New insights into homoeologous copy number variations in the hexaploid wheat genome

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.普通小麦（Bread wheat）是一类异源六倍体物种，其起源于三个染色体数目、基因组大小、转座因子（TE）含量、基因含量及共线性（synteny）均极为相似的二倍体物种之间连续两次近期的杂交事件。长期以来，学界普遍认为绝大多数基因以三套部分同源（homoeologous）拷贝的形式存在。然而，这些所谓的“三联体（triads）”仅占小麦基因的一半，剩余一半则属于在各亚基因组间拷贝数各异的部分同源基因家族。 本研究中，我们针对仅在单个亚基因组中发生一次缺失的“二联体（dyads）”或一次重复的“四联体（tetrads）”类部分同源基因家族，与三联体展开分析与比较，对二者的分布特征、保守性、功能、表达模式及表观遗传谱进行了系统研究。结果显示，二联体与四联体主要定位于染色体远端区域，且其表达水平与表达广度均低于三联体。此外，这两类基因家族显著富集于与环境适应相关的功能通路，且更易与抑制性组蛋白修饰H3K27me3相关联。 综上，上述结果表明，三联体主要对应持家基因，属于核心基因组范畴；而二联体与四联体则属于小麦族（Triticeae）非必需基因组。此外，通过对比不同类别的二联体与四联体，我们提出如下假说：与多数异源多倍体物种不同，普通小麦并不存在亚基因组优势与偏向性基因丢失现象。鉴于普通小麦的演化历程，其三套亚基因组间的差异更可能与两次连续且仍在进行的多倍体后二倍化浪潮相关，其中A与B亚基因组所受影响显著大于D亚基因组。