目的:分析异源多倍体基因组的一个复杂因素是减数分裂过程中同源染色体之间的物理相互作用的可能性,产生交叉(同源交换)或非交叉产物(同源基因转化)。通过比较来自两个二倍体祖细胞的序列中的SNP模式与来自异源多倍体亚基因组的序列中的SNP模式,首先在棉花中描述了同源基因转换。这些分析,然而,没有明确考虑其他可能导致与同源基因转换相似的SNP模式的进化情景,对推断的基因转换事件的真实性产生不确定性。
方法:这里,我们使用来自七个异源多倍体棉属物种(全部来自相同的多倍体事件)的高质量基因组组装的扩展系统发育采样,四个二倍体物种(两个与每个亚基因组密切相关),和二倍体外群,以得出一种可靠的方法,用于识别基因转换和同源交换的潜在基因组区域。
结果:我们发现在异源多倍体棉花中几乎没有同源基因转化的证据,在40个最受支持的事件中,只有两个被多个物种共享。我们做到了,然而,揭示一个单一的,在1号染色体的一端共享同源交换事件,该事件发生在异源多倍化后不久,但在后代物种分歧之前。
结论:总体而言,我们的分析表明,同源基因转换和同源交换在棉属中并不常见,在七个物种中,每个亚基因组影响零至24个基因(0.0-0.065%)。更一般地说,我们强调了使用简单的四分类单元测试来研究已建立的异源多倍体中同源基因转换模式的潜在问题。
OBJECTIVE: A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non-crossover products (homoeologous gene conversion). Homoeologous gene conversion was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar SNP patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events.
METHODS: Here, we use an expanded phylogenetic sampling of high-quality genome assemblies from seven allopolyploid Gossypium species (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange.
RESULTS: We found little evidence for homoeologous gene conversion in allopolyploid cottons, and that only two of the 40 best-supported events were shared by more than one species. We did, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species.
CONCLUSIONS: Overall, our analyses demonstrated that homoeologous gene conversion and homoeologous exchanges are uncommon in Gossypium, affecting between zero and 24 genes per subgenome (0.0-0.065%) across the seven species. More generally, we highlighted the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids.