Department of Biology, Duke University, Durham, North Carolina 27701
Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
Genetics. 2020 Apr;214(4):1031-1045. doi: 10.1534/genetics.120.303026. Epub 2020 Feb 7.
Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here, we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package syntR. The syntR algorithm performs as well as previous methods while being systematic, repeatable, and applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, ssp. and ssp. Using syntR, we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years, a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between one and three translocations involving only 8 of the 17 chromosomes. This nonrandom exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.
绘制物种间的染色体重排图谱可以帮助我们理解基因组进化、生殖隔离和物种形成。在这里，我们提出了一种新的算法，用于识别遗传图谱对中同源区域，该算法在随附的 R 包 syntR 中实现。syntR 算法的性能与以前的方法一样好，同时具有系统性、可重复性，并且适用于任何物种群的染色体重排作图。此外，我们对一年生向日葵进行了染色体重排的系统调查，这是一个以极端核型多样性而闻名的群体。我们为草原向日葵的两个亚种构建了高密度遗传图谱，分别为 ssp. 和 ssp. 。使用 syntR，我们确定了这两个亚种和以前发表的高密度遗传图谱之间的同源区块。我们使用这些同源区块重建一年生向日葵的祖先核型，并保守地估计每年有 7.9 次染色体重排，这是一个很高的染色体进化速率。尽管在这个群体中倒位的速率甚至高于易位的速率，但我们进一步发现，每个现存的核型都有一到三个易位，仅涉及 17 条染色体中的 8 条。这种非随机交换表明，特定的染色体容易发生易位，因此可能会导致向日葵中广泛的杂种不育。这些数据加深了我们对染色体进化的理解，并证实 具有异常高的染色体重排率，这可能有助于类似的快速多样化。
