Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

Description: Arthropod Transposable Elements Database
Year founded: 2018
Last update: 2018-8-02
Version: v1.0
Accessibility:
Manual:
Accessible
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Country/Region: China
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Peking University
Address: Beijing China
City: Beijing
Province/State: Beijing
Country/Region: China
Contact name (PI/Team): Jian Lu
Contact email (PI/Helpdesk): luj@pku.edu.cn

Publications

31064091
Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. [PMID: 31064091]
Wu C, Lu J.

Transposable elements (TEs) are ubiquitous in arthropods. However, analyses of large-scale and long-term coevolution between TEs and host genomes remain scarce in arthropods. Here, we choose 14 representative Arthropoda species from eight orders spanning more than 500 million years of evolution. By developing an unbiased TE annotation pipeline, we obtained 87 to 2266 TE reference sequences in a species, which is a considerable improvement compared to the reference TEs previously annotated in Repbase. We find that TE loads are diversified among species and were previously underestimated. The highly species- and time-specific expansions and contractions, and intraspecific sequence diversification are the leading driver of long terminal repeat (LTR) dynamics in Lepidoptera. Terminal inverted repeats (TIRs) proliferated substantially in five species with large genomes. A phylogenetic comparison reveals that the loads of multiple TE subfamilies are positively correlated with genome sizes. We also identified a few horizontally transferred TE candidates across nine species. In addition, we set up the Arthropod Transposable Elements database (ArTEdb) to provide TE references and annotations. Collectively, our results provide high-quality TE references and uncover that TE loads and expansion histories vary greatly among arthropods, which implies that TEs are an important driving force shaping the evolution of genomes through gain and loss.

Genes (Basel). 2019:10(5) | 1 Citations (from Europe PMC, 2020-10-31)

Ranking

All databases:
3560/4695 (24.196%)
Gene genome and annotation:
1006/1245 (19.277%)
3560
Total Rank
1
Citations
1
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Record metadata

Created on: 2020-10-10
Curated by:
Changcheng Wu [2020-10-15]
Dong Zou [2020-10-14]
Changcheng Wu [2020-10-10]