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Updated: Aug 18, 2025

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TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies.

Tong Yu1, Xiao Ma1, Zhuo Liu1

  • 1School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China.

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|December 9, 2022
PubMed
Summary

A new platform, TVIR, offers comprehensive genomic data for 59 vegetables, including functional genes and CRISPR sequences. This resource facilitates global vegetable research and data sharing for improved crop development.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Vegetables are crucial for human nutrition, necessitating systematic genomic study.
  • A centralized platform for vegetable genomic data sharing and analysis is vital.

Purpose of the Study:

  • To develop a comprehensive, user-friendly platform for vegetable genomic data.
  • To facilitate data sharing and comparative genomic analysis for 59 vegetable species.

Main Methods:

  • Genome sequencing and assembly for 59 vegetable species.
  • Identification and annotation of functional genes, including auxin, anthocyanin, flowering, resistance, glucosinolate, and N6-methyladenosine (m6A) genes.
  • Detection and deposition of clustered regularly interspaced short palindromic repeat (CRISPR) guide sequences and microRNAs (miRNAs).

Main Results:

  • The Vegetable Information Resource (TVIR) database was established, hosting genomic data for 59 vegetables.
  • TVIR contains extensive gene information, including 5215 auxin, 2437 anthocyanin, 15002 flowering, 79830 resistance, 2639 glucosinolate, and 2597 m6A genes.
  • The database includes 2,101,501 CRISPR sequences, 17,377 miRNAs, gene synteny, duplication, orthologs, and 2,346,850 gene annotations.
  • Transcriptome data for 98 vegetables were collected and collated.

Conclusions:

  • TVIR is the first large-scale collection of vegetable genomic data and bioinformatic analysis.
  • The platform provides tools for comparative genomic analysis and allows data download.
  • TVIR is poised to become a central hub for global vegetable research, with future updates planned.