Data and program download    



[Papers]
[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  *Yano et. al. (2020) Communications Biology 3:432
  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  *Yano et. al. (2020) Communications Biology 3:432
  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  *Yano et. al. (2020) Communications Biology 3:432
  [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  *Yano et. al. (2020) Communications Biology 3:432
  [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  *Yano et. al. (2020) Communications Biology 3:432, Yano et. al. (2018) Plant Cell Physiol. 59:e4
  [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]


Gene prediction pipeline  *Yano et. al. (2020) Communications Biology 3:432
  [ONT4genepredict]   (perl scripts)   [download]
  (This pipeline predicts protein-coding genes based on nanopore RNA-seq rawdata and generates GFF3 file.)