Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA.
Department of Computer Science, Saint Louis University, St. Louis, MO, 63103, USA.
BMC Genomics. 2018 Apr 24;19(1):282. doi: 10.1186/s12864-018-4683-0.
Chromosomal rearrangements have been shown to facilitate speciation through creating a barrier of gene flow. However, it is not known whether heterogeneous rates of chromosomal rearrangement at the genome scale contributed to the huge disparity of species richness among different groups of organisms, which is one of the most remarkable and pervasive patterns on Earth. The largest fungal phylum Ascomycota is an ideal study system to address this question because it comprises three subphyla (Saccharomycotina, Taphrinomycotina, and Pezizomycotina) whose species numbers differ by two orders of magnitude (59,000, 1000, and 150 respectively).
We quantified rates of genome rearrangement for 71 Ascomycota species that have well-assembled genomes. The rates of inter-species genome rearrangement, which were inferred based on the divergence rates of gene order, are positively correlated with species richness at both ranks of subphylum and class in Ascomycota. This finding is further supported by our quantification of intra-species rearrangement rates based on paired-end genome sequencing data of 216 strains from three representative species, suggesting a difference of intrinsic genome instability among Ascomycota lineages. Our data also show that different rates of imbalanced rearrangements, such as deletions, are a major contributor to the heterogenous rearrangement rates.
Various lines of evidence in this study support that a higher rate of rearrangement at the genome scale might have accelerated the speciation process and increased species richness during the evolution of Ascomycota species. Our findings provide a plausible explanation for the species disparity among Ascomycota lineages, which will be valuable to unravel the underlying causes for the huge disparity of species richness in various taxonomic groups.
染色体重排已被证明通过形成基因流动的屏障而促进物种形成。然而，目前尚不清楚基因组范围内染色体重排的异质性速率是否导致不同生物群之间物种丰富度的巨大差异，这是地球上最显著和普遍的模式之一。最大的真菌门子囊菌门是解决这个问题的理想研究系统，因为它包含三个亚门（酵母纲、栓菌纲和盘菌纲），其物种数量相差两个数量级（分别为 59,000、1000 和 150）。
我们量化了 71 种具有良好组装基因组的子囊菌物种的基因组重排率。基于基因顺序分歧率推断的种间基因组重排率与子囊菌门的亚门和纲两个等级的物种丰富度呈正相关。这一发现进一步得到了我们基于三个代表种的 216 个菌株的测序数据来量化种内重排率的支持，表明子囊菌谱系之间存在内在基因组不稳定性的差异。我们的数据还表明，不平衡重排（如缺失）的不同速率是异质重排率的主要贡献者。
本研究中的各种证据支持基因组水平上更高的重排率可能加速了子囊菌物种的形成过程，并在其进化过程中增加了物种丰富度。我们的发现为子囊菌谱系之间的物种差异提供了一个合理的解释，这对于揭示各种分类群中物种丰富度巨大差异的潜在原因将是有价值的。
