title: The Vigna unguiculata Gene Expression Atlas (VuGEA) from de novo assembly and quantification of RNA-seq data provides insights into seed maturation mechanisms.
abstract: 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 (http://vugea.noble.org), 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. Using this gene expression atlas, we inferred details of molecular processes that are active during seed development, and identified key putative regulators of seed maturation. Additionally, we found evidence for conservation of regulatory mechanisms involving miRNA in plant tissues subjected to drought and seeds undergoing desiccation.
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences (SIBS), The Chinese Academy of Sciences (CAS), Shanghai, 201602, China.|University of Chinese Academy of Sciences, Beijing, 100039, China.
authors.forename: Shaolun
authors.initials: S
authors.lastname: Yao
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences (SIBS), The Chinese Academy of Sciences (CAS), Shanghai, 201602, China.|University of Chinese Academy of Sciences, Beijing, 100039, China.
authors.forename: Chuan
authors.initials: C
authors.lastname: Jiang
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences (SIBS), The Chinese Academy of Sciences (CAS), Shanghai, 201602, China.
authors.forename: Ziyue
authors.initials: Z
authors.lastname: Huang
authors.affiliation: The Samuel Roberts Noble Foundation, Plant Biology Division, Ardmore, OK, 73401, USA.
authors.forename: Ivone
authors.initials: I
authors.lastname: Torres-Jerez
authors.affiliation: The Samuel Roberts Noble Foundation, Plant Biology Division, Ardmore, OK, 73401, USA.|The Samuel Roberts Noble Foundation, Computing Service Department, Ardmore, OK, 73401, USA.
authors.forename: Junil
authors.initials: J
authors.lastname: Chang
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences (SIBS), The Chinese Academy of Sciences (CAS), Shanghai, 201602, China.
authors.forename: Heng
authors.initials: H
authors.lastname: Zhang
authors.affiliation: The Samuel Roberts Noble Foundation, Plant Biology Division, Ardmore, OK, 73401, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Udvardi
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences (SIBS), The Chinese Academy of Sciences (CAS), Shanghai, 201602, China.
authors.forename: Renyi
authors.initials: R
authors.lastname: Liu
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences (SIBS), The Chinese Academy of Sciences (CAS), Shanghai, 201602, China.
authors.forename: Jerome
authors.initials: J
authors.lastname: Verdier
mesh_terms: D002874:Chromosome Mapping; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D012639:Seeds / Q000235:genetics / Q000378:metabolism*; D000070658:Vigna / Q000235:genetics / Q000378:metabolism*
keywords: 
  Vigna unguiculata
  ; cowpea; de novo assembly; drought; gene atlas; seed; transcriptome