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. 2021 Sep 23;17(1):98.
doi: 10.1186/s13007-021-00797-4.

AprGPD: the apricot genomic and phenotypic database

Chen Chen  1   2   3 , Huimin Liu  1   2   3 , Ningning Gou  1   2   3 , Mengzhen Huang  1   2   3 , Wanyu Xu  1   2   3 , Xuchun Zhu  1   2   3 , Mingyu Yin  1   2   3 , Haikun Bai  1   2   3 , Lin Wang  4   5   6 , Ta-Na Wuyun  7   8   9
Affiliations

AprGPD: the apricot genomic and phenotypic database

Chen Chen et al. Plant Methods. .

Abstract

Background: Apricot is cultivated worldwide because of its high nutritive content and strong adaptability. Its flesh is delicious and has a unique and pleasant aroma. Apricot kernel is also consumed as nuts. The genome of apricot has been sequenced, and the transcriptome, resequencing, and phenotype data have been increasely generated. However, with the emergence of new information, the data are expected to integrate, and disseminate.

Results: To better manage the continuous addition of new data and increase convenience, we constructed the apricot genomic and phenotypic database (AprGPD, http://apricotgpd.com ). At present, AprGPD contains three reference genomes, 1692 germplasms, 306 genome resequencing data, 90 RNA sequencing data. A set of user-friendly query, analysis, and visualization tools have been implemented in AprGPD. We have also performed a detailed analysis of 59 transcription factor families for the three genomes of apricot.

Conclusion: Six modules are displayed in AprGPD, including species, germplasm, genome, variation, product, tools. The data integrated by AprGPD will be helpful for the molecular breeding of apricot.

Keywords: AprGPD; Apricot; Expression; Genome; Phenotype; Transcription factors; Variation.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Nine species of apricot from China. 01–09 represent nine species. a The distributions, descriptions, and pictures of the nine species. b The tree type and relative height of nine species
Fig. 2
Fig. 2
Germplasm module. a Search tools; b Images and distribution of the sample; c Statistical chart of quantitative (frequency chart and boxplot) and qualitative traits (pie-chart)
Fig. 3
Fig. 3
Gene annotation submodule. a Gene annotation information; b Gene expression; c Gene variation information
Fig. 4
Fig. 4
Metabolic pathway submodule. a KEGG pathway, demo of Ko 00010; b The expression pattern of candidate genes; c The detailed information of genes in the pathway
Fig. 5
Fig. 5
Gene family submodule. a Information about the number of each gene family; b Details about the gene family members
Fig. 6
Fig. 6
Co-expression of genes. a Network: transcription factors (blue) and target gene ID (yellow); b Annotation of the co-expressed genes
Fig. 7
Fig. 7
Information of transcription factors in apricot. a Query tool; b Information of TFs; c Phylogenetic tree; d Gene structure and motif distribution; e Expression heatmap; f Distribution of TFs on eight chromosomes; g Syntenic relationships
Fig. 8
Fig. 8
Search and display information on variations. a Comparative search tool; b Variation information displayed in a table; c Statistical information on variation displayed using JBrowse, pie charts, and tables
Fig. 9
Fig. 9
The products involved in apricot. a The product image. b Details of corresponding apricot-derived product
See this image and copyright information in PMC

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