Melonet DB   for functional genomics research of muskmelon  
gene ID search  :    
[Last update: 28th, Oct, 2023]
Data and program download    

[1] Yano et. al. (2020) Communications Biology 3:432 [DOI: 10.1038/s42003-020-01172-0]
[2] Yano et. al. (2018) Plant Cell Physiol. 59:e4 [DOI: 10.1093/pcp/pcx193]

C.melo Harukei-3 genome assemly and annotation
  ver1.41 genome assembly   (fasta)   [donwload]   *assembled by long read Oxford Nanoore Technology R10/R9.4.1, BioNano, mate pair
  ver1.41 genome annotation   (GFF3)   [consensus ID]   [original ID]   
  ver1.41 transcript sequences   (fasta)   [consensus ID]   [original ID]   
  ver1.41 coding sequences   (fasta)   [consensus ID]   [original ID]   
  ver1.41 protein sequences   (fasta)   [consensus ID]   [original ID]   

Nanopore-based C.melo genomic contigs
  Awamidori (Shirouri) [NARO Genebank No. JP32187]   (fasta)   [donwload]   *assembled by Nanopore R9.4.1 long read
  Ougon-9 (Makuwa) [NARO Genebank No. JP32147]   (fasta)   [donwload]   *assembled by Nanopore R9.4.1 long read
  JSS-6 (Japanese wild melon) [NARO Genebank No. JP82421]   (fasta)   [donwload]   *assembled by Nanopore R9.4.1 long read
  Honey Dew [NARO Genebank No. JP32114]   (fasta)   [donwload]   *assembled by Nanopore R9.4.1 long read
  Spicy [NARO Genebank No. JP32115]   (fasta)   [donwload]   *assembled by Nanopore R9.4.1 long read
  Natsukei-1 [NARO Genebank No. JP32098]   (fasta)   [donwload]   *assembled by Nanopore R9.4.1 long read
  Fuyukei [NARO Genebank No. JP74158]   (fasta)   [donwload]   *assembled by Nanopore R9.4.1 long read

Genome sequencing data
  [Genome sequencing data of Harukei-3 melon]   (NCBI Bioproject accession No. PRJNA603155)   [LINK]
  (e.g. Oxford nanopore R9.4.1/R10, Pacbio RSII, Illumina Hiseq-2000, Illumina mate pair)
  [Illumina resequencing data of five melon accessions]   (NCBI Bioproject accession No. PRJNA603162)   [LINK]
  (e.g. Honey Dew, Spicy, Ougon-9, JSS-6)

Oxford nanopore RNA-seq data
  [Nanopore direct RNA-seq in muskmelon Harukei-3]   (NCBI Bioproject accession No. PRJNA603129)   [LINK]
  [Nanopore RNA-seq in melon leaves]   (NCBI Bioproject accession No. PRJNA603146)   [LINK]

Illumina RNA-seq data
  [Hiseq-2500 paired-end RNA-seq in 30 'Harukei-3' melon tissues or developmental stages]   (DDBJ accession No. DRA006228)   [LINK]
  (e.g. callus, expanded leaves, young leaves, root, tendril, stems, flower, fruit)
  [Hiseq-2500/X paired-end RNA-seq in 15 'Harukei-3' melon tissues or developmental stages]   (NCBI Bioproject accession No. PRJNA603204)   [LINK]
  (additional tissue-wide RNA-seq dataset such as germinating seeds, seedlings, ripened fruits)
  [Hiseq-X paired-end leaf RNA-seq in Harukei-3 melon from July to November 2018, 75 samples]   (NCBI Bioproject accession No. PRJNA603202)   [LINK]

Long read-based gene prediction pipeline
  [ONT4genepredict]   (perl scripts)   [download]   *updated 29th Mar 2021
  (This pipeline predicts protein-coding genes based on nanopore RNA-seq and generates GFF3 file.)

[29th Mar 2021] Bug fix + function update. Now, both cDNA RNA-seq and direct RNA-seq datasets (ONT or Pacbio) can be used as input. If ORF is predicted in both direction which may occur due to PCR amplication of cDNA, reliable one is selected and another may be discarded based on protein sequence homology information.