Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. Results: We repor...
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paper:paper_14747596_v17_n1_p_Vlasova2023-06-08T16:17:37Z Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes Westergaard, Gastón Germán Vazquez, Martín Pablo Mentaberry, Alejandro Néstor BAT93 Common bean Gene duplication LncRNAs Tissue expression Transcriptome long untranslated RNA transcriptome microsatellite DNA plant DNA transcriptome Article controlled study fruit development gene duplication gene expression genetic transcription genetic variability genome analysis genotype nonhuman Phaseolus vulgaris phylogenomics plant evolution plant genome plant seed pod transcriptomics DNA sequence gene duplication gene expression profiling genetics human Phaseolus phylogeny DNA, Plant Gene Duplication Gene Expression Profiling Genome, Plant Genotype Humans Microsatellite Repeats Phaseolus Phylogeny Seeds Sequence Analysis, DNA Transcriptome Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. Results: We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. Conclusions: The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop. © 2016 Vlasova et al. Fil:Westergaard, G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Vázquez, M.P. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Mentaberry, A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2016 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14747596_v17_n1_p_Vlasova http://hdl.handle.net/20.500.12110/paper_14747596_v17_n1_p_Vlasova |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
BAT93 Common bean Gene duplication LncRNAs Tissue expression Transcriptome long untranslated RNA transcriptome microsatellite DNA plant DNA transcriptome Article controlled study fruit development gene duplication gene expression genetic transcription genetic variability genome analysis genotype nonhuman Phaseolus vulgaris phylogenomics plant evolution plant genome plant seed pod transcriptomics DNA sequence gene duplication gene expression profiling genetics human Phaseolus phylogeny DNA, Plant Gene Duplication Gene Expression Profiling Genome, Plant Genotype Humans Microsatellite Repeats Phaseolus Phylogeny Seeds Sequence Analysis, DNA Transcriptome |
| spellingShingle |
BAT93 Common bean Gene duplication LncRNAs Tissue expression Transcriptome long untranslated RNA transcriptome microsatellite DNA plant DNA transcriptome Article controlled study fruit development gene duplication gene expression genetic transcription genetic variability genome analysis genotype nonhuman Phaseolus vulgaris phylogenomics plant evolution plant genome plant seed pod transcriptomics DNA sequence gene duplication gene expression profiling genetics human Phaseolus phylogeny DNA, Plant Gene Duplication Gene Expression Profiling Genome, Plant Genotype Humans Microsatellite Repeats Phaseolus Phylogeny Seeds Sequence Analysis, DNA Transcriptome Westergaard, Gastón Germán Vazquez, Martín Pablo Mentaberry, Alejandro Néstor Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes |
| topic_facet |
BAT93 Common bean Gene duplication LncRNAs Tissue expression Transcriptome long untranslated RNA transcriptome microsatellite DNA plant DNA transcriptome Article controlled study fruit development gene duplication gene expression genetic transcription genetic variability genome analysis genotype nonhuman Phaseolus vulgaris phylogenomics plant evolution plant genome plant seed pod transcriptomics DNA sequence gene duplication gene expression profiling genetics human Phaseolus phylogeny DNA, Plant Gene Duplication Gene Expression Profiling Genome, Plant Genotype Humans Microsatellite Repeats Phaseolus Phylogeny Seeds Sequence Analysis, DNA Transcriptome |
| description |
Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. Results: We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. Conclusions: The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop. © 2016 Vlasova et al. |
| author |
Westergaard, Gastón Germán Vazquez, Martín Pablo Mentaberry, Alejandro Néstor |
| author_facet |
Westergaard, Gastón Germán Vazquez, Martín Pablo Mentaberry, Alejandro Néstor |
| author_sort |
Westergaard, Gastón Germán |
| title |
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes |
| title_short |
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes |
| title_full |
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes |
| title_fullStr |
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes |
| title_full_unstemmed |
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes |
| title_sort |
genome and transcriptome analysis of the mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes |
| publishDate |
2016 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14747596_v17_n1_p_Vlasova http://hdl.handle.net/20.500.12110/paper_14747596_v17_n1_p_Vlasova |
| work_keys_str_mv |
AT westergaardgastongerman genomeandtranscriptomeanalysisofthemesoamericancommonbeanandtheroleofgeneduplicationsinestablishingtissueandtemporalspecializationofgenes AT vazquezmartinpablo genomeandtranscriptomeanalysisofthemesoamericancommonbeanandtheroleofgeneduplicationsinestablishingtissueandtemporalspecializationofgenes AT mentaberryalejandronestor genomeandtranscriptomeanalysisofthemesoamericancommonbeanandtheroleofgeneduplicationsinestablishingtissueandtemporalspecializationofgenes |
| _version_ |
1768542380049301504 |