An improved reference of the PN40024 grapevine genome assembly (PN40024.v4) and annotations

Dataset

DOI

Here, we provide an improved version of the PN40024 genome assembly, called PN40024.v4, which combines the top-quality Sanger contigs from the 12X version with Pacific Biosciences long reads (Sequel SMRT). Along with this new assembly, we also provide a new version of the gene annotation, called PN40024.v4.1 based on a newly developed annotation workflow and RNA-Seq/proteins datasets. Then, the gene annotation version PN40024.v4.3 was generated. This was generated from version PN40024.v4.1, and the structure of multiple gene family catalogues was curated using the Apollo tool (manual curation of a set of genes of functional interest to the community).

bwa-mem2, v2.0

Samtools, v1.9

MUMmer, v3.1

BEDTools, v2.26.0

Trimmomatic, v0.39

GMAP/GSNAP, v2020-09-12

PsiCLASS, v1.0.1

GlimmerHMM, v3.0.4

MAKER2, v3.01.03

ncbi-blast, 2.10.1+

BRAKER2, v2.1.5-master_20200915

GeneMark-ETP +, v4.61

AUGUSTUS, master_v3.3.3_20200914

DIAMOND, v0.9.24.125

SPALN, 2.3.3f

ProtHint, 2.5.0

BamTools, v2.5.1

GeneID, v1.4.5-master-20200916

EvidenceModeler, v1.1.1

PASA, v2.4.1

tRNAscan-SE, 2.0

Blast2GO, v1.5.1

InterProScan, v5.52-86.0

BUSCO, v5.1.2

Apollo, v2.6.4

CANU, v.1.6

LORDEC, v.0.5.3

minimap2, v2.17-r954-dirty

Flye, v2.4-gc9db046

Haplomerger2, v20180603

OPERA-LG, v2.0.6

GapCloser, v1.12

LR_Gapcloser, v1.0

PILON, v1.23-1-g41e0b8e

liftoff, v1.5.1

exonerate, v2.4.0

Identifier
DOI	https://doi.org/10.57745/F9N2FZ
Related Identifier	IsCitedBy https://doi.org/10.1093/g3journal/jkad067
Metadata Access	https://entrepot.recherche.data.gouv.fr/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.57745/F9N2FZ

Provenance
Creator	Velt, Amandine (ORCID: 0000-0003-2368-839X); Rustenholz, Camille
Publisher	Recherche Data Gouv
Contributor	Velt, Amandine; Rustenholz, Camille; Frommer, Bianca; Institut national de recherche pour l'agriculture, l'alimentation et l'environnement; Entrepôt Recherche Data Gouv
Publication Year	2022
Rights	etalab 2.0; info:eu-repo/semantics/openAccess; https://spdx.org/licenses/etalab-2.0.html
OpenAccess	true
Contact	Velt, Amandine (SVQV ; INRAE, University of Strasbourg ; France); Rustenholz, Camille (SVQV ; INRAE, University of Strasbourg ; France)

Representation
Resource Type	Dataset
Format	text/plain; application/octet-stream; application/pdf; text/tab-separated-values
Size	2424571; 8214235; 3055515; 3107075; 843442; 5376426; 270678; 11306600; 47853630; 167561621; 50437114; 59978458; 16550515; 53443120; 53766411; 20068772; 475619838; 4487
Version	2.2
Discipline	Agriculture, Forestry, Horticulture; Life Sciences; Agricultural Sciences; Agriculture, Forestry, Horticulture, Aquaculture; Agriculture, Forestry, Horticulture, Aquaculture and Veterinary Medicine; Medicine
Spatial Coverage	INRAE-University of Strasbourg, Colmar 68000, France