我们通常将包含两个相对完整的 LTRs 和已识别的 PPT 和 PBS 位点的元素,且两侧有 TSD 的 LTR 定义为 Intact LTR(A)。由于 LTR-RTs 两端序列非常相似,LTR-RTs 内可发生重组,导致内部元件消失,形成 solo LTR(C),而 solo LTR 的数量表明了一个基因组中 LTR 去除的频率和效率。此外 LTR 发生缺失、易位可形...
This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.doi:10.1186/s12864-024-10177-6Rui-Bin CaoRan ChenKe-Xin LiaoHe LiGang-Biao XuXiao-Long Jiang
The LTR-RTs were compared to identify how different LTR-RT types (Divo and Nana) are distributed across the chromosomes of C. eugenioides, as well as to determine the origin of the Nana element. Two other LTR-RTs, named Tork and Athila, were also identified and mapped. The efficiency of...
Long terminal repeat retrotransposons (LTR-RTs) are a large portion of most plant genomes, and can be used as a powerful molecular marker system. The first citrus reference genome (Citrus x clementina) has been publicly available since 2011; however, previous studies in citrus have not utilized ...
identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin Hyunjin Koo1, Soomin Kim1, Hyun‑Seung Park1, Sang‑Ji Lee1, Nam‑Chon Paek1, Jungnam Cho2 and Tae‑Jin Yang1* Abstract Long terminal repeat retrotransposons (LTR-RTs) make ...
Although plant genomes have experienced periodic proliferation and/or recent burst of LTRretrotransposons, the majority of LTR-RTs are inactivated by DNA methylation and small RNA-mediated silencing mechanisms, and/or were deleted/truncated by unequal homologous recombination and illegitimate recombination, ...
LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, and LtrDetector, and generates non-redundant LTR-RT library for genome annotations. ...
Thus, LTR_STRUC [34] and LTR_FINDER [27] software were first run to predict LTR-RTs for each genomes. Two workflows were performed, the first using conventional bioinformatics methods with filters proposed in InpactorDB [35], and the second one using the computational architecture with the ...
rice6.9.5.liban.rexdb.domtbl HMMScan raw output rice6.9.5.liban.rexdb.dom.faa protein sequences of domain, which can be used for phylogenetic analysis. rice6.9.5.liban.rexdb.dom.tsv inner domains of TEs/LTR-RTs, which might be used to filter domains based on their scores and coverage...
Long terminal repeat retrotransposons (LTR-RTs) make up a large fraction of most plant genomes, and they play important roles in genome evolution. A total of 3,959 full-length LTR-RTs were identified in the sequenced genome using both structure-based (LTR_FINDER) and homology-based (RepeatMask...