| URL: | http://pmite.hzau.edu.cn/ |
| Full name: | Plant Miniature Inverted Transposable Element database |
| Description: | P-MITE is a database of miniature inverted transposable elements (MITEs) de novo identified from over 40 plant genomes. It's intended to provide data about MITE sequences and families and other resources for biologists who are working on the related disciplines. It also provides softwares that could be downloaded and used for de novo identification of MITE in a new genome. This MITE database contains more than 2 million MITE-related sequences of 3,527 MITE families, identified from 41 sequenced plant genomes. |
| Year founded: | 2014 |
| Last update: | 2014-01-01 |
| Version: | v1.0 |
| Accessibility: |
Accessible
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| Country/Region: | China |
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| University/Institution: | Huazhong Agricultural University |
| Address: | Wuhan,430070,P. R. China |
| City: | Wuhan |
| Province/State: | Hubei |
| Country/Region: | China |
| Contact name (PI/Team): | Jiongjiong Chen |
| Contact email (PI/Helpdesk): | jjchen@mail.hzau.edu.cn |
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P-MITE: a database for plant miniature inverted-repeat transposable elements. [PMID: 24174541]
Miniature inverted-repeat transposable elements (MITEs) are prevalent in eukaryotic species including plants. MITE families vary dramatically and usually cannot be identified based on homology. In this study, we de novo identified MITEs from 41 plant species, using computer programs MITE Digger, MITE-Hunter and/or Repetitive Sequence with Precise Boundaries (RSPB). MITEs were found in all, but one (Cyanidioschyzon merolae), species. Combined with the MITEs identified previously from the rice genome, >2.3 million sequences from 3527 MITE families were obtained from 41 plant species. In general, higher plants contain more MITEs than lower plants, with a few exceptions such as papaya, with only 538 elements. The largest number of MITEs is found in apple, with 237 302 MITE sequences. The number of MITE sequences in a genome is significantly correlated with genome size. A series of databases (plant MITE databases, P-MITE), available online at http://pmite.hzau.edu.cn/django/mite/, was constructed to host all MITE sequences from the 41 plant genomes. The databases are available for sequence similarity searches (BLASTN), and MITE sequences can be downloaded by family or by genome. The databases can be used to study the origin and amplification of MITEs, MITE-derived small RNAs and roles of MITEs on gene and genome evolution. |