Chromosome-level assemblies of seven A. thaliana accessions using PacBio long-read sequencing.. Assembly of multiple Arabidopsis thaliana genomes

We report chromosome-level, reference-quality assemblies of seven Arabidopsis thaliana accessions selected across the geographic range of this model plant. Each genome assembly revealed between 13-17 Mb of rearranged and 5-6 Mb of novel sequence introducing copy-number changes in ~5000 genes, including ~1,900 genes which are not part of the current reference annotation. By analyzing the collinearity between the genomes, we identified nearly 600 hotspots of rearrangements covering ~8% of the genome. Hotspots of rearrangements are characterized by accession-specific accumulation of tandem duplications and are enriched for genes implicated in disease resistance and secondary metabolite biosynthesis. Concomitant loss of meiotic recombination in hybrids within these regions is consistent with the accumulation of rare and deleterious alleles and incompatibility loci. Together this suggests that hotspots of rearrangements are governed by different evolutionary dynamics as compared to the rest of the genome and facilitate rapid response to the ever-evolving challenges of biotic stress.

本研究报道了7个覆盖模式植物拟南芥（Arabidopsis thaliana）地理分布范围的种质系的染色体级参考级基因组组装结果。每个基因组组装均鉴定出13~17 Mb的重排序列与5~6 Mb的全新序列，这些序列带来了约5000个基因的拷贝数改变，其中约1900个基因未被纳入当前的基因组参考注释（reference annotation）。通过分析各基因组间的共线性（collinearity），我们共鉴定出近600个重排热点（rearrangement hotspots），覆盖约8%的基因组区域。重排热点具有种质系特异性串联重复（tandem duplication）累积的特征，且显著富集了与抗病性及次生代谢物生物合成相关的基因。这些区域在杂交个体中伴随出现的减数分裂重组（meiotic recombination）缺失现象，与稀有有害等位基因及不亲和位点（incompatibility loci）的累积特征相一致。综上，本研究结果表明，相较于基因组其余区域，重排热点受独特的进化动力学（evolutionary dynamics）调控，可帮助植物快速响应不断演化的生物胁迫（biotic stress）挑战。