Data and program download    



[INFO] Dataset shown below has been made public in the following papers:
Yano et. al. (2020) Communications Biology 3:432 [DOI: 10.1038/s42003-020-01172-0]
Yano et. al. (2018) Plant Cell Physiol. 59:e4 [DOI: 10.1093/pcp/pcx193]


Harukei-3 genome assemly and annotation
  ver1.41 genome assembly   (fasta)   [donwload]   
  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]   


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]


Software and Pipeline
  [ONT4genepredict]   (perl scripts)   [download]
  (This pipeline predicts protein-coding genes based on nanopore RNA-seq rawdata and generates GFF3 file.)