Abstract
As an economically important crop, apple is one of the most cultivated fruit trees in temperate regions worldwide. Recently, a large number of high-quality transcriptomic and epigenomic datasets for apple were made available to the public, which could be helpful in inferring gene regulatory relationships and thus predicting gene function at the genome level. Through integration of the available apple genomic, transcriptomic, and epigenomic datasets, we constructed co-expression networks, identified functional modules, and predicted chromatin states. A total of 112 RNA-seq datasets were integrated to construct a global network and a conditional network (tissue-preferential network). Furthermore, a total of 1,076 functional modules with closely related gene sets were identified to assess the modularity of biological networks and further subjected to functional enrichment analysis. The results showed that the function of many modules was related to development, secondary metabolism, hormone response, and transcriptional regulation. Transcriptional regulation is closely related to epigenetic marks on chromatin. A total of 20 epigenomic datasets, which included ChIP-seq, DNase-seq, and DNA methylation analysis datasets, were integrated and used to classify chromatin states. Based on the ChromHMM algorithm, the genome was divided into 620,122 fragments, which were classified into 24 states according to the combination of epigenetic marks and enriched-feature regions. Finally, through the collaborative analysis of different omics datasets, the online database AppleMDO (http://bioinformatics.cau.edu.cn/AppleMDO/) was established for cross-referencing and the exploration of possible novel functions of apple genes. In addition, gene annotation information and functional support toolkits were also provided. Our database might be convenient for researchers to develop insights into the function of genes related to important agronomic traits and might serve as a reference for other fruit trees.
Highlights
Apple (Malus domestica Borkh.), a member of the Rosaceae family, is one of the most cultivated fruit trees in temperate regions worldwide, and its origin and evolution are inseparable from the progress of human civilization (Duan et al, 2017)
Based on the ChromHMM algorithm, the genome was divided into 620,122 fragments, which were classified into 24 states according to the combination of epigenetic marks and enriched-feature regions (Table 3, Supplementary Figure 6)
Global network Tissue-preferential network Protein-protein interaction Functional module Chromatin state Cytochrome P450 Protein kinase Ubiquitin Transcription factor/regulator Carbohydrate-active enzyme Epigenetic regulator gene ontology (GO) annotation KEGG annotation Pfam domain Orthologues in A. thaliana Orthologues in P. persica Orthologues in P. communis Orthologues in P. bretschneideri Orthologues in R. multiflora Orthologues in R. occidentalis Orthologues in F. vesca Orthologues in V. vinifera Orthologues in S. lycopersicum Orthologues in P. trichocarpa Orthologues in N. benthamiana Orthologues in O. sativa Orthologues in Z. mays
Summary
Apple (Malus domestica Borkh.), a member of the Rosaceae family, is one of the most cultivated fruit trees in temperate regions worldwide, and its origin and evolution are inseparable from the progress of human civilization (Duan et al, 2017). A variety of epigenomic profiles of different epigenetic markers have been produced for apple, using DNase-seq, ChIP-seq, and Bisulfite-seq. These datasets can be used to identify potential regulatory elements in the genome at the whole-genome level. The fruitENCODE database (http://137.189.43.55/encode.html) provides a genome browser for a variety of fruits, including apple, to view DNA methylation, DNase I hypersensitivity sites (DHSs), and histone modification (Lu et al, 2018). We developed a multi-dimensional omics database for apple co-expression networks and chromatin states (AppleMDO), which will help in the cross-referencing and exploration of some novel functions of genes and provide a reference for other fruits
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