Chardonnay genome assembly and annotations

Annotations relating to the Chardonnay genome assembly (the study is published here: https://doi.org/10.1371/journal.pgen.1007807). The assembly is also available at NCBI: BioProject: PRJNA399599.

chardonnay_p-ctg.fasta / chardonnay_h-ctg.fasta:

Contig assembly for Chardonnay. chardonnay_p-ctg.fasta = primary contigs (haploid representation), chardonnay_h-ctg.fasta = haplotigs (alt contigs for phased regions in haploid assembly).

p-h.maker.gff / p-h.maker.proteins.faa / p-h.maker.transcripts.fna:

Maker-predicted gene annotations.

p-h.maker.draft-names.tsv / p-h.orthomcl.orthoGroups.tsv / p-h.KEGG.tsv:

Draft names (based on UniprotKB blastP hits), OrthoMCL annotations, and KEGG annotations for maker-predicted genes.

p-h.repeats.gff:

RepeatMasker-based repeat annotations.

chardonnay_primary_contigs_chromosome-order.fa / chardonnay_haplotigs_chromosome-order.fa:

Contigs placed in chromosome-order (using PN40024 as reference).

chardonnay_primary_contig_mappings.tsv / chardonnay_haplotig_mappings.tsv:

Mapping coordinates for chromosome-ordered contigs.

kmer-based_parentage.primary_contigs.bed / kmer-based_parentage.haplotigs.bed:

Parentage assignments using the kmer-based method described in the study.

SNP-based_parentage.primary_contigs.bed / SNP-based_parentage.haplotigs.bed:

Parentage assignments using SNP-based method (view haplotig assignments against primary contigs) described in the study.

p-ctg.gene-expansion-candidates.tsv / h-ctg.gene-expansion-candidates.tsv / p-ctg.gene-expansion-candidates.bed / h-ctg.gene-expansion-candidates.bed:

Gene expansion candidates (TSV = 1 row per predicted orthogroup, BED = annotations for viewing).

PN_and_CH.FAR2.msa.png:

Multi Sequence Alignment for expansion of FAR2-like genes in described in Chardonnay genome assembly publication described in the study.