Evaluating MAKER-P in the Context of Two Closely Related Peanut Genomes

We used the MAKER-P software to predict genes for the genomes of two wild ancestors of tetraploid cultivated peanut, Arachis hypogaea. The wild diploid ancestors, Arachis duranensis and Arachis ipaensis, separated from one another approximately two million years ago, and merged only ~5-10 thousand years ago, to produce the immediate progenitor of the tetraploid crop species. Availability of gene annotations from the two wild species, at this relatively close evolutionary distance, allows us to identify a set of evolutionary changes that have occurred within this timeframe. We see many changes, both large and small. We infer that the A. duranensis genome has shrunk relative to the A. ipaensis genome (and probably relative to the common ancestor), following a set of inversions and rearrangements in A. duranensis - after which intergenic material was removed from A. duranensis in the inverted regions, due to increased recombinations in formerly pericentromeric regions. Other changes include independent gene and transposon losses and gains in both genomes, particularly affecting clustered genes such as NBS-LRRs, but affecting many gene families. The net gains and losses were not equal, giving approximately 13% more gene models in A. ipaensis. The net increase in gene count in A. ipaensis is due primarily to a combination of greater expansions of gene families in A. ipaensis through local duplications, or greater losses of genes within clusters in A. duranensis.