School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, 570228, Haikou, P.R. China.
School of life sciences, Hainan University, 570228, Haikou, P.R. China.
BMC Genomics. 2024 Sep 16;25(1):864. doi: 10.1186/s12864-024-10779-0.
Greater yam is a key staple crop grown in tropical and subtropical regions, while its asexual propagation mode had led to non-flowering mutations. How transposable elements contribute to its genetic variations is rarely analyzed. We used transcriptome and whole genome sequencing data to identify active transposable elements (TEs) and genetic variation caused by these active TEs. Our aim was to shed light on which TEs would lead to its intraspecies variation.
Annotation of de novo assembly transcripts indicated that 0.8 - 0.9% of transcripts were TE related, with LTR retrotransposons (LTR-RTs) accounted for 65% TE transcripts. A large portion of these transcripts were non-autonomous TEs, which had incomplete functional domains. The majority of mapped transcripts were distributed in genic deficient regions, with 9% of TEs overlapping with genic regions. Moreover, over 90% TE transcripts exhibited low expression levels and insufficient reads coverage to support full-length structure assembly. Subfamily analysis of Copia and Gypsy, the two LTR-RTs revealed that a small number of subfamilies contained a significantly larger number of members, which play a key role in generating TE transcript. Based on resequencing data, 15,002 L-RT insertion loci were detected for active LTR-RT members. The insertion loci of LTR-RTs were highly divergent among greater yam accessions.
This study showed the ongoing transcription and transpositions of TEs in greater yam, despite low transcription levels and incomplete proteins insufficient for autonomous transposition. While our research did not directly link these TEs to specific yam traits such as tuber yield and propagation mode, it lays a crucial foundation for further research on how these TE insertion polymorphisms (TIPs) might be related to variations in greater yam traits and its tuber propagation mode. Future research may explore the potential roles of TEs in trait variations, such as tuber yield and stress resistance, in greater yam.
淮山是热带和亚热带地区的主要粮食作物之一，其无性繁殖方式导致了非开花突变。转座元件如何导致其遗传变异很少被分析。我们使用转录组和全基因组测序数据来识别活跃的转座元件（TEs）和这些活跃的 TEs 引起的遗传变异。我们的目的是阐明哪些 TEs 会导致其种内变异。
从头组装转录本的注释表明，0.8-0.9%的转录本与转座元件相关，其中 LTR 反转录转座子（LTR-RTs）占 TE 转录本的 65%。这些转录本中有很大一部分是非自主转座元件，它们缺乏完整的功能域。大多数映射的转录本分布在基因缺失区域，其中 9%的 TEs 与基因区域重叠。此外，超过 90%的 TE 转录本表达水平较低，读取覆盖率不足以支持全长结构组装。Copia 和 Gypsy 这两种 LTR-RTs 的亚家族分析表明，少数亚家族包含数量显著较多的成员，这些成员在产生 TE 转录本方面发挥着关键作用。基于重测序数据，检测到 15002 个活跃 LTR-RT 成员的 L-RT 插入位点。LTR-RTs 的插入位点在不同的淮山品种之间高度分化。
本研究表明，TEs 在淮山中有持续的转录和转位，尽管转录水平较低，且缺乏完整的、足以自主转位的蛋白质。虽然我们的研究没有直接将这些 TEs 与淮山的特定特性（如块茎产量和繁殖方式）联系起来，但它为进一步研究这些 TE 插入多态性（TIPs）与淮山特性及其块茎繁殖方式的变异之间的关系奠定了重要基础。未来的研究可能会探索 TEs 在特性变异（如块茎产量和抗逆性）中的潜在作用。
