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. 2023 Sep 15;23(1):430.
doi: 10.1186/s12870-023-04406-5.

The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp

Shulin Chen  1 , Manyi Sun  2 , Shaozhuo Xu  1 , Cheng Xue  1 , Shuwei Wei  3 , Pengfei Zheng  1 , Kaidi Gu  1 , Zhiwen Qiao  1 , Zhiying Liu  1 , Mingyue Zhang  4 , Jun Wu  5
Affiliations

The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp

Shulin Chen et al. BMC Plant Biol. .

Abstract

Background: Pears are among the most important temperate fruit trees in the world, with significant research efforts increasing over the last years. However, available omics data for pear cannot be easily and quickly retrieved to enable further studies using these biological data.

Description: Here, we present a publicly accessible multi-omics pear resource platform, the Pear Genomics Database (PGDB). We collected and collated data on genomic sequences, genome structure, functional annotation, transcription factor predictions, comparative genomics, and transcriptomics. We provide user-friendly functional modules to facilitate querying, browsing and usage of these data. The platform also includes basic and useful tools, including JBrowse, BLAST, phylogenetic tree building, and additional resources providing the possibility for bulk data download and quick usage guide services.

Conclusions: The Pear Genomics Database (PGDB, http://pyrusgdb.sdau.edu.cn ) is an online data analysis and query resource that integrates comprehensive multi-omics data for pear. This database is equipped with user-friendly interactive functional modules and data visualization tools, and constitutes a convenient platform for integrated research on pear.

Keywords: Database; Genome; Pear; Re-sequencing; Transcriptome.

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Conflict of interest statement

The authors declare they have no competing interests.

Figures

Fig. 1
Fig. 1
Overview of the PGDB website architecture
Fig. 2
Fig. 2
Search page of the PGDB. (a) Search for genetic information and sequences. (b) Genetic information search results, including gene details, GO ①, KEGG ② and InterPro ③ functional annotations, sequences ④, and homologous genes ⑤
Fig. 3
Fig. 3
Synteny page of the PGDB. (a) Querying synteny blocks between genomes and drawing synteny images. (b) The synteny blocks in the query and compared chromosomes. (c) The genes contained in each synteny block. (d) The collinear image drawn online
Fig. 4
Fig. 4
The BLAST and the JBrowse tools available in the PGDB. (a) BLAST page to search for regions of similarity between sequences. (b) The BLAST results page. (c) Visualization of genomic regions using the Genome browser. (d) Detailed information about a single region
See this image and copyright information in PMC

References

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