C.melo Harukei-3 genome assemly and annotation *Yano et. al. (2020) Communications Biology 3:432
|
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]
|
|
Long read-based gene prediction pipeline *Yano et. al. (2020) Communications Biology 3:432
[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.
|
|
|
