InpactorDB: A Plant LTR Retrotransposon Reference Library.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• LTR retrotransposons (LTR-RTs) are significant components of plant genomes, influencing genome structure and evolution.
• Their mobility and amplification play roles in gene and genome evolution, making them valuable evolutionary markers.
• A lack of readily available, curated, and classified LTR-RT reference sequences hinders plant research.

Purpose of the Study:

• To introduce InpactorDB, a comprehensive database of LTR retrotransposon sequences.
• To provide a standardized method for identifying and classifying LTR-RTs in newly sequenced plant genomes.
• To make LTR-RT reference sequences freely accessible to the plant research community.

Main Methods:

• Compilation of LTR retrotransposon sequences from 181 plant species across 98 families.
• Development and application of the Inpactor tool for standardized identification and classification of LTR-RTs.
• Creation of a non-redundant database containing 67,241 LTR-RT elements.

Main Results:

• InpactorDB provides 67,241 non-redundant LTR-RT elements from 181 plant species.
• The Inpactor tool enables consistent identification and classification of LTR-RTs in new genomes.
• The database is freely available online, addressing a critical need in plant genomics.

Conclusions:

• InpactorDB significantly enhances the accessibility of curated LTR-RT data for plant research.
• The standardized Inpactor tool facilitates consistent analysis of LTR retrotransposons across diverse plant species.
• This resource will advance studies on plant genome evolution and the role of LTR-RTs.