Genome of an allotetraploid wild peanut <i>Arachis monticola</i>: a de novo assembly

Abstract

Arachis monticola (2n = 4x = 40) is the only allotetraploid wild peanut within the Arachis genus and section, with an AABB-type genome of ∼2.7 Gb in size. The AA-type subgenome is derived from diploid wild peanut Arachis duranensis, and the BB-type subgenome is derived from diploid wild peanut Arachis ipaensis. A. monticola is regarded either as the direct progenitor of the cultivated peanut or as an introgressive derivative between the cultivated peanut and wild species. The large polyploidy genome structure and enormous nearly identical regions of the genome make the assembly of chromosomal pseudomolecules very challenging. Here we report the first reference quality assembly of the A. monticola genome, using a series of advanced technologies. The final whole genome of A. monticola is ∼2.62 Gb and has a contig N50 and scaffold N50 of 106.66 Kb and 124.92 Mb, respectively. The vast majority (91.83%) of the assembled sequence was anchored onto the 20 pseudo-chromosomes, and 96.07% of assemblies were accurately separated into AA- and BB- subgenomes. We demonstrated efficiency of the current state of the strategy for de novo assembly of the highly complex allotetraploid species, wild peanut (A. monticola), based on whole-genome shotgun sequencing, single molecule real-time sequencing, high-throughput chromosome conformation capture technology, and BioNano optical genome maps. These combined technologies produced reference-quality genome of the allotetraploid wild peanut, which is valuable for understanding the peanut domestication and evolution within the Arachis genus and among legume crops.