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. <strong>chardonnay_p-ctg.fasta / chardonnay_h-ctg.fasta:</strong> 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). <strong>p-h.maker.gff / p-h.maker.proteins.faa / p-h.maker.transcripts.fna:</strong> Maker-predicted gene annotations. <strong>p-h.maker.draft-names.tsv / p-h.orthomcl.orthoGroups.tsv / p-h.KEGG.tsv:</strong> Draft names (based on UniprotKB blastP hits), OrthoMCL annotations, and KEGG annotations for maker-predicted genes. <strong>p-h.repeats.gff:</strong> RepeatMasker-based repeat annotations. <strong>chardonnay_primary_contigs_chromosome-order.fa / chardonnay_haplotigs_chromosome-order.fa:</strong> Contigs placed in chromosome-order (using PN40024 as reference). <strong>chardonnay_primary_contig_mappings.tsv / chardonnay_haplotig_mappings.tsv:</strong> Mapping coordinates for chromosome-ordered contigs. <strong>kmer-based_parentage.primary_contigs.bed / kmer-based_parentage.haplotigs.bed:</strong> Parentage assignments using the kmer-based method described in the study. <strong>SNP-based_parentage.primary_contigs.bed / SNP-based_parentage.haplotigs.bed:</strong> Parentage assignments using SNP-based method (view haplotig assignments against primary contigs) described in the study. <strong>p-ctg.gene-expansion-candidates.tsv / h-ctg.gene-expansion-candidates.tsv / p-ctg.gene-expansion-candidates.bed / h-ctg.gene-expansion-candidates.bed:</strong> Gene expansion candidates (TSV = 1 row per predicted orthogroup, BED = annotations for viewing). <strong>PN_and_CH.FAR2.msa.png: </strong> Multi Sequence Alignment for expansion of FAR2-like genes in described in Chardonnay genome assembly publication described in the study.本数据集关联霞多丽（Chardonnay）基因组组装的注释信息，相关研究已发表于：https://doi.org/10.1371/journal.pgen.1007807。该组装数据亦可在NCBI获取：BioProject编号：PRJNA399599。 <strong>chardonnay_p-ctg.fasta / chardonnay_h-ctg.fasta:</strong> 霞多丽基因组重叠群组装结果。其中chardonnay_p-ctg.fasta 为单倍型代表性主重叠群（primary contigs），chardonnay_h-ctg.fasta 为单倍型组装中相位区域的替代重叠群（haplotigs）。 <strong>p-h.maker.gff / p-h.maker.proteins.faa / p-h.maker.transcripts.fna:</strong> 基于Maker工具预测的基因注释文件。 <strong>p-h.maker.draft-names.tsv / p-h.orthomcl.orthoGroups.tsv / p-h.KEGG.tsv:</strong> 针对Maker预测基因的三类注释信息：基于UniprotKB的BlastP比对结果得到的暂定基因名、OrthoMCL同源分组注释，以及KEGG通路注释。 <strong>p-h.repeats.gff:</strong> 基于RepeatMasker的重复序列注释文件。 <strong>chardonnay_primary_contigs_chromosome-order.fa / chardonnay_haplotigs_chromosome-order.fa:</strong> 已按染色体顺序排布的重叠群序列（以PN40024作为参考基因组进行排序）。 <strong>chardonnay_primary_contig_mappings.tsv / chardonnay_haplotig_mappings.tsv:</strong> 染色体顺序排布的重叠群的坐标映射文件。 <strong>kmer-based_parentage.primary_contigs.bed / kmer-based_parentage.haplotigs.bed:</strong> 采用本研究所述的基于kmer的方法得到的亲子关系分配注释文件。 <strong>SNP-based_parentage.primary_contigs.bed / SNP-based_parentage.haplotigs.bed:</strong> 采用本研究所述的基于单核苷酸多态性（SNP）的方法得到的亲子关系分配注释文件（可对照主重叠群查看单体型序列的分配结果）。 <strong>p-ctg.gene-expansion-candidates.tsv / h-ctg.gene-expansion-candidates.tsv / p-ctg.gene-expansion-candidates.bed / h-ctg.gene-expansion-candidates.bed:</strong> 基因扩张候选区域相关文件：TSV格式文件为每个预测同源分组对应一行数据，BED格式文件用于可视化展示注释信息。 <strong>PN_and_CH.FAR2.msa.png:</strong> 本研究提及的霞多丽基因组组装论文中，针对FAR2类基因扩张的多序列比对结果图。