AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States

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 () 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.

γ-Aminobutyric Acid Participates in the Adult-Phase Adventitious Rooting Recalcitrance

“…The gene-specific primers were designed using Primer software (version 5.0) (Table S1). Thirteen PIN gene family members, that showed detectable expression in apple stem or shoot apex, were selected for qPCR analysis (https ://bioin forma tics.cau.edu.cn/Apple MDO/gene_famil y/famil y_membe r.php?gene_famil y=Trans porte r&&famil y_id=AEC) (Da et al 2019). One microgram of total RNA was used in reverse transcription in a total volume of 20 μL.…”

Should Starch Metabolism Be a Key Point of the Climacteric vs. Non-climacteric Fruit Definition?

“…For banana, there is the Banana Genome Hub, containing a transcriptomics search tool (Droc et al, 2013 ). For apple, there is a similar web site, called AppleMDO, published recently by Da et al ( 2019 ). For collecting grape RNAseq data and making them searchable, a new platform has been created, called Grape-RNA (Wang et al, 2020 ) and for Citrus sinensis a recent data basis has been created too (Feng et al, 2019 ).…”

Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

“…StringTie was used to assembly and quantify transcripts [ 84 ]. The co-expression network of the DEGs was analyzed using AppleMDO webtools [ 85 ].…”