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Kong X, Zhang Y, Wang Z, Bao S, Feng Y, Wang J, Yu Z, Long F, Xiao Z, Hao Y, Gao X, Li Y, Ding Y, Wang J, Lei T, Xu C, Wang J. Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae. HORTICULTURE RESEARCH 2023; 10:uhad073. [PMID: 37303613 PMCID: PMC10251138 DOI: 10.1093/hr/uhad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/10/2023] [Indexed: 06/13/2023]
Abstract
An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7-78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6-46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.
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Affiliation(s)
| | | | | | | | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Feng Long
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zejia Xiao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yinfeng Li
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
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Barrett CF, McKain MR, Sinn BT, Ge XJ, Zhang Y, Antonelli A, Bacon CD. Ancient Polyploidy and Genome Evolution in Palms. Genome Biol Evol 2019; 11:1501-1511. [PMID: 31028709 PMCID: PMC6535811 DOI: 10.1093/gbe/evz092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2019] [Indexed: 12/23/2022] Open
Abstract
Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
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Affiliation(s)
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Yuqu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Royal Botanical Gardens Kew, Richmond, United Kingdom
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
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3
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Zhang LM, Leng CY, Luo H, Wu XY, Liu ZQ, Zhang YM, Zhang H, Xia Y, Shang L, Liu CM, Hao DY, Zhou YH, Chu CC, Cai HW, Jing HC. Sweet Sorghum Originated through Selection of Dry, a Plant-Specific NAC Transcription Factor Gene. THE PLANT CELL 2018; 30:2286-2307. [PMID: 30309900 PMCID: PMC6241255 DOI: 10.1105/tpc.18.00313] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/04/2018] [Accepted: 10/02/2018] [Indexed: 05/20/2023]
Abstract
Sorghum (Sorghum bicolor) is the fifth most popular crop worldwide and a C4 model plant. Domesticated sorghum comes in many forms, including sweet cultivars with juicy stems and grain sorghum with dry, pithy stems at maturity. The Dry locus, which controls the pithy/juicy stem trait, was discovered over a century ago. Here, we found that Dry gene encodes a plant-specific NAC transcription factor. Dry was either deleted or acquired loss-of-function mutations in sweet sorghum, resulting in cell collapse and altered secondary cell wall composition in the stem. Twenty-three Dry ancestral haplotypes, all with dry, pithy stems, were found among wild sorghum and wild sorghum relatives. Two of the haplotypes were detected in domesticated landraces, with four additional dry haplotypes with juicy stems detected in improved lines. These results imply that selection for Dry gene mutations was a major step leading to the origin of sweet sorghum. The Dry gene is conserved in major cereals; fine-tuning its regulatory network could provide a molecular tool to control crop stem texture.
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Affiliation(s)
- Li-Min Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chuan-Yuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiao-Yuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhi-Quan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Inner Mongolia Research Centre for Prataculture, Chinese Academy of Sciences, Beijing 100093, China
| | - Yu-Miao Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Xia
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Dong-Yun Hao
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, Jilin 130124, China
| | - Yi-Hua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng-Cai Chu
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong-Wei Cai
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Forage Crop Research Institute, Japan Grassland Agricultural and Forage Seed Association, Nasushiobara, Tochigi 329-2742, Japan
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Inner Mongolia Research Centre for Prataculture, Chinese Academy of Sciences, Beijing 100093, China
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4
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Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals. Nat Commun 2016; 7:12767. [PMID: 27698483 PMCID: PMC5059443 DOI: 10.1038/ncomms12767] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/29/2016] [Indexed: 01/19/2023] Open
Abstract
The plant metabolome is characterized by extensive diversity and is often regarded as a bridge between genome and phenome. Here we report metabolic and phenotypic genome-wide studies (mGWAS and pGWAS) in rice grain that, in addition to previous metabolic GWAS in rice leaf and maize kernel, show both distinct and overlapping aspects of genetic control of metabolism within and between species. We identify new candidate genes potentially influencing important metabolic and/or morphological traits. We show that the differential genetic architecture of rice metabolism between different tissues is in part determined by tissue specific expression. Using parallel mGWAS and pGWAS we identify new candidate genes potentially responsible for variation in traits such as grain colour and size, and provide evidence of metabotype-phenotype linkage. Our study demonstrates a powerful strategy for interactive functional genomics and metabolomics in plants, especially the cloning of minor QTLs for complex phenotypic traits.
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Ochoa Cruz EA, Cruz GMQ, Vieira AP, Van Sluys MA. Virus-like attachment sites as structural landmarks of plants retrotransposons. Mob DNA 2016; 7:14. [PMID: 27471551 PMCID: PMC4963935 DOI: 10.1186/s13100-016-0069-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/07/2016] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. Among them, long terminal repeat retrotransposons (LTR-RTs) are the largest component of most plant genomes, the Gypsy and Copia superfamilies being the most common. Recently it has been found that Del lineage, an LTR-RT of Gypsy superfamily, has putative virus-like attachment (vl-att) sites. This signature, originally described for retroviruses, is recognized by retroviral integrase conferring specificity to the integration process. RESULTS Here we retrieved 26,092 putative complete LTR-RTs from 10 lineages found in 10 fully sequenced angiosperm genomes and found putative vl-att sites that are a conserved structural landmark across these genomes. Furthermore, we reveal that each plant genome has a distinguishable LTR-RT lineage amplification pattern that could be related to the vl-att sites diversity. We used these patterns to generate a specific quick-response (QR) code for each genome that could be used as a barcode of identification of plants in the future. CONCLUSIONS The universal distribution of vl-att sites represents a new structural feature common to plant LTR-RTs and retroviruses. This is an important finding that expands the information about the structural similarity between LTR-RT and retroviruses. We speculate that the sequence diversity of vl-att sites could be important for the life cycle of retrotransposons, as it was shown for retroviruses. All the structural vl-att site signatures are strong candidates for further functional studies. Moreover, this is the first identification of specific LTR-RT content and their amplification patterns in a large dataset of LTR-RT lineages and angiosperm genomes. These distribution patterns could be used in the future with biotechnological identification purposes.
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Affiliation(s)
- Edgar Andres Ochoa Cruz
- Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), 05508-090 São Paulo, SP Brasil
| | | | - Andréia Prata Vieira
- Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), 05508-090 São Paulo, SP Brasil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), 05508-090 São Paulo, SP Brasil
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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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7
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Sundararajan A, Dukowic-Schulze S, Kwicklis M, Engstrom K, Garcia N, Oviedo OJ, Ramaraj T, Gonzales MD, He Y, Wang M, Sun Q, Pillardy J, Kianian SF, Pawlowski WP, Chen C, Mudge J. Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays. FRONTIERS IN PLANT SCIENCE 2016; 7:1433. [PMID: 27713757 PMCID: PMC5031598 DOI: 10.3389/fpls.2016.01433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/08/2016] [Indexed: 05/20/2023]
Abstract
Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC1, GC2, and GC3, collectively termed GCx) to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Surprisingly, GCx bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GCx genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I) are biased against both high GCx genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GCx genes.
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Affiliation(s)
| | | | | | | | - Nathan Garcia
- National Center for Genome Resources, Santa FeNM, USA
| | | | | | | | - Yan He
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Minghui Wang
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Qi Sun
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Jaroslaw Pillardy
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
- *Correspondence: Joann Mudge,
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Getnet Z, Husen A, Fetene M, Yemata G. Growth, Water Status, Physiological, Biochemical and Yield Response of Stay Green Sorghum (Sorghum bicolor (L.) Moench) Varieties-A Field Trial Under Drought-Prone Area in Amhara Regional State, Ethiopia. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/ja.2015.188.202] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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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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10
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Borrell AK, Mullet JE, George-Jaeggli B, van Oosterom EJ, Hammer GL, Klein PE, Jordan DR. Drought adaptation of stay-green sorghum is associated with canopy development, leaf anatomy, root growth, and water uptake. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6251-63. [PMID: 25381433 PMCID: PMC4223986 DOI: 10.1093/jxb/eru232] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Stay-green sorghum plants exhibit greener leaves and stems during the grain-filling period under water-limited conditions compared with their senescent counterparts, resulting in increased grain yield, grain mass, and lodging resistance. Stay-green has been mapped to a number of key chromosomal regions, including Stg1, Stg2, Stg3, and Stg4, but the functions of these individual quantitative trait loci (QTLs) remain unclear. The objective of this study was to show how positive effects of Stg QTLs on grain yield under drought can be explained as emergent consequences of their effects on temporal and spatial water-use patterns that result from changes in leaf-area dynamics. A set of four Stg near-isogenic lines (NILs) and their recurrent parent were grown in a range of field and semicontrolled experiments in southeast Queensland, Australia. These studies showed that the four Stg QTLs regulate canopy size by: (1) reducing tillering via increased size of lower leaves, (2) constraining the size of the upper leaves; and (3) in some cases, decreasing the number of leaves per culm. In addition, they variously affect leaf anatomy and root growth. The multiple pathways by which Stg QTLs modulate canopy development can result in considerable developmental plasticity. The reduction in canopy size associated with Stg QTLs reduced pre-flowering water demand, thereby increasing water availability during grain filling and, ultimately, grain yield. The generic physiological mechanisms underlying the stay-green trait suggest that similar Stg QTLs could enhance post-anthesis drought adaptation in other major cereals such as maize, wheat, and rice.
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Affiliation(s)
- Andrew K Borrell
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, Warwick, QLD 4370, Australia
| | - John E Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Barbara George-Jaeggli
- Department of Agriculture, Fisheries and Forestry Queensland (DAFFQ), Hermitage Research Facility, Warwick, QLD 4370, Australia
| | | | - Graeme L Hammer
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Patricia E Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - David R Jordan
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, Warwick, QLD 4370, Australia
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Cruz GMQ, Metcalfe CJ, de Setta N, Cruz EAO, Vieira AP, Medina R, Van Sluys MA. Virus-like attachment sites and plastic CpG islands:landmarks of diversity in plant Del retrotransposons. PLoS One 2014; 9:e97099. [PMID: 24849372 PMCID: PMC4029996 DOI: 10.1371/journal.pone.0097099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att) sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to the integration process, different att sites types therefore implies lineage specificity. While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. All eudicot copies grouped into one single clade while the monocots harbour a more diverse collection of elements. Furthermore, full-length Del elements and truncated copies were unevenly distributed amongst chromosomes. Elements of Del lineage are organized in plants into three clusters and each cluster is composed of elements with distinct LTR features. Our results suggest that the Del lineage efficiently amplified in the monocots and that one branch is probably a newly emerging sub-lineage. Finally, sequences in all groups are under purifying selection. These results show the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification.
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Affiliation(s)
- Guilherme M. Q. Cruz
- Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | - Cushla J. Metcalfe
- Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | | | - Edgar A. O. Cruz
- Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | - Andréia Prata Vieira
- Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | - Rosario Medina
- Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
- * E-mail:
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12
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Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One 2014; 9:e85761. [PMID: 24614886 PMCID: PMC3948623 DOI: 10.1371/journal.pone.0085761] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/06/2013] [Indexed: 01/08/2023] Open
Abstract
Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.
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Holton TA, Vijayakumar V, Khaldi N. Bioinformatics: Current perspectives and future directions for food and nutritional research facilitated by a Food-Wiki database. Trends Food Sci Technol 2013. [DOI: 10.1016/j.tifs.2013.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Vandenbrink JP, Goff V, Jin H, Kong W, Paterson AH, Feltus FA. Identification of bioconversion quantitative trait loci in the interspecific cross Sorghum bicolor × Sorghum propinquum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2367-2380. [PMID: 23836384 DOI: 10.1007/s00122-013-2141-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 06/01/2013] [Indexed: 06/02/2023]
Abstract
For lignocellulosic bioenergy to be economically viable, genetic improvements must be made in feedstock quality including both biomass total yield and conversion efficiency. Toward this goal, multiple studies have considered candidate genes and discovered quantitative trait loci (QTL) associated with total biomass accumulation and/or grain production in bioenergy grass species including maize and sorghum. However, very little research has been focused on genes associated with increased biomass conversion efficiency. In this study, Trichoderma viride fungal cellulase hydrolysis activity was measured for lignocellulosic biomass (leaf and stem tissue) obtained from individuals in a F5 recombinant inbred Sorghum bicolor × Sorghum propinquum mapping population. A total of 49 QTLs (20 leaf, 29 stem) were associated with enzymatic conversion efficiency. Interestingly, six high-density QTL regions were identified in which four or more QTLs overlapped. In addition to enzymatic conversion efficiency QTLs, two QTLs were identified for biomass crystallinity index, a trait which has been shown to be inversely correlated with conversion efficiency in bioenergy grasses. The identification of these QTLs provides an important step toward identifying specific genes relevant to increasing conversion efficiency of bioenergy feedstocks. DNA markers linked to these QTLs could be useful in marker-assisted breeding programs aimed at increasing overall bioenergy yields concomitant with selection of high total biomass genotypes.
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Affiliation(s)
- Joshua P Vandenbrink
- Department of Genetics and Biochemistry, Clemson University, 105 Collings Street, Clemson, SC 29634, USA
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15
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Wilhelm EP, Howells RM, Al-Kaff N, Jia J, Baker C, Leverington-Waite MA, Griffiths S, Greenland AJ, Boulton MI, Powell W. Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1321-36. [PMID: 23381809 DOI: 10.1007/s00122-013-2055-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/20/2013] [Indexed: 05/18/2023]
Abstract
The introgression of Reduced height (Rht)-B1b and Rht-D1b into bread wheat (Triticum aestivum) varieties beginning in the 1960s led to improved lodging resistance and yield, providing a major contribution to the 'green revolution'. Although wheat Rht-1 and surrounding sequence is available, the genetic composition of this region has not been examined in a homoeologous series. To determine this, three Rht-1-containing bacterial artificial chromosome (BAC) sequences derived from the A, B, and D genomes of the bread wheat variety Chinese Spring (CS) were fully assembled and analyzed. This revealed that Rht-1 and two upstream genes were highly conserved among the homoeologs. In contrast, transposable elements (TEs) were not conserved among homoeologs with the exception of intronic miniature inverted-repeat TEs (MITEs). In relation to the Triticum urartu ancestral line, CS-A genic sequences were highly conserved and several colinear TEs were present. Comparative analysis of the CS wheat BAC sequences with assembled Poaceae genomes showed gene synteny and amino acid sequences were well preserved. Further 5' and 3' of the wheat BAC sequences, a high degree of gene colinearity is present among the assembled Poaceae genomes. In the 20 kb of sequence flanking Rht-1, five conserved non-coding sequences (CNSs) were present among the CS wheat homoeologs and among all the Poaceae members examined. Rht-A1 was mapped to the long arm of chromosome 4 and three closely flanking genetic markers were identified. The tools developed herein will enable detailed studies of Rht-1 and linked genes that affect abiotic and biotic stress response in wheat.
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Affiliation(s)
- Edward P Wilhelm
- National Institute of Agricultural Botany, Huntingdon Rd., Cambridge CB3 0LE, UK.
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16
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Feltus FA, Vandenbrink JP. Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:80. [PMID: 23122416 PMCID: PMC3502489 DOI: 10.1186/1754-6834-5-80] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 10/05/2012] [Indexed: 05/19/2023]
Abstract
For lignocellulosic bioenergy to become a viable alternative to traditional energy production methods, rapid increases in conversion efficiency and biomass yield must be achieved. Increased productivity in bioenergy production can be achieved through concomitant gains in processing efficiency as well as genetic improvement of feedstock that have the potential for bioenergy production at an industrial scale. The purpose of this review is to explore the genetic and genomic resource landscape for the improvement of a specific bioenergy feedstock group, the C4 bioenergy grasses. First, bioenergy grass feedstock traits relevant to biochemical conversion are examined. Then we outline genetic resources available bioenergy grasses for mapping bioenergy traits to DNA markers and genes. This is followed by a discussion of genomic tools and how they can be applied to understanding bioenergy grass feedstock trait genetic mechanisms leading to further improvement opportunities.
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Affiliation(s)
- Frank Alex Feltus
- Department of Genetics & Biochemistry, Clemson University, 105 Collings Street. BRC #302C, Clemson, SC, 29634, USA
| | - Joshua P Vandenbrink
- Department of Genetics & Biochemistry, Clemson University, 105 Collings Street. BRC #302C, Clemson, SC, 29634, USA
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18
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de Setta N, Metcalfe CJ, Cruz GMQ, Ochoa EA, Van Sluys MA. Noise or Symphony: Comparative Evolutionary Analysis of Sugarcane Transposable Elements with Other Grasses. PLANT TRANSPOSABLE ELEMENTS 2012. [DOI: 10.1007/978-3-642-31842-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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19
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Ficklin SP, Feltus FA. Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice. PLANT PHYSIOLOGY 2011; 156:1244-56. [PMID: 21606319 PMCID: PMC3135956 DOI: 10.1104/pp.111.173047] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Accepted: 05/20/2011] [Indexed: 05/17/2023]
Abstract
One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.
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Vermerris W. Survey of genomics approaches to improve bioenergy traits in maize, sorghum and sugarcane. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:105-19. [PMID: 21205186 DOI: 10.1111/j.1744-7909.2010.01020.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bioenergy crops currently provide the only source of alternative energy with the potential to reduce the use of fossil transportation fuels in a way that is compatible with existing engine technology, including in developing countries. Even though bioenergy research is currently receiving considerable attention, many of the concepts are not new, but rather build on intense research efforts from 30 years ago. A major difference with that era is the availability of genomics tools that have the potential to accelerate crop improvement significantly. This review is focused on maize, sorghum and sugarcane as representatives of bioenergy grasses that produce sugar and/or lignocellulosic biomass. Examples of how genetic mapping, forward and reverse genetics, high-throughput expression profiling and comparative genomics can be used to unravel and improve bioenergy traits will be presented.
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Affiliation(s)
- Wilfred Vermerris
- University of Florida Genetics Institute and Agronomy Department, Cancer/Genetics Research Complex, PO Box 103610, Gainesville, FL 32610, USA.
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21
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Rodionov AV, Nosov NN, Kim ES, Machs EM, Punina EO, Probatova NS. The origin of polyploid genomes of bluegrasses Poa L. and Gene flow between northern pacific and sub-Antarctic Islands. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410120021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Liu Q, Zhu Z. Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection. BMC PLANT BIOLOGY 2010; 10:256. [PMID: 21092127 PMCID: PMC3095335 DOI: 10.1186/1471-2229-10-256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 11/20/2010] [Indexed: 05/02/2023]
Abstract
BACKGROUND Nod26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are unique to plants. According to homology modeling and phylogenetic analysis, the NIP subfamily can be further divided into three subgroups with distinct biological functions (NIP I, NIP II, and NIP III). In some grasses, the NIP III subgroup proteins (NIP2s) were demonstrated to be permeable to solutes with larger diameter, such as silicic acid and arsenous acids. However, to date there is no data-mining or direct experimental evidences for the permeability of such larger solutes for dicot NIP2s, although they exhibit similar three-dimensional structures as those in grasses. It is therefore intriguing to investigate the molecular mechanisms that drive the evolution of plant NIP2s. RESULTS The NIP III subgroup is more ancient with a divergence time that predates the monocot-dicot split. The proliferation of NIP2 genes in modern grass species is primarily attributed to whole genome and segmental chromosomal duplication events. The structure of NIP2 genes is relatively conserved, possessing five exons and four introns. All NIP2s possess an ar/R filter consisting of G, S, G, and R, except for the cucumber CsNIP2;2, where a small G in the H2 is substituted with the bulkier C residue. Our maximum likelihood analysis revealed that NIP2s, especially the loop A (LA) region, have undergone strong selective pressure for adaptive evolution. The analysis at the amino acid level provided strong statistical evidences for the functional divergence between monocot and dicot NIP III subgroup proteins. In addition, several SDPs (Specificity Determining Positions) responsible for functional specificity were predicted. CONCLUSIONS The present study provides the first evidences of functional divergence between dicot and monocot NIP2s, and suggests that positive selection, as well as a radical shift of evolutionary rate at some critical amino acid sites is the primary driver. These findings will expand our understanding to evolutionary mechanisms driving the functional diversification of monocot and dicot NIP III subgroup proteins.
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Affiliation(s)
- Qingpo Liu
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Hangzhou 311300, China
| | - Zhujun Zhu
- College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, Hangzhou 311300, China
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Drader T, Kleinhofs A. A synteny map and disease resistance gene comparison between barley and the model monocot Brachypodium distachyon. Genome 2010; 53:406-17. [PMID: 20616871 DOI: 10.1139/g10-014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Grass species have coevolved with current economically important crop pathogens over millions of years. During this time, speciation of current domestic crops has occurred, resulting in related yet divergent genomes. Here, we present a synteny map between the crop species Hordeum vulgare and the recently sequenced Brachypodium distachyon genome, focusing on regions known to harbor important barley disease resistance genes. The resistance genes have orthologous genes in Brachypodium that show conservation of the form and likely the function of the genes. The level of colinearity between the genomes is highly dependent on the region of interest and, at the DNA level or protein level, the gene of interest. The stem rust resistance gene Rpg1 has an ortholog with a high level of identity at the amino acid level, while the stem rust resistance gene Rpg5 has two orthologs with a high level of identity, one corresponding to the NBS-LRR domain and the other to the serine/threonine protein kinase domain, on different contigs. Interestingly, the predicted product of the Brachypodium Rpg1 ortholog contained a WD40 domain at the C-terminal end. The stem rust resistance gene rpg4 (actin depolymerizing factor 2) also has an ortholog with a high level of identity, in which one of the three residues indicated by allele sequencing in barley cultivars to be important in disease resistance is conserved. The syntenous region of the seedling spot blotch resistance locus, Rcs5, has a high level of colinearity that may prove useful in efforts to identify and clone this gene. A synteny map and orthologous resistance gene comparisons are presented.
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Affiliation(s)
- Tom Drader
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA.
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Li X, Wu HX, Southerton SG. Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants. BMC Evol Biol 2010; 10:190. [PMID: 20565927 PMCID: PMC2907377 DOI: 10.1186/1471-2148-10-190] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 06/21/2010] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. RESULTS The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. CONCLUSIONS Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.
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Affiliation(s)
- Xinguo Li
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
| | - Harry X Wu
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
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25
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Peng Z, Lu T, Li L, Liu X, Gao Z, Hu T, Yang X, Feng Q, Guan J, Weng Q, Fan D, Zhu C, Lu Y, Han B, Jiang Z. Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences. BMC PLANT BIOLOGY 2010; 10:116. [PMID: 20565830 PMCID: PMC3017805 DOI: 10.1186/1471-2229-10-116] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 06/18/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies. RESULTS Here we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study. CONCLUSION Analysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.
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Affiliation(s)
- Zhenhua Peng
- Chinese Academy of Forestry, Wanshou Shan, Beijing 100091, PR China
- International Network for Bamboo and Rattan, 8 Fu Tong Dong Da Jie, Chaoyang District, Beijing 100102, PR China
| | - Tingting Lu
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Lubin Li
- Chinese Academy of Forestry, Wanshou Shan, Beijing 100091, PR China
| | - Xiaohui Liu
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Zhimin Gao
- International Network for Bamboo and Rattan, 8 Fu Tong Dong Da Jie, Chaoyang District, Beijing 100102, PR China
| | - Tao Hu
- Chinese Academy of Forestry, Wanshou Shan, Beijing 100091, PR China
| | - Xuewen Yang
- International Network for Bamboo and Rattan, 8 Fu Tong Dong Da Jie, Chaoyang District, Beijing 100102, PR China
| | - Qi Feng
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Jianping Guan
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Qijun Weng
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Danlin Fan
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Chuanrang Zhu
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Ying Lu
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Bin Han
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
| | - Zehui Jiang
- Chinese Academy of Forestry, Wanshou Shan, Beijing 100091, PR China
- International Network for Bamboo and Rattan, 8 Fu Tong Dong Da Jie, Chaoyang District, Beijing 100102, PR China
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Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA. GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics 2010; 11:308. [PMID: 20470436 PMCID: PMC2895627 DOI: 10.1186/1471-2164-11-308] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 05/16/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates. RESULTS Here we demonstrate that in certain organisms the amount of GC at the wobble position (GC3) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC3 content: they (1) provide more targets for methylation, (2) exhibit more variable expression, (3) more frequently possess upstream TATA boxes, (4) are predominant in certain classes of genes (e.g., stress responsive genes) and (5) have a GC3 content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC3 bimodality in grasses. CONCLUSIONS Our findings suggest that high levels of GC3 typify a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC3 bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation.
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Affiliation(s)
- Tatiana V Tatarinova
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
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27
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Maas LF, McClung A, McCouch S. Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:895-908. [PMID: 19949767 DOI: 10.1007/s00122-009-1219-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 11/03/2009] [Indexed: 05/08/2023]
Abstract
A days to heading QTL (dth1.1) located on the short arm of rice chromosome 1 was sub-divided into eight sub-introgression lines (SILs) to analyze the genetic basis of transgressive variation for flowering time. Each SIL contained one or more introgression(s) from O. rufipogon in the genetic background of the elite Oryza sativa cultivar, Jefferson. Each introgression was defined at high resolution using molecular markers and those in the dth1.1 region were associated with the presence of one or more flowering time genes (GI, SOC1, FT-L8, EMF1, and PNZIP). SILs and controls were evaluated for flowering time under both short- and long-day growing conditions. Under short-day lengths, lines with introgressions carrying combinations of linked flowering time genes (GI/SOC1, SOC1/FT-L8, GI/SOC1/FT-L8 and EMF1/PNZIP) from the late parent, O. rufipogon, flowered earlier than the recurrent parent, Jefferson, while recombinant lines carrying smaller introgressions marked by the presence of GI, SOC1, EMF1 or PNZIP alone no longer flowered early. Under long-day length, lines carrying SOC1/FT-L8, SOC1 or PNZIP flowered early, while those carrying GI or EMF1 delayed flowering. Across all experiments and in the field, only SIL_SOC1/FT-L8 was consistently early. A preliminary yield evaluation indicated that the transgressive early flowering observed in several of the SILs was also associated with a measurable and positive effect on yield. These SILs represent a new source of variation that can be used in breeding programs to manipulate flowering time in rice cultivars without the reduction in yield that is often associated with early maturing phenotypes.
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Affiliation(s)
- Luis F Maas
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853, USA
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Kim ES, Bolsheva NL, Samatadze TE, Nosov NN, Nosova IV, Zelenin AV, Punina EO, Muravenko OV, Rodionov AV. The unique genome of two-chromosome grasses Zingeria and Colpodium, its origin, and evolution. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409110076] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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