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科学家实现四倍体马铃薯的单倍型基因组组装
2022-03-06 17:13

德国马克斯普朗克植物育种研究所Korbinian Schneeberger研究组完成了四倍体马铃薯染色体规模的单倍型基因组组装。2022年3月3日出版的《自然-遗传学》发表了这项成果。

研究人员基于高质量长读长、717个花粉基因组的单细胞测序和Hi-C数据对马铃薯栽培品种“Otava”的3.1 Gb进行了单倍型水平(精度为99.6%)的染色体规模组装。出乎意料的是,由于近亲繁殖,约50%的基因组在血缘上是相同的,这与约20%基因组的高度丰富结构重排形成鲜明对比。在38,214个基因中,只有54%存在于所有四种单倍型中,每个基因平均有3.2个拷贝。

以叶转录组为例,11%的基因至少在一种单倍型中表达不同,其中25%的基因可能通过等位基因特异性DNA甲基化进行调控。该工作揭示了马铃薯近代的育种历史、其四倍体基因组的功能组织,并有助于加快利用基因组学辅助育种的进程。

据了解,马铃薯是世界上种植最广泛的块茎作物。然而,重建其同源四倍体基因组的四种单倍型仍具有挑战。

附:英文原文

Title: Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Author: Sun, Hequan, Jiao, Wen-Biao, Krause, Kristin, Campoy, Jos A., Goel, Manish, Folz-Donahue, Kat, Kukat, Christian, Huettel, Bruno, Schneeberger, Korbinian

Issue&Volume: 2022-03-03

Abstract: Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.

DOI: 10.1038/s41588-022-01015-0

Source: https://www.nature.com/articles/s41588-022-01015-0

Nature Genetics:《自然—遗传学》,创刊于1992年。隶属于施普林格·自然出版集团,最新IF:41.307
官方网址:https://www.nature.com/ng/
投稿链接:https://mts-ng.nature.com/cgi-bin/main.plex


本期文章:《自然—遗传学》:Online/在线发表

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