A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.)

Abstract

BackgroundCowpea (Vigna unguiculata (L.) Walp.) is the most important food and forage legume in the semi-arid tropics of sub-Saharan Africa where approximately 80% of worldwide production takes place primarily on low-input, subsistence farm sites. Among the major goals of cowpea breeding and improvement programs are the rapid manipulation of agronomic traits for seed size and quality and improved resistance to abiotic and biotic stresses to enhance productivity. Knowing the suite of transcription factors (TFs) and transcriptionally active proteins (TAPs) that control various critical plant cellular processes would contribute tremendously to these improvement aims.ResultsWe used a computational approach that employed three different predictive pipelines to data mine the cowpea genome and identified over 4400 genes representing 136 different TF and TAP families. We compare the information content of cowpea to two evolutionarily close species common bean (Phaseolus vulgaris), and soybean (Glycine max) to gauge the relative informational content. Our data indicate that correcting for genome size cowpea has fewer TF and TAP genes than common bean (4408 / 5291) and soybean (4408/ 11,065). Members of the GROWTH-REGULATING FACTOR (GRF) and Auxin/indole-3-acetic acid (Aux/IAA) gene families appear to be over-represented in the genome relative to common bean and soybean, whereas members of the MADS (Minichromosome maintenance deficient 1 (MCM1), AGAMOUS, DEFICIENS, and serum response factor (SRF)) and C2C2-YABBY appear to be under-represented. Analysis of the AP2-EREBP APETALA2-Ethylene Responsive Element Binding Protein (AP2-EREBP), NAC (NAM (no apical meristem), ATAF1, 2 (Arabidopsis transcription activation factor), CUC (cup-shaped cotyledon)), and WRKY families, known to be important in defense signaling, revealed changes and phylogenetic rearrangements relative to common bean and soybean that suggest these groups may have evolved different functions.ConclusionsThe availability of detailed information on the coding capacity of the cowpea genome and in particular the various TF and TAP gene families will facilitate future comparative analysis and development of strategies for controlling growth, differentiation, and abiotic and biotic stress resistances of cowpea.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4306-1) contains supplementary material, which is available to authorized users.

The genome of cowpea (Vigna unguiculata[L.] Walp.)

“…Using the same computational pipeline as for V. unguiculata (Vu), the repeats of the V. angularis (Yang et al, 2015;Va) and V. radiata (Kang et al, 2014;Vr) genomes also were annotated. Previous analyses placed cowpea phylogenetically closer to mung bean (Vr) than to adzuki bean (Va; She et al, 2015), although the Va and Vr genomes are relatively similar in size, with cowpea, respectively, 11 and 12% larger.…”

“…A highly fragmented draft assembly and BAC sequence assemblies of IT97K-499-35 were previously generated . Although these resources enabled progress on cowpea genetics (Yao et al, 2016;Carvalho et al, 2017;Misra et al, 2017;Huynh et al, 2018;Lo et al, 2018), they lacked the contiguity and completeness required for accurate genome annotation, detailed investigation of candidate genes or thorough genome comparisons. Here, we re-estimated the genome size of V. unguiculata and produced a genome assembly using single-molecule real-time sequencing combined with optical and genetic mapping.…”

The genome of cowpea (Vigna unguiculata [L.] Walp.)

“…A highly fragmented draft assembly and BAC sequence assemblies of IT97K‐499‐35 were previously generated (Muñoz‐Amatriaín et al ., ). Although these resources enabled progress on cowpea genetics (Yao et al ., ; Carvalho et al ., ; Misra et al ., ; Huynh et al ., ; Lo et al ., ), they lacked the contiguity and completeness required for accurate genome annotation, detailed investigation of candidate genes or thorough genome comparisons. Here, we re‐estimated the genome size of V. unguiculata and produced a genome assembly using single‐molecule real‐time sequencing combined with optical and genetic mapping.…”

Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

“…The potential sequences were retrieved using custom Perl scripts that incorporated modules from BioPerl 1.7.1 [108, 109]. Any coding sequence (CDS) or nucleotide (NT) sequences were translated into amino acid sequences across six reading frames using a custom BioPerl script [110]. The sequences were searched using SANSParallel [111, 112] against the UniprotKB database [113], with 50 hit sequences displayed per query, and the “very slow” setting.…”