DataSheet_1_Transposable elements are associated with genome-specific gene expression in bread wheat.pdf

IntroductionRecent studies in wheat emphasized the importance of TEs, which occupy ~85% of the wheat genome, as a major source of intraspecific genetic variation due to their recent activity and involvement in genomic rearrangements. The contribution of TEs to structural and functional variations in bread wheat genes is not fully understood.
MethodsHere, publicly available RNA-Seq databases of bread wheat were integrated to identify TE insertions within gene bodies (exons\ introns) and assess the impact of TE insertions on gene expression variations of homoeologs gene groups. Overall, 70,818 homoeologs genes were analyzed: 55,170 genes appeared in each one of the three subgenomes (termed ABD), named triads; 12,640 genes appeared in two of the three subgenomes (in A and B only, termed AB; or in A and D only, termed AD; or in B and D only, termed BD);, named dyads; and 3,008 genes underwent duplication in one of the three subgenomes (two copies in: subgenome A, termed AABD; subgenome B, termed ABBD; or subgenome D, termed ABDD), named tetrads.
ResultsTo this end, we found that ~36% of the 70,818 genes contained at least one TE insertion within the gene body, mostly in triads. Analysis of 14,258 triads revealed that the presence of TE insertion in at least one of the triad genes (7,439 triads) was associated with balanced expression (similar expression levels) between the homoeolog genes. TE insertions within the exon or in the untranslated regions (UTRs) of one or more of the homoeologs in a triad were significantly associated with homoeolog expression bias. Furthermore, we found a statistically significant correlation between the presence\absence of TEs insertions belonging to six TE superfamilies and 17 TE subfamilies and the suppression of a single homoeolog gene. A significant association was observed between the presence of TE insertions from specific superfamilies and the expression of genes that are associated with biotic and abiotic stress responses.
ConclusionOur data strongly indicate that TEs might play a prominent role in controlling gene expression in a genome-specific manner in bread wheat.

引言 近期针对小麦的研究强调了转座因子（Transposable Elements, TEs）的重要性：这类因子占据约85%的小麦基因组，由于其近期的转座活性与参与基因组重排过程，成为种内遗传变异的主要来源。目前，转座因子对普通面包小麦基因的结构与功能变异的贡献尚未完全阐明。
方法 本研究整合了公开可用的RNA测序（RNA-Seq）数据库，以鉴定基因区域（外显子、内含子）内的转座因子插入事件，并评估转座因子插入对部分同源基因（homoeolog）群基因表达变异的影响。本次分析共涵盖70818个部分同源基因：其中55170个基因存在于三个亚基因组（记为ABD）的每一个中，这类基因被称为三联体（triads）；12640个基因仅存在于三个亚基因组中的两个（仅A和B亚基因组，记为AB；仅A和D亚基因组，记为AD；仅B和D亚基因组，记为BD），这类基因被称为二联体（dyads）；另有3008个基因在三个亚基因组中的某一个发生了复制（如在亚基因组A中存在两个拷贝，记为AABD；亚基因组B中存在两个拷贝，记为ABBD；亚基因组D中存在两个拷贝，记为ABDD），这类基因被称为四联体（tetrads）。
结果 基于上述研究设计，本研究发现70818个基因中约36%的基因在其基因区域内存在至少一处转座因子插入，且此类插入多发生于三联体基因中。对14258个三联体基因的分析显示：在7439个三联体基因中，至少有一个部分同源基因存在转座因子插入，这与各部分同源基因间的平衡表达（表达水平相近）显著相关。三联体中一个或多个部分同源基因的外显子或非翻译区（Untranslated Regions, UTRs）内存在转座因子插入，与部分同源基因表达偏倚显著相关。此外，本研究发现，属于6个转座因子超家族和17个转座因子亚家族的转座因子插入的有无，与单个部分同源基因的表达抑制存在统计学上的显著相关性。同时，特定超家族的转座因子插入与参与生物胁迫和非生物胁迫响应的基因的表达水平显著相关。
结论 本研究数据有力表明，转座因子可能以基因组特异性的方式，在普通面包小麦的基因表达调控中发挥重要作用。