ArticleGenome biology2016
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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97 citing papers in PubMed, 236 citations in OpenAlex.
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- Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4).GigaScience · 2025Article
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- The Kirkhouse Trust: Successes and Challenges in Twenty Years of Supporting Independent, Contemporary Grain Legume Breeding Projects in India and African Countries.Plants (Basel, Switzerland) · 2024Review
- Functional, transcriptomic, and lipidomic studies of theMicrobiology spectrum · 2024Article
- A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture.G3 (Bethesda, Md.) · 2023Article
- Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance.The plant genome · 2023Article
- Whole-genome resequencing of common bean elite breeding lines.Scientific reports · 2023Article
- Impact of drought and salt stress on galactinol and raffinose family oligosaccharides in common bean (AoB PLANTS · 2023Article
- A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture.bioRxiv : the preprint server for biology · 2023Article
- Identification and Characterization of Common Bean (Plants (Basel, Switzerland) · 2023Article
- Comparative Transcriptome Analysis of Tolerant and Sensitive Genotypes of Common Bean (Plants (Basel, Switzerland) · 2023Article
- Article
37 more citing papers are in PubMed but not listed here.
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38 authors at 17 institutions in 8 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLegumes 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.
resultsWe 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.
conclusionsThe 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.
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