Homoeologous exchanges occur through intragenic recombination generating novel transcripts and proteins in wheat and other polyploids

第一作者：Zhibin Zhang

第一单位：东北师范大学

通讯作者：Avraham A. Levy

 Abstract 

背景回顾：Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species.

提出问题：However, the molecular mechanisms that govern HEs are not well understood.

主要研究：Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses.

结果：In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them.

结论：HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.

 摘  要 

同源染色体之间的重组又称之为同源交换（homeologous exchange，HE），在某些植物种间杂交和异源多倍体的基因组结构塑造和基因表达方面发挥重要的作用。然而，作用于同源交换的分子机制还不是很透彻。本文中，作者通过细胞学和全基因组测序的方法研究了六倍体面包小麦的两个二倍体祖先种杂交产生的一个新的异源四倍体（AADD）子代中的同源交换。作者共鉴定了37个同源交换，并且精确定位了同源交换连接。同源交换存在典型的同源重组热点，偏向于在染色体臂的低拷贝、亚端粒区，并且与已知的重组热点基序有关联。但是，相较于同源重组会优先发生于编码区域的上游或者下游，同源交换显著富集于基因区，从而产生了很多新的重组转录本，预测会产生新的蛋白融合变体。为了测试该现象是否普遍存在于植物中，作者进一步分析了异源多倍体芸薹、水稻、拟南芥、香蕉以及花生，鉴定了一套高分辨率的同源交换连接数据集。结果显示，所有物种的同源交换区域均检测到了基因内重组和嵌合基因，并且在大多数物种中这种情况很突出。因此，同源交换为异源多倍体产生新的转录本和蛋白序列提供了一个演化机制。

 通讯作者 

**Avraham A. Levy**

研究方向：

doi: 10.1073/pnas.2003505117

Journal: PNAS

Published date: June 09, 2020