文献类型：期刊文献

英文题名：SPTEdb: a database for transposable elements in salicaceous plants

作者：Yi, Fei[1,2] Jia, Zirui[1] Xiao, Yao[1] Ma, Wenjun[1] Wang, Junhui[1]

第一作者：Yi, Fei

通信作者：Ma, WJ[1];Wang, JH[1]

机构：[1]Chinese Acad Forestry, Res Inst Forestry, State Key Lab Tree Genet & Breeding, Key Lab Tree Breeding & Cultivat State Forestry A, Beijing 100091, Peoples R China;[2]Three Gorges Univ, Coll Biol & Pharmaceut Sci, Yichang 443002, Peoples R China

年份：2018

卷号：2018

期号：2018

外文期刊名：DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION

收录：;Scopus(收录号：2-s2.0-85054778778);WOS:【SCI-EXPANDED(收录号:WOS:000427200400001)】；

基金：This work was supported by Open Foundation of State Key Laboratory of Tree Genetics and Breeding (Chinese Academy of Forestry) (TGB2016003); National Natural Science Foundation of China (31600541) and Science Foundation of China Postdoctor (160132). Funding for open access charge: National Natural Science Foundation of China.

语种：英文

摘要：Although transposable elements (TEs) play significant roles in structural, functional and evolutionary dynamics of the salicaceous plants genome and the accurate identification, definition and classification of TEs are still inadequate. In this study, we identified 18 393 TEs from Populus trichocarpa, Populus euphratica and Salix suchowensis using a combination of signature-based, similarity-based and De novo method, and annotated them into 1621 families. A comprehensive and user-friendly web-based database, SPTEdb, was constructed and served for researchers. SPTEdb enables users to browse, retrieve and download the TEs sequences from the database. Meanwhile, several analysis tools, including BLAST, HMMER, GetORF and Cut sequence, were also integrated into SPTEdb to help users to mine the TEs data easily and effectively. In summary, SPTEdb will facilitate the study of TEs biology and functional genomics in salicaceous plants.