, Wang X, Paterson AH. Genome and gene duplications and gene expression divergence: a view from plants. Ann N Y Acad Sci 2012; 1256:1-14. [PMID: 22257007 DOI: 10.1111/j.1749-6632.2011.06384.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
With many plant genomes sequenced, it is now clear that one distinguishing feature of angiosperm (flowering plant) genomes is their high frequency of whole-genome duplication. Single-gene duplication is also widespread in angiosperm genomes. Following various mechanisms of gene duplication, genes are often retained or lost in a biased manner, which has suggested recent models for gene family evolution, such as functional buffering and the gene balance hypothesis in addition to now-classical models, including neofunctionalization and subfunctionalization. Evolutionary consequences of gene duplication, often studied through analyzing gene expression divergence, have enhanced understanding of the biological significance of different mechanisms of gene duplication.
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Affiliation(s)
- Yupeng Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
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Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 2012; 40:e49. [PMID: 22217600 PMCID: PMC3326336 DOI: 10.1093/nar/gkr1293] [Citation(s) in RCA: 3474] [Impact Index Per Article: 289.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.
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Affiliation(s)
- Yupeng Wang
- Plant Genome Mapping Laboratory, Institute of Bioinformatics, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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Wang Y, Wang X, Tang H, Tan X, Ficklin SP, Feltus FA, Paterson AH. Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One 2011; 6:e28150. [PMID: 22164235 PMCID: PMC3229532 DOI: 10.1371/journal.pone.0028150] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 11/02/2011] [Indexed: 11/18/2022] Open
Abstract
Background Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. Results In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Conclusion Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution.
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Affiliation(s)
- Yupeng Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
- College of Life Sciences, Hebei United University, Tangshan, Hebei, China
| | - Haibao Tang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Xu Tan
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Stephen P. Ficklin
- Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - F. Alex Feltus
- Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
- Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia, United States of America
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Zhang H, Zhang CQ, Sun ZZ, Yu W, Gu MH, Liu QQ, Li YS. A major locus qS12, located in a duplicated segment of chromosome 12, causes spikelet sterility in an indica-japonica rice hybrid. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1247-56. [PMID: 21792631 DOI: 10.1007/s00122-011-1663-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 07/09/2011] [Indexed: 05/06/2023]
Abstract
Chromosome segment duplications are integral in genome evolution by providing a source for the origin of new genes. In the rice genome, besides an ancient polyploidy event known in the rice common ancestor, it had been identified that there was a special segmental duplication involving chromosomes 11 and 12, but the biological role of this duplication remains unknown. In this study, by using a set of chromosome segment substitution lines (CSSLs) and near isogenic lines (NILs) derived from the indica cultivar 9311 and japonica cultivar Nipponbare, a major QTL (qS12) resulting in hybrid male sterility was mapped within ~400 kb region adjacent to the special duplicated segment on the short arm of chromosome 12. Compared to the japonica cultivar Nipponbare, the two sides of the qS12 candidate region were inverted in the indica cultivar 9311. Among 47 of the 111 rice genotypes evaluated by molecular markers, the inverted sides were detected, and found completely homologous to indica cultivar 9311. These results suggested that the two inverted sides protect the sequence in the qS12 regions from recombination. On the short-arm of chromosome 12, two QTLs S-e and S25, in addition to qS12, were previously detected as a distinct segregation distortion and pollen semi-sterility loci. We propose these three hybrid sterility loci are the same locus, and the duplicated segment on chromosome 12 may play a prominent role in diversification, i.e., sub-speciation of cultivated rice.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Developmental Biology of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
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Ratnaparkhe MB, Wang X, Li J, Compton RO, Rainville LK, Lemke C, Kim C, Tang H, Paterson AH. Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny. THE NEW PHYTOLOGIST 2011; 192:164-178. [PMID: 21707619 DOI: 10.1111/j.1469-8137.2011.03800.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
• Plant genomes contain numerous disease resistance genes (R genes) that play roles in defense against pathogens. Scarcity of genetic polymorphism makes peanut (Arachis hypogaea) especially vulnerable to a wide variety of pathogens. • Here, we isolated and characterized peanut bacterial artificial chromosomes (BACs) containing a high density of R genes. Analysis of two genomic regions identified several TIR-NBS-LRR (Toll-interleukin-1 receptor, nucleotide-binding site, leucine-rich repeat) resistance gene analogs or gene fragments. We reconstructed their evolutionary history characterized by tandem duplications, possibly facilitated by transposon activities. We found evidence of both intergenic and intragenic gene conversions and unequal crossing-over, which may be driving forces underlying the functional evolution of resistance. • Analysis of the sequence mutations, protein secondary structure and three-dimensional structures, all suggest that LRR domains are the primary contributor to the evolution of resistance genes. The central part of LRR regions, assumed to serve as the active core, may play a key role in the resistance function by having higher rates of duplication and DNA conversion than neighboring regions. The assumed active core is characterized by significantly enriched leucine residue composition, accumulation of positively selected sites, and shorter beta sheets. • Homologous resistance gene analog (RGA)-containing regions in peanut, soybean, Medicago, Arabidopsis and grape have only limited gene synteny and microcollinearity.
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Affiliation(s)
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
- Center for Genomics and Computational Biology, School of Life Sciences, School of Sciences, Hebei United University, Tangshan, Hebei 063000, China
| | - Jingping Li
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Rosana O Compton
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Lisa K Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Haibao Tang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
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Wang X, Torres MJ, Pierce G, Lemke C, Nelson LK, Yuksel B, Bowers JE, Marler B, Xiao Y, Lin L, Epps E, Sarazen H, Rogers C, Karunakaran S, Ingles J, Giattina E, Mun JH, Seol YJ, Park BS, Amasino RM, Quiros CF, Osborn TC, Pires JC, Town C, Paterson AH. A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations. BMC Genomics 2011; 12:470. [PMID: 21955929 PMCID: PMC3193055 DOI: 10.1186/1471-2164-12-470] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 09/28/2011] [Indexed: 11/17/2022] Open
Abstract
Background Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity. Results A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating high-information-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity. Conclusions A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes. All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/; Temporarily password-protected: account: pgml; password: 123qwe123.
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Affiliation(s)
- Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, 30602, USA
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Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IAP, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 2011; 43:1035-9. [PMID: 21873998 DOI: 10.1038/ng.919] [Citation(s) in RCA: 1281] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 08/03/2011] [Indexed: 11/09/2022]
Abstract
We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
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Affiliation(s)
- Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China
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Jacquemin J, Chaparro C, Laudié M, Berger A, Gavory F, Goicoechea JL, Wing RA, Cooke R. Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species. Mol Biol Evol 2011; 28:3139-50. [PMID: 21616911 DOI: 10.1093/molbev/msr144] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Whole genome duplication (WGD) and subsequent evolution of gene pairs have been shown to have shaped the present day genomes of most, if not all, plants and to have played an essential role in the evolution of many eukaryotic genomes. Analysis of the rice (Oryza sativa ssp. japonica) genome sequence suggested an ancestral WGD ∼50-70 Ma common to all cereals and a segmental duplication between chromosomes 11 and 12 as recently as 5 Ma. More recent studies based on coding sequences have demonstrated that gene conversion is responsible for the high sequence conservation which suggested such a recent duplication. We previously showed that gene conversion has been a recurrent process throughout the Oryza genus and in closely related species and that orthologous duplicated regions are also highly conserved in other cereal genomes. We have extended these studies to compare megabase regions of genomic (coding and noncoding) sequences between two cultivated (O. sativa, Oryza glaberrima) and one wild (Oryza brachyantha) rice species using a novel approach of topological incongruency. The high levels of intraspecies conservation of both gene and nongene sequences, particularly in O. brachyantha, indicate long-range conversion events less than 4 Ma in all three species. These observations demonstrate megabase-scale conversion initiated within a highly rearranged region located at ∼2.1 Mb from the chromosome termini and emphasize the importance of gene conversion in cereal genome evolution.
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Affiliation(s)
- J Jacquemin
- Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Institut de Recherche pour le Développement/Université de Perpignan Via Domitia, Université de Perpignan, Perpignan-Cedex, France.
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Fawcett JA, Innan H. Neutral and non-neutral evolution of duplicated genes with gene conversion. Genes (Basel) 2011; 2:191-209. [PMID: 24710144 PMCID: PMC3924837 DOI: 10.3390/genes2010191] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 01/20/2011] [Accepted: 02/12/2011] [Indexed: 01/11/2023] Open
Abstract
Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes. It contributes to create unique patters of DNA polymorphism within species and divergence between species. A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments. In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates. Here, we review theoretical models to understand the evolution of duplicates in both neutral and non-neutral cases. We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples.
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Affiliation(s)
- Jeffrey A Fawcett
- Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan.
| | - Hideki Innan
- Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan.
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Ricachenevsky FK, Sperotto RA, Menguer PK, Sperb ER, Lopes KL, Fett JP. ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa) paralogs. BMC PLANT BIOLOGY 2011; 11:20. [PMID: 21266036 PMCID: PMC3041735 DOI: 10.1186/1471-2229-11-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 01/25/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Duplications are very common in the evolution of plant genomes, explaining the high number of members in plant gene families. New genes born after duplication can undergo pseudogenization, neofunctionalization or subfunctionalization. Rice is a model for functional genomics research, an important crop for human nutrition and a target for biofortification. Increased zinc and iron content in the rice grain could be achieved by manipulation of metal transporters. Here, we describe the ZINC-INDUCED FACILITATOR-LIKE (ZIFL) gene family in plants, and characterize the genomic structure and expression of rice paralogs, which are highly affected by segmental duplication. RESULTS Sequences of sixty-eight ZIFL genes, from nine plant species, were comparatively analyzed. Although related to MSF_1 proteins, ZIFL protein sequences consistently grouped separately. Specific ZIFL sequence signatures were identified. Monocots harbor a larger number of ZIFL genes in their genomes than dicots, probably a result of a lineage-specific expansion. The rice ZIFL paralogs were named OsZIFL1 to OsZIFL13 and characterized. The genomic organization of the rice ZIFL genes seems to be highly influenced by segmental and tandem duplications and concerted evolution, as rice genome contains five highly similar ZIFL gene pairs. Most rice ZIFL promoters are enriched for the core sequence of the Fe-deficiency-related box IDE1. Gene expression analyses of different plant organs, growth stages and treatments, both from our qPCR data and from microarray databases, revealed that the duplicated ZIFL gene pairs are mostly co-expressed. Transcripts of OsZIFL4, OsZIFL5, OsZIFL7, and OsZIFL12 accumulate in response to Zn-excess and Fe-deficiency in roots, two stresses with partially overlapping responses. CONCLUSIONS We suggest that ZIFL genes have different evolutionary histories in monocot and dicot lineages. In rice, concerted evolution affected ZIFL duplicated genes, possibly maintaining similar expression patterns between pairs. The enrichment for IDE1 boxes in rice ZIFL gene promoters suggests a role in Zn-excess and Fe-deficiency up-regulation of ZIFL transcripts. Moreover, this is the first description of the ZIFL gene family in plants and the basis for functional studies on this family, which may play important roles in Zn and Fe homeostasis in plants.
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Affiliation(s)
- Felipe K Ricachenevsky
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, P.O.Box 15005, Porto Alegre, 91501-970, Brazil
| | - Raul A Sperotto
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, P.O.Box 15005, Porto Alegre, 91501-970, Brazil
| | - Paloma K Menguer
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, 91501-970, Brazil
| | - Edilena R Sperb
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, 91501-970, Brazil
| | - Karina L Lopes
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, 91501-970, Brazil
| | - Janette P Fett
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, P.O.Box 15005, Porto Alegre, 91501-970, Brazil
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, 91501-970, Brazil
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