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

<i>Arachis monticola</i> (2n = 4x = 40) is the only allotetraploid wild peanut within section Arachis, with an AABB-type genome of about ~2.7 Gb. The AA-type subgenome is derived from diploid wild peanut <i>Arachis duranensis</i>, and the BB-type subgenome is derived from diploid wild peanut <i>Arachis ipaensis</i>. <i>A. monticola</i> 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 <i>A. monticola</i> genome, using a series of advanced technologies. The final whole genome of <i>A. monticola</i> 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 (SMRT) sequencing, high-throughput chromosome conformation capture (Hi-C) technology and BioNano optical genome map. These combined technologies produced reference-quality genome of the allotetraploid wild peanut, which is valuable for understanding the peanut domestication and evolution within Arachis genus and among legume crops.山地花生（Arachis monticola）的染色体组型为2n=4x=40，是落花生组（section Arachis）中唯一的异源四倍体野生花生，其AABB型基因组大小约为2.7 Gb。其中AA型亚基因组源自二倍体野生花生杜兰落花生（Arachis duranensis），BB型亚基因组源自二倍体野生花生伊帕落花生（Arachis ipaensis）。山地花生（A. monticola）被认为既是栽培花生的直接祖先，也可能是栽培花生与野生物种之间的渐渗衍生类群。其庞大的多倍体基因组结构以及大量高度同源的相似基因组区域，使得染色体假分子的组装极具挑战性。本研究利用一系列先进技术，首次报道了山地花生（A. monticola）基因组的参考级组装结果。最终组装得到的山地花生全基因组大小约为2.62 Gb，重叠群N50和支架N50分别为106.66 Kb和124.92 Mb。组装序列的绝大多数（91.83%）被锚定至20条伪染色体上，且96.07%的组装序列可准确区分为AA型和BB型亚基因组。本研究验证了基于全基因组鸟枪法测序、单分子实时（SMRT）测序、高通量染色体构象捕获（Hi-C）技术以及BioNano光学基因组图谱的策略，在高度复杂的异源多倍体物种野生花生（A. monticola）的从头组装中的有效性。上述联合技术成功获得了该异源四倍体野生花生的参考级基因组，这对于解析落花生属内以及豆科作物间的花生驯化与演化过程具有重要价值。