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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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TGIF-DB: terse genomics interface for developing botany.

Daisuke Tsugama1, Tetsuo Takano2

  • 1Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo, 188-0002, Japan. dtsugama@anesc.u-tokyo.ac.jp.

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|May 14, 2021
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Summary

This study enhances gene function annotations for pearl millet, garden asparagus, chickpea, and Tartary buckwheat by leveraging model plant data. A new website, TGIF-DB, provides access to these improved genomic resources for crop research.

Keywords:
ArabidopsisChickpeaGarden asparagusGenomicsPearl milletPlantRiceTartary buckwheat

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Area of Science:

  • Plant genomics
  • Comparative genomics
  • Bioinformatics

Background:

  • Pearl millet, garden asparagus, chickpea, and Tartary buckwheat are important crops with available genome sequences but limited gene function annotations.
  • Understanding gene function is crucial for crop improvement and agricultural development.

Purpose of the Study:

  • To improve functional annotations of genes in pearl millet, garden asparagus, chickpea, and Tartary buckwheat.
  • To systematically provide these enhanced annotations and sequences via a dedicated website.
  • To promote genomics research for these under-annotated crop species.

Main Methods:

  • Downloaded genome and transcript sequences for the target crops from public databases.
  • Associated crop transcripts with functional annotations from model plants (Arabidopsis thaliana, Oryza sativa) using BLASTX.
  • Identified conserved protein domains using HMMER scan against the Pfam database.

Main Results:

  • Successfully improved functional annotations for genes in pearl millet, garden asparagus, chickpea, and Tartary buckwheat.
  • Developed the Terse Genomics Interface for Developing Botany (TGIF-DB) website to host and display the data.
  • Data deposited in the figshare repository for accessibility.

Conclusions:

  • The study provides valuable, enhanced gene functional annotations for several important crop species.
  • The TGIF-DB website serves as a centralized resource for accessing these genomic data.
  • Facilitating genomics research for these crops can lead to advancements in agriculture.