PDF(Pubmed)
Abstract：
Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB\'s relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.
摘要：
转座因子（TE）是普遍存在的基因组成分，由于高度重复而难以研究。在这里，我们根据长读数测序数据组装了232个染色体水平的基因组。将232个基因组与15个现有组件耦合，我们开发了一个pan-TE地图，包括栽培和野生亚洲水稻。我们检测到177.084个高质量的TE变异，并使用外群推断它们的派生状态。我们发现TEs是水稻驯化和分化过程中表型变异的来源之一。我们确定了1246个基因，其表达变异与TE相关，但与单核苷酸多态性（SNP）无关。比如OsRbohB,并使用双荧光素酶（LUC）报告测定系统验证了OsRbohB的相对表达活性。我们的pan-TE图谱使我们能够检测到与农艺性状相关的多个新基因座。总的来说，我们的发现强调了TEs对驯化的贡献，水稻的分化和农艺性状，通过我们生成的高质量亚洲泛TE图谱，基因克隆和分子育种具有巨大潜力。
