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Wang W, Huang R, Wu G, Sun J, Zhu Y, Wang H. Transcriptomic and QTL Analysis of Seed Germination Vigor under Low Temperature in Weedy Rice WR04-6. PLANTS (BASEL, SWITZERLAND) 2023; 12:871. [PMID: 36840221 PMCID: PMC9961040 DOI: 10.3390/plants12040871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Low temperature is one of the major factors affecting rice germination, and low temperature germination (LTG) is an important agronomic trait. Although significant progress has been made in the study of rice LTG, the molecular mechanism of LTG remains poorly understood. To explore more rice LTG gene resources, we first demonstrated that weedy rice WR04-6 (Oryza sativa f. spontanea) had significantly higher LTG ability at 10 °C than the cultivated rice Qishanzhan (QSZ Oryza sativa L. ssp. indica). RNA-seq was used to investigate the gene expression of WR04-6 and QSZ at 10 °C for 10, 12 and 14 days after imbibition (DAI) of seed germination. The results of Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that the differentially expressed genes (DEGs) between WR04-6 and QSZ were mainly concentrated on the response to starch catabolic processes and the response to abscisic acid (ABA). This is consistent with the results of α-amylase activity, ABA and gibberellins (GA) treatment. A recombinant inbred line (RIL) population derived from a cross between WR04-6 and QSZ and its high-density SNP genetic map were used to detect quantitative trait loci (QTL) for LTG rates. The results showed that two new QTLs were located on chromosome 3 and chromosome 12. Combined with the mapped QTLs and RNA-seq DEGs, sixteen candidate genes potentially associated with LTG were identified. Validation of the expression of the candidates by qRT-PCR were consistent with the RNA-seq data. These results will enable us to understand the genetic basis of LTG in weedy rice and provide new genetic resources for the generation of rice germplasm with improved LTG.
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Affiliation(s)
- Wenjia Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ruizhi Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Gengwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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2
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Ye X, Hu H, Zhou H, Jiang Y, Gao S, Yuan Z, Stiller J, Li C, Chen G, Liu Y, Wei Y, Zheng YL, Wang YG, Liu C. Differences between diploid donors are the main contributing factor for subgenome asymmetry measured in either gene ratio or relative diversity in allopolyploids. Genome 2021; 64:847-856. [PMID: 33661713 DOI: 10.1139/gen-2020-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences were not detected between these two types of polyploid genotypes, although they differ in times exposed to evolutionary selection. The estimated ratio of shared genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes than those for the natural genotypes, which is expected as it is now well-known that many genes in a species are not shared among all individuals. As the exact diploid parent for a given subgenome is unknown, the estimated ratios of shared genes for the natural genotypes would also include difference among individual genotypes of the diploid donor species. Further, we detected the presence of SA in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. These results indicate that SA may, to a large degree, reflect differences between its diploid donors or that changes occurred during polyploid evolution are defined by their donor genomes.
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Affiliation(s)
- Xueling Ye
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Haiyan Hu
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Hong Zhou
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yunfeng Jiang
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Shang Gao
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Zhongwei Yuan
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jiri Stiller
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Chengwei Li
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - You-Gan Wang
- Science and Engineering Facility, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
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3
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Wang J, Yu J, Sun P, Li C, Song X, Lei T, Li Y, Yuan J, Sun S, Ding H, Duan X, Shen S, Shen Y, Li J, Meng F, Xie Y, Wang J, Hou Y, Zhang J, Zhang X, Li XQ, Paterson AH, Wang X. Paleo-polyploidization in Lycophytes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020; 18:333-340. [PMID: 33157303 PMCID: PMC7801247 DOI: 10.1016/j.gpb.2020.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/13/2019] [Accepted: 04/17/2019] [Indexed: 11/26/2022]
Abstract
Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13-15 million years ago (MYA) and another about 125-142 MYA, during the evolution of the genome of Selaginella moellendorffii, a model lycophyte. In addition, comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleo-polyploidization events than seed plants. Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages-lycophytes and seed plants-of vascular plants.
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Affiliation(s)
- Jinpeng Wang
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China; National Key Laboratory for North China Crop Improvement and Regulation, Agriculture University of Hebei, Baoding 071001, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Jigao Yu
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Pengchuan Sun
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Chao Li
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Xiaoming Song
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China; National Key Laboratory for North China Crop Improvement and Regulation, Agriculture University of Hebei, Baoding 071001, China
| | - Tianyu Lei
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Yuxian Li
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Jiaqing Yuan
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Sangrong Sun
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Hongling Ding
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Xueqian Duan
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Shaoqi Shen
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Yanshuang Shen
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Jing Li
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Fanbo Meng
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Yangqin Xie
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Jianyu Wang
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Yue Hou
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Jin Zhang
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Athens, 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
| | - Xiyin Wang
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China; National Key Laboratory for North China Crop Improvement and Regulation, Agriculture University of Hebei, Baoding 071001, China.
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4
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Wang J, Yu J, Li Y, Wei C, Guo H, Liu Y, Zhang J, Li X, Wang X. Sequential Paleotetraploidization shaped the carrot genome. BMC PLANT BIOLOGY 2020; 20:52. [PMID: 32005164 PMCID: PMC6995200 DOI: 10.1186/s12870-020-2235-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/31/2019] [Indexed: 06/02/2023]
Abstract
BACKGROUND Carrot (Daucus carota subsp. carota L.) is an important root crop with an available high-quality genome. The carrot genome is thought to have undergone recursive paleo-polyploidization, but the extent, occurrences, and nature of these events are not clearly defined. RESULTS Using a previously published comparative genomics pipeline, we reanalysed the carrot genome and characterized genomic fractionation, as well as gene loss and retention, after each of the two tetraploidization events and inferred a dominant and sensitive subgenome for each event. In particular, we found strong evidence of two sequential tetraploidization events, with one (Dc-α) approximately 46-52 million years ago (Mya) and the other (Dc-β) approximately 77-87 Mya, both likely allotetraploidization in nature. The Dc-β event was likely common to all Apiales plants, occurring around the divergence of Apiales-Bruniales and after the divergence of Apiales-Asterales, likely playing an important role in the derivation and divergence of Apiales species. Furthermore, we found that rounds of polyploidy events contributed to the expansion of gene families responsible for plastidial methylerythritol phosphate (MEP), the precursor of carotenoid accumulation, and shaped underlying regulatory pathways. The alignment of orthologous and paralogous genes related to different events of polyploidization and speciation constitutes a comparative genomics platform for studying Apiales, Asterales, and many other related species. CONCLUSIONS Hierarchical inference of homology revealed two tetraploidization events that shaped the carrot genome, which likely contributed to the successful establishment of Apiales plants and the expansion of MEP, upstream of the carotenoid accumulation pathway.
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Affiliation(s)
- Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- College of Mathematics and Science, Handan University, Handan, 056005 Hebei China
| | - Jigao Yu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Yuxian Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Chendan Wei
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - He Guo
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Ying Liu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Jin Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Xiuqing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Frederiction, New Brunswick E3B 4Z7 Canada
| | - Xiyin Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
- School of Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075 China
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5
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Detection of QTL for panicle architecture in $$\hbox {F}_{2}$$ population of rice. J Genet 2019. [DOI: 10.1007/s12041-019-1088-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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6
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Bruno E, Choi YS, Chung IK, Kim KM. QTLs and analysis of the candidate gene for amylose, protein, and moisture content in rice (Oryza sativa L.). 3 Biotech 2017; 7:40. [PMID: 28439810 DOI: 10.1007/s13205-017-0687-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/03/2017] [Indexed: 11/28/2022] Open
Abstract
In this study, we determined using NIRS the heritability percentage of amylose, protein, and moisture content in polished and unpolished rice in a CNDH population derived from a cross between Cheongcheong and Nagdong rice varieties. The results revealed a higher heritability percentage for the amylose content and compromised heritability for protein and moisture contents. We also conducted QTL analysis of rice for these major components and identified their chromosomal locations on a physical map. We found a total of four QTLs affecting the amylose, protein, and moisture contents of grain on chromosome 7. We constructed physical maps of seven DNA markers responsible for amylose content, six responsible for protein content, and three responsible for moisture content. Furthermore, we classified these genes according to their functions and found 17 genes (over 77%) to be involved in secondary metabolite synthesis, two genes (about 9%), each related to cell function and abiotic stress, and one gene (about 5%) involved in redox signaling.
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Affiliation(s)
- Ester Bruno
- Department of Food Security and Agricultural Development, Kyungpook National University, Daegu, 41566, Korea
| | - Yun-Sik Choi
- Department of Pharmaceutical Science & Technology, Catholic University of Daegu, Gyeongsan-Si, Gyeongbuk, 38430, Korea
| | - Il Kyung Chung
- Department of Biotechnology, Catholic University of Daegu, Gyeongsan-Si, Gyeongbuk, 38430, Korea
| | - Kyung-Min Kim
- Department of Food Security and Agricultural Development, Kyungpook National University, Daegu, 41566, Korea.
- School of Applied Biosciences, College of Agriculture & Life Sciences, Kyungpook National University, Daegu, 41566, Korea.
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7
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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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8
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PolyCat: a resource for genome categorization of sequencing reads from allopolyploid organisms. G3-GENES GENOMES GENETICS 2013; 3:517-25. [PMID: 23450226 PMCID: PMC3583458 DOI: 10.1534/g3.112.005298] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 01/10/2013] [Indexed: 01/05/2023]
Abstract
Read mapping is a fundamental part of next-generation genomic research but is complicated by genome duplication in many plants. Categorizing DNA sequence reads into their respective genomes enables current methods to analyze polyploid genomes as if they were diploid. We present PolyCat-a pipeline for mapping and categorizing all types of next-generation sequence data produced from allopolyploid organisms. PolyCat uses GSNAP's single-nucleotide polymorphism (SNP)-tolerant mapping to minimize the mapping efficiency bias caused by SNPs between genomes. PolyCat then uses SNPs between genomes to categorize reads according to their respective genomes. Bisulfite-treated reads have a significant reduction in nucleotide complexity because nucleotide conversion events are confounded with transition substitutions. PolyCat includes special provisions to properly handle bisulfite-treated data. We demonstrate the functionality of PolyCat on allotetraploid cotton, Gossypium hirsutum, and create a functional SNP index for efficiently mapping sequence reads to the D-genome sequence of G. raimondii. PolyCat is appropriate for all allopolyploids and all types of next-generation genome analysis, including differential expression (RNA sequencing), differential methylation (bisulfite sequencing), differential DNA-protein binding (chromatin immunoprecipitation sequencing), and population diversity.
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9
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Molecular aspects of flower development in grasses. ACTA ACUST UNITED AC 2011; 24:247-82. [PMID: 21877128 DOI: 10.1007/s00497-011-0175-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 08/11/2011] [Indexed: 10/17/2022]
Abstract
The grass family (Poaceae) of the monocotyledons includes about 10,000 species and represents one of the most important taxa among angiosperms. Their flower morphology is remarkably different from those of other monocotyledons and higher eudicots. The peculiar floral structure of grasses is the floret, which contains carpels and stamens, like eudicots, but lacks petals and sepals. The reproductive organs are surrounded by two lodicules, which correspond to eudicot petals, and by a palea and lemma, whose correspondence to eudicot organs remains controversial. The molecular and genetic analysis of floral morphogenesis and organ specification, primarily performed in eudicot model species, led to the ABCDE model of flower development. Several genes required for floral development in grasses correspond to class A, B, C, D, and E genes of eudicots, but others appear to have unique and diversified functions. In this paper, we outline the present knowledge on the evolution and diversification of grass genes encoding MIKC-type MADS-box transcription factors, based on information derived from studies in rice, maize, and wheat. Moreover, we review recent advances in studying the genes involved in the control of flower development and the extent of structural and functional conservation of these genes between grasses and eudicots.
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10
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Gene conversion in angiosperm genomes with an emphasis on genes duplicated by polyploidization. Genes (Basel) 2011; 2:1-20. [PMID: 24710136 PMCID: PMC3924838 DOI: 10.3390/genes2010001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 12/06/2010] [Accepted: 01/06/2011] [Indexed: 11/16/2022] Open
Abstract
Angiosperm genomes differ from those of mammals by extensive and recursive polyploidizations. The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution. Though most genes may escape conversion by their homologs, concerted evolution of duplicated genes can last for millions of years or longer after their origin. Indeed, paralogous genes on two rice chromosomes duplicated an estimated 60–70 million years ago have experienced gene conversion in the past 400,000 years. Gene conversion preserves similarity of paralogous genes, but appears to accelerate their divergence from orthologous genes in other species. The mutagenic nature of recombination coupled with the buffering effect provided by gene redundancy, may facilitate the evolution of novel alleles that confer functional innovations while insulating biological fitness of affected plants. A mixed evolutionary model, characterized by a primary birth-and-death process and occasional homoeologous recombination and gene conversion, may best explain the evolution of multigene families.
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11
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Van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K. The flowering world: a tale of duplications. TRENDS IN PLANT SCIENCE 2009; 14:680-8. [PMID: 19818673 DOI: 10.1016/j.tplants.2009.09.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 08/31/2009] [Accepted: 09/07/2009] [Indexed: 05/02/2023]
Abstract
Flowering plants contain many genes, most of which were created during the past 200 or so million years through small- and large-scale duplications. Paleo-polyploidy events, in particular, have been the subject of much recent research. There is a growing consensus that one or more genome doubling or merging events occurred early during the evolution of the flowering plants, and that many lineages have since undergone additional, independent and more recent duplication events. Here, we review the difficulties in determining the number of genome duplications and discuss how the completion of some additional genome sequences of species occupying key phylogenetic positions has led to a better understanding of the timing of certain duplication events. This is important if we want to demonstrate the significance of genome duplications for the evolution and radiation of (different groups of) flowering plants.
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Affiliation(s)
- Yves Van de Peer
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052 Gent, Belgium.
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12
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Li Z, Zhang H, Ge S, Gu X, Gao G, Luo J. Expression pattern divergence of duplicated genes in rice. BMC Bioinformatics 2009; 10 Suppl 6:S8. [PMID: 19534757 PMCID: PMC2697655 DOI: 10.1186/1471-2105-10-s6-s8] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Genome-wide duplication is ubiquitous during diversification of the angiosperms, and gene duplication is one of the most important mechanisms for evolutionary novelties. As an indicator of functional evolution, the divergence of expression patterns following duplication events has drawn great attention in recent years. Using large-scale whole-genome microarray data, we systematically analyzed expression divergence patterns of rice genes from block, tandem and dispersed duplications. Results We found a significant difference in expression divergence patterns for the three types of duplicated gene pairs. Expression correlation is significantly higher for gene pairs from block and tandem duplications than those from dispersed duplications. Furthermore, a significant correlation was observed between the expression divergence and the synonymous substitution rate which is an approximate proxy of divergence time. Thus, both duplication types and divergence time influence the difference in expression divergence. Using a linear model, we investigated the influence of these two variables and found that the difference in expression divergence between block and dispersed duplicates is attributed largely to their different divergence time. In addition, the difference in expression divergence between tandem and the other two types of duplicates is attributed to both divergence time and duplication type. Conclusion Consistent with previous studies on Arabidopsis, our results revealed a significant difference in expression divergence between the types of duplicated genes and a significant correlation between expression divergence and synonymous substitution rate. We found that the attribution of duplication mode to the expression divergence implies a different evolutionary course of duplicated genes.
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Affiliation(s)
- Zhe Li
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center for Bioinformatics, Peking University, Beijing 100871, PR China.
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Mackiewicz P, Wyroba E. Phylogeny and evolution of Rab7 and Rab9 proteins. BMC Evol Biol 2009; 9:101. [PMID: 19442299 PMCID: PMC2693434 DOI: 10.1186/1471-2148-9-101] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 05/14/2009] [Indexed: 11/14/2022] Open
Abstract
Background An important role in the evolution of intracellular trafficking machinery in eukaryotes played small GTPases belonging to the Rab family known as pivotal regulators of vesicle docking, fusion and transport. The Rab family is very diversified and divided into several specialized subfamilies. We focused on the VII functional group comprising Rab7 and Rab9, two related subfamilies, and analysed 210 sequences of these proteins. Rab7 regulates traffic from early to late endosomes and from late endosome to vacuole/lysosome, whereas Rab9 participates in transport from late endosomes to the trans-Golgi network. Results Although Rab7 and Rab9 proteins are quite small and show heterogeneous rates of substitution in different lineages, we found a phylogenetic signal and inferred evolutionary relationships between them. Rab7 proteins evolved before radiation of main eukaryotic supergroups while Rab9 GTPases diverged from Rab7 before split of choanoflagellates and metazoans. Additional duplication of Rab9 and Rab7 proteins resulting in several isoforms occurred in the early evolution of vertebrates and next in teleost fishes and tetrapods. Three Rab7 lineages emerged before divergence of monocots and eudicots and subsequent duplications of Rab7 genes occurred in particular angiosperm clades. Interestingly, several Rab7 copies were identified in some representatives of excavates, ciliates and amoebozoans. The presence of many Rab copies is correlated with significant differences in their expression level. The diversification of analysed Rab subfamilies is also manifested by non-conserved sequences and structural features, many of which are involved in the interaction with regulators and effectors. Individual sites discriminating different subgroups of Rab7 and Rab9 GTPases have been identified.
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Affiliation(s)
- Paweł Mackiewicz
- University of Wrocław, Faculty of Biotechnology, Department of Genomics, 63/77 Przybyszewskiego Street, 51-148 Wrocław, Poland.
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Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes. Mol Phylogenet Evol 2009; 51:515-30. [PMID: 19166953 DOI: 10.1016/j.ympev.2008.12.024] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 12/23/2008] [Accepted: 12/29/2008] [Indexed: 12/27/2022]
Abstract
Phylogenetic utility of two nuclear genes (GBSSI-2 and DHAR) was explored in genus Fragaria in order to clarify phylogenetic relationships among taxa and to elucidate the origin of the polyploid species. Orthology of the amplified products was assessed by several methods. Our results strongly suggest the loss of one GBSSI duplicated copy (GBSSI-1) in the Fragariinae subtribe. Phylogenetic analyses provided new insights into the evolutionary history of Fragaria, such as evidence supporting the presence of three main diploid genomic pools in the genus and demonstrating the occurrence of independent events of polyploidisation. In addition, the data provide evidence supporting an allopolyploid origin of the hexaploid F. moschata, and the octoploids F. chiloensis, F. iturupensis and F. virginiana. Accordingly, a new pattern summarizing our present knowledge on the Fragaria evolutionary history is proposed. Additionally, sequence analyses also revealed relaxed constraints on homoeologous copies at high ploidy level, as demonstrated by deletion events within DHAR coding sequences of some allo-octoploid haplotypes.
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Paterson AH, Bowers JE, Feltus FA, Tang H, Lin L, Wang X. Comparative genomics of grasses promises a bountiful harvest. PLANT PHYSIOLOGY 2009; 149:125-31. [PMID: 19126703 PMCID: PMC2613718 DOI: 10.1104/pp.108.129262] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 11/05/2008] [Indexed: 05/18/2023]
Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
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17
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Lyons E, Freeling M. How to usefully compare homologous plant genes and chromosomes as DNA sequences. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 53:661-73. [PMID: 18269575 DOI: 10.1111/j.1365-313x.2007.03326.x] [Citation(s) in RCA: 308] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
There are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non-coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text.
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Affiliation(s)
- Eric Lyons
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Zhang YP, Ge S. Molecular evolution study in China: progress and future promise. Philos Trans R Soc Lond B Biol Sci 2007; 362:973-86. [PMID: 17317644 PMCID: PMC2435564 DOI: 10.1098/rstb.2007.2027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
China has a large land area with highly diverse topography, climate and vegetation, and animal resources and is ranked eighth in the world and first in the Northern Hemisphere on richness of biodiversity. Even though little work on molecular evolution had been reported a decade ago, studies on both the evolution of macromolecules and the molecular phylogeny have become active in China in recent years. This review highlights some of the interesting and important developments in molecular evolution study in China. Chinese scientists have made significant contribution on the methods inferring phylogeny and biogeography of animals and plants in East Asia using molecular data. Studies on population and conservation genetics of animals and plants, such as Golden monkey and Chinese sturgeon, provided useful information for conserving the endangered species. East and South Asia has been demonstrated to be one of the centres of domestication. Origin and evolution of genes and gene families have been explored, which shed new insight on the genetic mechanism of adaptation. In the genomic era, Chinese researchers also made a transition from single-gene to a genomic investigation approach. Considering the fact that amazing progress has been made in the past few years, and more and more talented young scientists are entering field, the future of molecular evolution study in China holds much promise.
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Affiliation(s)
- Ya-ping Zhang
- Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 JiaoChangDongLu, Kunming, Yunnan 650223, People's Republic of China.
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Schaller GE, Binder BM. Biochemical Characterization of Plant Ethylene Receptors Following Transgenic Expression in Yeast. Methods Enzymol 2007; 422:270-87. [PMID: 17628144 DOI: 10.1016/s0076-6879(06)22013-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ethylene receptors of plants are related to and originated from bacterial histidine kinases. As such they represent a system by which one can study not only how the ethylene signal is perceived and its signal transduced, but also how bacterial two-component systems have been adapted for signal transduction in a eukaryote. Much of the biochemical characterization of the ethylene receptors, including the demonstration of kinase activity, ethylene binding, and interaction with other signaling components, has relied on the ability of the receptors to be functionally expressed in transgenic yeast. This chapter describes some of the key approaches used for such work, with a special emphasis on techniques employed to analyze ethylene binding. In many cases the approaches used in transgenic yeast may also be used for studies of the receptors in the native plant.
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Affiliation(s)
- G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
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Wang X, Shi X, Li Z, Zhu Q, Kong L, Tang W, Ge S, Luo J. Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics 2006; 7:447. [PMID: 17038171 PMCID: PMC1626491 DOI: 10.1186/1471-2105-7-447] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2006] [Accepted: 10/12/2006] [Indexed: 11/27/2022] Open
Abstract
Background The identification of chromosomal homology will shed light on such mysteries of genome evolution as DNA duplication, rearrangement and loss. Several approaches have been developed to detect chromosomal homology based on gene synteny or colinearity. However, the previously reported implementations lack statistical inferences which are essential to reveal actual homologies. Results In this study, we present a statistical approach to detect homologous chromosomal segments based on gene colinearity. We implement this approach in a software package ColinearScan to detect putative colinear regions using a dynamic programming algorithm. Statistical models are proposed to estimate proper parameter values and evaluate the significance of putative homologous regions. Statistical inference, high computational efficiency and flexibility of input data type are three key features of our approach. Conclusion We apply ColinearScan to the Arabidopsis and rice genomes to detect duplicated regions within each species and homologous fragments between these two species. We find many more homologous chromosomal segments in the rice genome than previously reported. We also find many small colinear segments between rice and Arabidopsis genomes.
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Affiliation(s)
- Xiyin Wang
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
- College of Mathematics, Hebei Polytechnic University, Tangshan, Hebei 063009, China
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Xiaoli Shi
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
| | - Zhe Li
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
| | - Qihui Zhu
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lei Kong
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
| | - Wen Tang
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
| | - Song Ge
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jingchu Luo
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
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Freeling M, Thomas BC. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 2006; 16:805-14. [PMID: 16818725 DOI: 10.1101/gr.3681406] [Citation(s) in RCA: 314] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Controversy surrounds the apparent rising maximums of morphological complexity during eukaryotic evolution, with organisms increasing the number and nestedness of developmental areas as evidenced by morphological elaborations reflecting area boundaries. No "predictable drive" to increase this sort of complexity has been reported. Recent genetic data and theory in the general area of gene dosage effects has engendered a robust "gene balance hypothesis," with a theoretical base that makes specific predictions as to gene content changes following different types of gene duplication. Genomic data from both chordate and angiosperm genomes fit these predictions: Each type of duplication provides a one-way injection of a biased set of genes into the gene pool. Tetraploidies and balanced segments inject bias for those genes whose products are the subunits of the most complex biological machines or cascades, like transcription factors (TFs) and proteasome core proteins. Most duplicate genes are removed after tetraploidy. Genic balance is maintained by not removing those genes that are dose-sensitive, which tends to leave duplicate "functional modules" as the indirect products (spandrels) of purifying selection. Functional modules are the likely precursors of coadapted gene complexes, a unit of natural selection. The result is a predictable drive mechanism where "drive" is used rigorously, as in "meiotic drive." Rising morphological gain is expected given a supply of duplicate functional modules. All flowering plants have survived at least three large-scale duplications/diploidizations over the last 300 million years (Myr). An equivalent period of tetraploidy and body plan evolution may have ended for animals 500 million years ago (Mya). We argue that "balanced gene drive" is a sufficient explanation for the trend that the maximums of morphological complexity have gone up, and not down, in both plant and animal eukaryotic lineages.
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Affiliation(s)
- Michael Freeling
- Department of Plant and Molecular Biology, University of California-Berkeley, Berkeley, California 94720, USA.
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Thomas BC, Pedersen B, Freeling M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 2006; 16:934-46. [PMID: 16760422 PMCID: PMC1484460 DOI: 10.1101/gr.4708406] [Citation(s) in RCA: 300] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Approximately 90% of Arabidopsis' unique gene content is found in syntenic blocks that were formed during the most recent whole-genome duplication. Within these blocks, 28.6% of the genes have a retained pair; the remaining genes have been lost from one of the homeologs. We create a minimized genome by condensing local duplications to one gene, removing transposons, and including only genes within blocks defined by retained pairs. We use a moving average of retained and non-retained genes to find clusters of retention and then identify the types of genes that appear in clusters at frequencies above expectations. Significant clusters of retention exist for almost all chromosomal segments. Detailed alignments show that, for 85% of the genome, one homeolog was preferentially (1.6x) targeted for fractionation. This homeolog fractionation bias suggests an epigenetic mechanism. We find that islands of retention contain "connected genes," those genes predicted-by the gene balance hypothesis-to be resistant to removal because the products they encode interact with other products in a dose-sensitive manner, creating a web of dependency. Gene families that are overrepresented in clusters include those encoding components of the proteasome/protein modification complexes, signal transduction machinery, ribosomes, and transcription factor complexes. Gene pair fractionation following polyploidy or segmental duplication leaves a genome enriched for "connected" genes. These clusters of duplicate genes may help explain the evolutionary origin of coregulated chromosomal regions and new functional modules.
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Affiliation(s)
- Brian C. Thomas
- College of Natural Resources, University of California–Berkeley, Berkeley, California 94720, USA
| | - Brent Pedersen
- Department of Environmental Science, Policy & Management, University of California–Berkeley, Berkeley, California 94720, USA
| | - Michael Freeling
- Department of Plant & Microbial Biology, University of California–Berkeley, Berkeley, California 94720, USA
- Corresponding author.E-mail ; fax (510) 642-4995
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Paterson AH. Leafing through the genomes of our major crop plants: strategies for capturing unique information. Nat Rev Genet 2006; 7:174-84. [PMID: 16485017 DOI: 10.1038/nrg1806] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Crop plants not only have economic significance, but also comprise important botanical models for evolution and development. This is reflected by the recent increase in the percentage of publicly available sequence data that are derived from angiosperms. Further genome sequencing of the major crop plants will offer new learning opportunities, but their large, repetitive, and often polyploid genomes present challenges. Reduced-representation approaches - such as EST sequencing, methyl filtration and Cot-based cloning and sequencing - provide increased efficiency in extracting key information from crop genomes without full-genome sequencing. Combining these methods with phylogenetically stratified sampling to allow comparative genomic approaches has the potential to further accelerate progress in angiosperm genomics.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
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Abstract
The economic and scientific importance of the cereals has motivated a rich history of research into their genetics, development, and evolution. The nearly completed sequence of the rice genome is emblematic of a transition to high-throughput genomics and computational biology that has also pervaded study of many other cereals. The relatively close (ca. <50 million years old) relationships among morphologically diverse cereals native to environments that sample much of global geographic diversity make the cereals particularly attractive for comparative studies of plant genome evolution. Extensive germplasm resources, largely a byproduct of their economic importance, together with growing collections of defined mutants, provide foundations for a host of post-genomic studies to shed more light on the relationship between sequence and function in this important group. Using the rapidly growing capabilities of several informatics resources, genomic data from model cereals are likely to be leveraged tremendously in the study and improvement of a wide range of crop plants that sustain much of the world's population, including many which still lack primary genomic resources.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
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