Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis)

Abstract

Peanut (<i>Arachis hypogaea</i> L.), an important leguminous crop, is widely cultivated in tropical and subtropical regions. Peanut is an allotetraploid, having A and B subgenomes that maybe have originated in its diploid progenitors <i>Arachis duranensis</i> (A-genome) and <i>Arachis ipaensis</i> (B-genome), respectively. We previously sequenced the former and here present the draft genome of the latter, expanding our knowledge of the unique biology of <i>Arachis</i>. The assembled genome of <i>A. ipaensis</i> is ~1.39 Gb with 39,704 predicted protein-encoding genes. A gene family analysis revealed that the FAR1 family may be involved in regulating peanut special fruit development. Genomic evolutionary analyses estimated that the two progenitors diverged ~3.3 million years ago and suggested that <i>A. ipaensis</i> experienced a whole-genome duplication event after the divergence of <i>Glycine max</i>. We identified a set of disease resistance-related genes and candidate genes for biological nitrogen fixation. In particular, two and four homologous genes that may be involved in the regulation of nodule development were obtained from <i>A. ipaensis</i> and <i>A. duranensis</i>, respectively. We outline a comprehensive network involved in drought adaptation. Additionally, we analyzed the metabolic pathways involved in oil biosynthesis and found genes related to fatty acid and triacylglycerol synthesis. Importantly, three new <i>FAD2</i> homologous genes were identified from <i>A. ipaensis</i> and one was completely homologous at the amino acid level with FAD2 from <i>A. hypogaea</i>. The availability of the <i>A. ipaensis</i> and <i>A. duranensis</i> genomic assemblies will advance our knowledge of the peanut genome.