C.melo Harukei-3 genome assemly and annotation
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Nanopore-based C.melo genomic contigs
Awamidori (Shirouri) [NARO Genebank No. JP32187]
(fasta)
[donwload]
*assembled by Nanopore R9.4.1 long read
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Ougon-9 (Makuwa) [NARO Genebank No. JP32147]
(fasta)
[donwload]
*assembled by Nanopore R9.4.1 long read
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JSS-6 (Japanese wild melon) [NARO Genebank No. JP82421]
(fasta)
[donwload]
*assembled by Nanopore R9.4.1 long read
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Honey Dew [NARO Genebank No. JP32114]
(fasta)
[donwload]
*assembled by Nanopore R9.4.1 long read
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Spicy [NARO Genebank No. JP32115]
(fasta)
[donwload]
*assembled by Nanopore R9.4.1 long read
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Natsukei-1 [NARO Genebank No. JP32098]
(fasta)
[donwload]
*assembled by Nanopore R9.4.1 long read
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Fuyukei [NARO Genebank No. JP74158]
(fasta)
[donwload]
*assembled by Nanopore R9.4.1 long read
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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)
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[Illumina resequencing data of five melon accessions]
(NCBI Bioproject accession No. PRJNA603162)
[LINK]
(e.g. Honey Dew, Spicy, Ougon-9, JSS-6)
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Oxford nanopore RNA-seq data
[Nanopore direct RNA-seq in muskmelon Harukei-3]
(NCBI Bioproject accession No. PRJNA603129)
[LINK]
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[Nanopore RNA-seq in melon leaves]
(NCBI Bioproject accession No. PRJNA603146)
[LINK]
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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)
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[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)
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[Hiseq-X paired-end leaf RNA-seq in Harukei-3 melon from July to November 2018, 75 samples]
(NCBI Bioproject accession No. PRJNA603202)
[LINK]
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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.
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