*URL has been changed to "https://melonet-db.dna.affrc.go.jp/ap/top". Please change bookmark.
*24th Oct, 2019: database is updated based on Harukei3 genome reference ver1.35


 

 
 
 
 
INTRODUCTION    
Melon (Cucumis melo L.) is an economically important crop of Cucurbitaceae family that is widely produced in the world. While melon is an important source of vitamins and minerals for human, it exhibits a wide range of naturally occurring genetic variation including both climacteric (ethylene-producing) and non-climacteric (non ethylene-producing) fruit ripening types. The Japanese muskmelon cultivar 'Earls favorite Harukei-3' is known for its excellent sweetness and rich aroma, and hence used for breeding of expensive (high-grade) muskmelon in Japan. Because of the economic importance in horticulture, we are using this 'Harukei-3' melon as a standard material for genetic and molecular biological studies. These include bioresource development such as artificially induced mutant population. However, to determine target gene(s) in translational research, it is often required to estimate gene function based on sequence information and/or gene expression patterns. Herein, we developed this web site designated as 'Melonet-DB'. Currently, several interactive tools are implemented as follows.

[1] Harukei3 genome viewer
JBrowse viewer for the 'Harukei-3' genome reference ver1.35 has been updated at 23th Oct. 2019.

[2] Gene expression map viewer (Expression atlas)
This tool is designed to visually analyze and understand tissue-specific expression pattern of melon genes in 'Harukei-3' melon. Previously, it was based on 30 RNA-seq samples (Yano et. al. 2018 Plant Cell Physiol. 59:e4). Update version now includes transcriptome dataset of 45 RNA-seq samples including ethylene-emitting post harvest fruit tissues. A newly assembled 'Harukei-3' genome reference ver1.35 was used for the informatics study in addition to the first melon genome reference DHL92.

[3] Coexpression viewer
This tool is designed to analyze coexpression relationship between genes. This database is based on RNA-seq transcriptome dataset of 'Harukei-3' melon used in [1]. In addition to the cytoscape version, the d3.js version has been updated.

[4] Mutation analysis tools
These tools are aimed at to analyze whether nucleotide change(s) cause amino acid substitution, frame shift, or splicing variation within gene. Several formats including VCF are supported.

[5] Sequence analysis tools
These tools are designed to analyze DNA sequence. Blast or "oligo DNA mapper" identify homologous genes or genomic positions, respectively, based on query sequence. "CDS/Protein seq search" retrieves DNA or protein sequence based on gene ID.

[6] Primer design tools
These tools are designed to analyze primer sequence. "Primer finder" finds the best possible unique PCR primer pair based on target query sequence.

[7] Gene ID search
Gene ID search program has been updated to explore genes in newly assembled 'Harukei-3' genome reference ver1.35. Consensus gene ID nomenclature is attached when 1-to-1 ortholog relationship was found in genes between two genome references, 'Harukei-3' and DHL92. For genes that are predicted only in Harukei-3 reference, original ID is used.

[*] As trial update prior to publication, some information of 'Harukei-3' genome reference ver1.35 (e.g. gene/protein sequence, RNA-seq transcriptome) is updated in this database. Please refrain from using these information for presentation before our publication. Every access to this DB is considered agreed to the condition.


Administrator : Ryoichi Yano [National Agriculture and Food Research Organization / University of Tsukuba]