GFF/GTF files

/GFF/GTF files
GFF/GTF files2021-04-09T10:05:13+00:00

Tomato (Solanum lycopersicum cv. ‘Heinz’)

  • Incomplete ITAG4.1 annotation file – After mapping several RNA-seq libraries against the SL4.0/ITAG4.1 annotation we found 2780 genes missing (compared to ITAG 4.0) including the ripening regulator RIN.

  • New alignments – We extracted the cDNA sequences of all the genes from the ITAG4.0 version that do not appear in the ITAG4.1 (2780 genes), and aligned them against the SL4.0 assembly. In this alignment, performed with STARlong, 2752 genes aligned only once in the genome, 9 genes did not align and 19 genes aligned more than once.

  • Complete ITAG4.1 version – The 2752 genes that align only once to the genome were included in the gtf file (below) with the label «ITAG4.0_transposition» in the source field. The coordinates of the included genes were extracted analyzing the SAM file cigar for each gene. Please notice that the 2752 genes that we included only have the «gene» feature.

ITAG4.1_complete.gtf

Grapevine (Vitis vinifera cv. ‘Pinot Noir’)

  • GFF for MYB14/MYB15 DAP-seq mapping – a new annotation file combining all V1 gene models with the updated STS VCost.v3 gene models was created. The merged annotation file, V1_COST_STS annotation was used for the mapping of MYB14/MYB15 DAP-seq data (Orduña et al., 2020).

MYB14/15 DAP-seq gff
  • VCost.INTEGRAPEv1.gff3 – VCost.v3_v26.gff3 annotation file with gene names from the Grape Gene Referene Catalogue (v1).

INTEGRAPE V.cost gff

Silkworm Mulberry (Morus alba)

We have been updating the Morus alba genome annotation gff with our genes of interest. The original article is from Jiao et al. (2020)

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