花生
生物
基因组
顺序装配
花生
参考基因组
倍性
康蒂格
全基因组测序
基因
遗传学
植物
转录组
基因表达
作者
Dongmei Yin,Changmian Ji,Xingli Ma,Hang Li,Wan-Ke Zhang,Song Li,Fuyan Liu,Kunkun Zhao,Fapeng Li,Ke Li,Longlong Ning,Jialin He,Yuejun Wang,Fei Zhao,Yilin Xie,Hongkun Zheng,Xingguo Zhang,Yijing Zhang,Jinsong Zhang
出处
期刊:GigaScience
[Oxford University Press]
日期:2018-06-01
卷期号:7 (6)
被引量:60
标识
DOI:10.1093/gigascience/giy066
摘要
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.
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