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Database (Oxford). 2015 Feb 27;2015. pii: bav004. doi: 10.1093/database/bav004. Print 2015.

MnTEdb, a collective resource for mulberry transposable elements.

Author information

1
State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China.
2
State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China hejia@swu.edu.cn.

Abstract

Mulberry has been used as an economically important food crop for the domesticated silkworm for thousands of years, resulting in one of the oldest and well-known plant-herbivore interactions. The genome of Morus notabilis has now been sequenced and there is an opportunity to mine the transposable element (TE) data. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the mulberry genome, a specific, comprehensive and user-friendly web-based database, MnTEdb, was constructed. It was built based on a detailed and accurate identification of all TEs in mulberry. A total of 5925 TEs belonging to 13 superfamilies and 1062 families were deposited in this database. MnTEdb enables users to search, browse and download the mulberry TE sequences. Meanwhile, data mining tools, including BLAST, GetORF, HMMER, Sequence Extractor and JBrowse were also integrated into MnTEdb. MnTEdb will assist researchers to efficiently take advantage of our newly annotated TEs, which facilitate their studies in the origin, amplification and evolution of TEs, as well as the comparative analysis among the different species. Database URL: http://morus.swu.edu.cn/mntedb/.

PMID:
25725060
PMCID:
PMC4343074
DOI:
10.1093/database/bav004
[Indexed for MEDLINE]
Free PMC Article

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