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. 2023 Jul 6:2023:baad050.
doi: 10.1093/database/baad050.

PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study

Jian Hu  1   2   3 , Baisha Huang  1   2   3 , Hao Yin  1   2   3 , Kaijie Qi  1   2   3 , Yuanyuan Jia  1 , Zhihua Xie  1   2   3 , Yuan Gao  3 , Hongxiang Li  1   2   3 , Qionghou Li  1   2   3 , Zewen Wang  1   2   3 , Ying Zou  1   2   3 , Shaoling Zhang  1   2   3 , Xin Qiao  1   2   3
Affiliations

PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study

Jian Hu et al. Database (Oxford). .

Abstract

Pear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges to cope with the burgeoning sets of multiomics data are rapidly increasing. Here, we constructed the Pear Multiomics Database (PearMODB) by integrating genome, transcriptome, epigenome and population variation data, and aimed to provide a portal for accessing and analyzing pear multiomics data. A variety of online tools were built including gene search, BLAST, JBrowse, expression heatmap, synteny analysis and primer design. The information of DNA methylation sites and single-nucleotide polymorphisms can be retrieved through the custom JBrowse, providing an opportunity to explore the genetic polymorphisms linked to phenotype variation. Moreover, different gene families involving transcription factors, transcription regulators and disease resistance (nucleotide-binding site leucine-rich repeat) were identified and compiled for quick search. In particular, biosynthetic gene clusters (BGCs) were identified in pear genomes, and specialized webpages were set up to show detailed information of BGCs, laying a foundation for studying metabolic diversity among different pear varieties. Overall, PearMODB provides an important platform for pear genomics, genetics and breeding studies. Database URL http://pearomics.njau.edu.cn.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
The framework and available function modules of PearMODB. Core system and programming language, logo, main functional modules, corresponding core programs of PearMODB are shown from left to right.
Figure 2.
Figure 2.
The home page of PearMODB. (A) Drop-down menus to explore different function modules and brief introduction. (B) Representative cultivars of five major cultivated species and wild pear species. (C) Brief introduction about pear cultivation and yield. (D) Available tools on PearMODB.
Figure 3.
Figure 3.
Gene search tool. (A) Gene search page. (B) Chromosomal location and sequences of the target gene. (C) Spatiotemporal expression profile of target gene.
Figure 4.
Figure 4.
BLAST tool. (A) BLAST search page. (B) BLAST result page.
Figure 5.
Figure 5.
JBrowse tool. (A) Available tracks for different types of genomic features. (B) A window showing detailed information of the target gene model. (C) SNPs information for 113 pear accessions. (D) Tracks of three types of DNA methylation.
Figure 6.
Figure 6.
Expression Heatmap page. (A) The block for organism selection and gene id input. (B) Gene expression profile of example genes in 17 tissues or development stages of P. bretschneideri cv. ‘Dangshansuli’.
Figure 7.
Figure 7.
Synteny Browser page. (A) Macrosynteny visualization between the two pear variety genomes. (B) Dot plot corresponding to the macrosynteny visualization. (C) Distribution of the number of syntenic blocks with different lengths. (D) Microsynteny visualization of the target gene. (E) Dot plot of collinearity relationships of 17 chromosomes between ‘Dangshansuli’ and ‘Duli’. (F) Macrosynteny visualization of Chr11 between ‘Dangshansuli’ and ‘Duli’. (G) Microsynteny visualization of the selected syntenic block.
Figure 8.
Figure 8.
A comparison of gene number of different families in seven pear genomes.
Figure 9.
Figure 9.
BGCs page. (A) Whole set of BGCs in a pear genome. (B) Gene members and functional characteristics of BGCs. (C) Co-expression relationships between BGCs. (D) Co-expression network of genes within a selected cluster (rectangle) and their co-expression relationships with genes from other clusters (ellipse).
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