An RNA-Seq based gene expression atlas of the common bean

Abstract

BackgroundCommon bean (Phaseolus vulgaris) is grown throughout the world and comprises roughly 50% of the grain legumes consumed worldwide. Despite this, genetic resources for common beans have been lacking. Next generation sequencing, has facilitated our investigation of the gene expression profiles associated with biologically important traits in common bean. An increased understanding of gene expression in common bean will improve our understanding of gene expression patterns in other legume species.ResultsCombining recently developed genomic resources for Phaseolus vulgaris, including predicted gene calls, with RNA-Seq technology, we measured the gene expression patterns from 24 samples collected from seven tissues at developmentally important stages and from three nitrogen treatments. Gene expression patterns throughout the plant were analyzed to better understand changes due to nodulation, seed development, and nitrogen utilization. We have identified 11,010 genes differentially expressed with a fold change ≥ 2 and a P-value < 0.05 between different tissues at the same time point, 15,752 genes differentially expressed within a tissue due to changes in development, and 2,315 genes expressed only in a single tissue. These analyses identified 2,970 genes with expression patterns that appear to be directly dependent on the source of available nitrogen. Finally, we have assembled this data in a publicly available database, The Phaseolus vulgaris Gene Expression Atlas (Pv GEA), http://plantgrn.noble.org/PvGEA/ . Using the website, researchers can query gene expression profiles of their gene of interest, search for genes expressed in different tissues, or download the dataset in a tabular form.ConclusionsThese data provide the basis for a gene expression atlas, which will facilitate functional genomic studies in common bean. Analysis of this dataset has identified genes important in regulating seed composition and has increased our understanding of nodulation and impact of the nitrogen source on assimilation and distribution throughout the plant.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-866) contains supplementary material, which is available to authorized users.

The Micro-RNA172c-APETALA2-1 Node as a Key Regulator of the Common Bean-Rhizobium etli Nitrogen Fixation Symbiosis

“…3, B-G). O'Rourke et al (2014) identified common bean nodulation genes that were highly expressed in young and/or mature nodules and that are homologous to cognate nodulation genes previously identified in other legume species. From these, we selected six early nodulation genes for expression analysis: the TF genes NF-YA1 (Phvul.001G196800.1), NSP2 (Phvul.009G122700.1), and NIN (Phvul.009G115800); CYCLOPS (Phvul.002G128600.1), coding for a nuclear protein that interacts with CCaMK; FLOTILLIN-LIKE2 (FLOT2; Phvul.009G090700.1), coding for a lipid raft component; and ENOD40 (Phvul.008G291800), which lacks an open reading frame but encodes two small peptides and may function as a cell-cell signaling molecule for nodulation ; Oldroyd and Kouchi et al, 2010;Murray, 2011;Oldroyd, 2013).…”

“…To explore if this circuit is functioning in common bean, we first identified Hb genes encoded by the common bean genome: five symbiotic leg-hemoglobin (Lb) genes having greatly increased expression in effective nodules and four nonsymbiotic Hb genes (O'Rourke et al, 2014;Supplemental Fig. S7).…”

“…Therefore, our data differ from those of Yan et al (2013) and lead us to conclude that AP2-1 repression of Hb-1 genes is not relevant for common bean nodulation. Our exploration of other common bean symbiotic genes repressed by AP2-1 included the identification of TFBS statistically overrepresented in the promoter regions of 402 common bean genes reported by O'Rourke et al (2014) as nodule-enhanced genes. The expression pattern of these genes is similar to that of miR172c and opposite to that of AP2-1, which shows low expression in mature nodules and high expression in roots, suggesting these as candidates for transcriptional repression by AP2-1.…”

“…In soybean, 10 AP2 TF genes have been proposed as miR172 targets (Song et al, 2011). A recent analysis of the common bean transcriptome by RNA sequencing (RNAseq) combined with available gene calls (O'Rourke et al, 2014) identified 202 transcripts encoding AP2-type TFs. The phylogenetic tree generated using sequence alignments of the common bean AP2 proteins is depicted in Figure 1A.…”

“…We performed target prediction analysis for all the common bean AP2 gene transcripts identified in the Pv GEA (O'Rourke, et al, 2014) using the Web server psRNATarget (http://plantgrn.noble.org/psRNATarget/; Dai and Zhao, 2011). Stringent criteria were used to predict targets; that is, an alignment spanning at least 18 bp with maximum penalty score of 3.…”