Genome of an allotetraploid wild peanut Arachis monticola: 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.

Comparison ofArachis monticolawith Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

“…Previously, we have assembled the whole genome sequence of wild peanut A. monticola , a tetraploid species, based on a combined set of data using illumina short read sequencing, single molecule real time (SMRT) sequencing, Bionano genome map, and high throughput chromosome conformation capture (Hi‐C) technologies . In this study, we further performed full annotation of the assembled genome.…”

“…The availability of reference genomes from both wild and cultivated tetraploids enabled us to explore genomic differences between subgenomes in the tetraploids and their respective A and B‐genome‐like diploids . The A. monticola genome showed higher levels of collinearity in both euchromatic and pericentromeric regions of homoeologous chromosomes than A and B‐genome‐like diploids (Figure S1, Supporting Information) .…”

Translational genomics for achieving higher genetic gains in groundnut

“…These genomes predicted 1.2 Gb genome size for A. duranensis (36,734 genes) and 1.5 Gb genome size for A. ipaensis (41,840 genes) making total to the estimated genome size for cultivated groundnut (~ 2.7 Gb). In 2018, the genome assembly has been made available for the allotetraploid wild groundnut (~ 2.62 Gb; 20 pseudomolecules), A. monticola PI 263,393, which is considered either the direct progenitor for the cultivated tetraploid groundnut or as an independent derivative between the cultivated groundnut and wild species (Yin et al 2018). This study even deployed highly sophisticated and advanced technologies such as Hi-C technology to develop this high-quality genome assembly for the wild tetraploid.…”

Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.)

“…Recently, breakthroughs have been made in peanut genome sequencing. From 2016 to 2018, the genomes of the two diploid progenitors and one allotetraploid wild species, A.monticola, were successfully sequenced [20][21][22][23]. Based on the genomic sequences of the two diploid progenitors, genome-wide g-SSRs were identified and developed, and a high-density SSR physical map of wild peanut species was constructed [24].…”