Journal Article

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Vlasova, Anna, Zehnsdorf, Maik, Herrera-Estrella, Alfredo, Santalla, Marta, Vianello-Brondani, Rosana P., Dohm, Juliane C., Delgado-Salinas, Alfonso, García, José Luís, Sánchez, Federico, Erb, Ionas, Rendón-Anaya, Martha, Garcia-Mas, Jordi, Vázquez, Martín P., Andreu, Nuria, Notredame, Cedric, Saburido-Alvarez, Soledad, Himmelbauer, Heinz, Gonzalez, Irene, Mentaberry, Alejandro, Capella-Gutiérrez, Salvador, Câmara, Francisco, Gabaldón, Toni, Westergaard, Gastón, Hernández-Oñate, Miguel, Sanseverino, Walter, Guigó, Roderic, Cozzuto, Luca, Alioto, Tyler, Corvelo, André, Kedra, Darek, Prieto-Barja, Pablo, Gómez-Garrido, Jessica, Aguilar, O. Mario, Minoche, André E., Pappas, Georgios J., Aguilar-Morón, María A., Delaye, Luis, Lowy, Ernesto

2016

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V
• Subject: Acids / Andes region / Angiosperms / Animal Genetics and Genomics / Artificial chromosomes / Automation / beans / Bioinformatics / Biomedical and Life Sciences / Coffee / Crops / DNA, Plant - genetics / Domestication / evolution / Evolutionary Biology / fruiting / Gene clusters / Gene Duplication / Gene expression / Gene Expression Profiling / Gene families / Gene pool / genetic resistance / Genome, Plant / Genomes / Genomics / Genotype / Genotypes / Human Genetics / Humans / Legumes / Life Sciences / Microbial Genetics and Genomics / Microsatellite Repeats - genetics / multigene family / non-coding RNA / Phaseolus - genetics / Phaseolus vulgaris / Phylogeny / Plant breeding / Plant Genetics and Genomics / pods / Proteins / Seeds / Seeds - genetics / Sequence Analysis, DNA / Specialization / tissues / Transcription / transcription (genetics) / transcriptome / Transcriptome - genetics / transcriptomics