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

Vikram A Misra,Michael P Timko,Yu Wang

doi:10.1186/s12864-017-4306-1

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.

Highlights

Cowpea (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
About 97% of all previously reported cowpea expressed sequence tags (ESTs) can be found in the assembly by Basic Local Alignment and Search Tool Nucleotide (BLASTN) and a large proportion of the assembly is composed of scaffold sequences containing two or more overlapping contigs [27]
To identify genes encoding transcription factors (TFs) and transcriptionally active proteins (TAPs) present in the draft cowpea genome assembly, we used three different identification pipelines: the PlantTFcat pipeline [40], the iTAK pipeline [41] and a novel pipeline developed for this study that uses a strict set of rules for gene family membership as defined by Lang et al (2010) [44]

Summary

Introduction

Cowpea (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. Estimates by the Food and Agriculture Organization (FAO) of the United Nations [3] indicate that 5.59 million metric tons of cowpea was produced worldwide, the majority of which (81%) is produced by low-input subsistence farmers in Western Africa [3,4,5], followed by Eastern (8.68%) and Central Africa (4.37%) [3]. In these regions cowpea grains are an important source of protein and carbohydrates [5, 6]. Cowpea can withstand dry conditions and low quality soils relatively well [12]

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