A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization
A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization
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六倍体小麦的共表达网络揭示了多倍体化后同源减数分裂基因的表达基本平衡，并且没有显着的基因丢失
DOI：
10.1101/695759
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Alabdullah A
中科院分区：
文献类型：
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作者：
Alabdullah A
多倍化在植物进化中起着重要作用。然而，在多倍化后，减数分裂过程必须适应以确保增加的染色体数目的适当分离以产生平衡的配子。有人认为，减数分裂基因（MG）重复返回到一个单一的副本后，全基因组复制，以稳定多倍体基因组。因此，在小麦的多倍化，一个六倍体物种与三个相关的（同源）基因组，稳定化过程可能涉及同源染色体（同源）的MG的含量和表达的快速变化。为了检验这一假设，使用共表达网络分析和基于同源性的方法在小麦中鉴定了候选MG的集合。总共使用了来自包括小麦减数分裂花药在内的一系列组织的130个RNA-Seq样品来定义基因的共表达模块。三个模块与减数分裂组织样品显著相关，但与其他组织类型不相关。这些模块富集了与细胞周期、DNA复制和染色质修饰相关的GO术语，并包含已知MG的直系同源物。总体而言，这些减数分裂相关模块中有74.4%的基因具有三个同源拷贝，这与其他组织相关模块相似。在通过直系同源而非共表达鉴定的小麦MG中，与祖先小麦物种相比，大多数（93.7%）以相同的拷贝数（78.4%）保留在六倍体小麦中或拷贝数增加（15.3%）。此外，减数分裂相关模块内的基因表现出更平衡的同源物之间的表达水平比非减数分裂相关模块中的基因。总之，我们的研究结果不支持广泛的基因丢失，也不支持小麦多倍体化后MG同源基因表达的变化。MG共表达网络的构建允许识别枢纽基因，并为未来的研究提供了关键目标。
Polyploidization has played an important role in plant evolution. However, upon polyploidization, the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to stabilize the polyploid genome. Therefore, upon the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the stabilization process may have involved rapid changes in content and expression of MGs on homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were identified in wheat using co-expression network analysis and orthology informed approaches. In total, 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue samples but not with other tissue types. These modules were enriched for GO terms related to cell cycle, DNA replication, and chromatin modification and contained orthologs of known MGs. Overall, 74.4% of genes within these meiosis-related modules had three homeologous copies which was similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-expression, the majority (93.7%) were either retained in hexaploid wheat at the same number of copies (78.4%) or increased in copy number (15.3%) compared to ancestral wheat species. Furthermore, genes within meiosis-related modules showed more balanced expression levels between homeologs than genes in non-meiosis-related modules. Taken together, our results do not support extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The construction of the MG co-expression network allowed identification of hub genes and provided key targets for future studies.