African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt.
Methods Mol Biol. 2023;2703:71-82. doi: 10.1007/978-1-0716-3389-2_6.
To meet the critical demand of LTR-RTs data-driven research, we updated the CicerSpTEdb database to version 2.0, which includes more accurate intact LTR-RT elements with annotation of internal domains. We also added the ability to BLAST against TEs of Cicer species. As a result, 3701 intact LTR-RTs were detected in the studied genomes, including 2840 Copia and 861 Gypsy elements. Of the 3701 intact LTR-RTs, 588 were in C. arietinum, including 475 Copia and 113 Gypsy. While 1373 were detected in C. reticulatum, including 1041 Copia and 332 Gypsy. Furthermore, 1740 were found in C. echinospermum, including 1324 Copia and 416 Gypsy. Based on LTR-RT clades, the analysis classified the 3701 identified intact LTR-RTs in the studied genomes as Ale (850), SIRE (740), unknown (455), Ikeros (323), Reina (290), Tork (290), Ivana (282), Tekay (197), Athila (128), TAR (99), CRM (31), and Ogre (16) elements. The newly updated CicerSpTEdb2.0 will be a valuable resource for TEs of Cicer species and their comparative genomics.Database URL: http://cicersptedb.easyomics.org/index.php.
为了满足 LTR-RTs 数据驱动研究的关键需求，我们更新了 CicerSpTEdb 数据库至 2.0 版本，其中包含了更准确的具有内部结构域注释的完整 LTR-RT 元件。我们还增加了针对鹰嘴豆属 TE 的 BLAST 功能。结果，在研究的基因组中检测到 3701 个完整的 LTR-RT，包括 2840 个 Copia 和 861 个 Gypsy 元件。在 3701 个完整的 LTR-RT 中，588 个存在于鹰嘴豆中，包括 475 个 Copia 和 113 个 Gypsy。而在 C. reticulatum 中检测到 1373 个，包括 1041 个 Copia 和 332 个 Gypsy。此外，在 C. echinospermum 中发现了 1740 个，包括 1324 个 Copia 和 416 个 Gypsy。基于 LTR-RT 进化枝，分析将研究基因组中鉴定的 3701 个完整 LTR-RT 分为 Ale（850）、SIRE（740）、未知（455）、Ikeros（323）、Reina（290）、Tork（290）、Ivana（282）、Tekay（197）、Athila（128）、TAR（99）、CRM（31）和 Ogre（16）元件。新更新的 CicerSpTEdb2.0 将成为鹰嘴豆属 TE 及其比较基因组学的有价值资源。数据库网址：http://cicersptedb.easyomics.org/index.php。
