The Black-eyed pea Gene Expression Atlas (VuGEA) from de novo assembly and quantification of RNA-seq data

Legume research and cultivar development are important for sustainable food production, especially of high-protein seed. Thanks to the development of deep-sequencing technologies, crop species have been taken to the front line, even without completion of their genome sequences. Black-eyed pea (Vigna unguiculata) is a legume species widely grown in semi-arid regions, which has high potential to provide stable seed protein production in a broad range of environments, including drought conditions. The black-eyed pea reference genotype has been used to generate a gene expression atlas of the major plant tissues (i.e. leaf, root, stem, flower, pod and seed), with a developmental time-series for pods and seeds. From these various organs, 27 cDNA libraries were generated and sequenced, resulting in more than one billion reads. Following filtering, these reads were de novo assembled into 36,529 transcript sequences that were annotated and quantified across the different tissues. A set of 24,866 unique transcript sequences, called unigenes, was identified. All the information related to transcript identification, annotation and quantification were stored into a gene expression atlas webserver, providing a user-friendly interface and necessary tools to analyse transcript expression in black-eyed pea organs and to compare data with other legume species.


Heatmap of tissue-specific and preferentially expressed genes in Blackeyed pea. The color scale indicates the z-score associated with all the Black-eyed pea transcripts preferentially or specifically expressed in a particular organ.

Using this gene expression atlas, researchers at the Chinese Academy of Sciences inferred details of molecular processes that are active during seed development, and identified key putative regulators of seed maturation. Additionally, they found evidence for conservation of regulatory mechanisms involving miRNA in plant tissues subjected to drought and seeds undergoing desiccation.


Yao S, Jiang C, Huang Z, Torres-Jerez I, Chang J, Zhang H, Udvardi M, Liu R, Verdier J. (2016) The Vigna unguiculata Gene Expression Atlas (VuGEA) from de novo assembly and quantification of RNA-seq data provides insights into seed maturation mechanisms. Plant J [Epub ahead of print]. [abstract]

Leave a Reply

Your email address will not be published. Required fields are marked *


Time limit is exhausted. Please reload CAPTCHA.