Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825,767,562 bp in 8,260 scaffolds with an N50 scaffold size of 713,602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49,124 high confidence gene models representing 37,740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158,367 Solanaceae genes and 1,897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome r..., Readme.txt523_3_assembly_ALLPATHS_v4.1.fastaGenome assembly of S. chacoense M6, containing 8,260 scaffold sequencesM6_v4.1_PM.faPseudomolecules of S. chacoense M6, containing 12 chromosomesM6_v4.1_masked_PM.faMasked pseudomolecules of S. chacoense M6, containing 12 chromosomesM6_v4.1_scaffold.agpAGP file describing the assembly of S. chacoense M6 scaffolds within the pseudomoleculesM6_v4.1_PM_plus_chrUn.faPseudomolecules of S. chacoense M6, containing 12 chromosomes and chrUn (unanchored scaffolds)short_summary_BUSCO_output.txtOutput file from running BUSCO on the genome assemblyfull_table_BUSCO_output.tsvOutput file from running BUSCO on the genome assemblym6.hc.gene_models.chr_corrected.gff3Generic feature format file (gff3) of high-confidence genes in S. chacoense M6 (Corrected version as of 06/2018)m6.hc.gene_models.all_chrs_corrected.gff3Generic feature format file (gff3) of high-confidence genes in S. chacoense M6, including ChrUnpasa_m6.hc.gene_models.cdna.faTranscript sequences ...,

栽培马铃薯（Solanum tuberosum L.）是高度杂合的同源四倍体，给基因组分析与育种工作带来诸多挑战。野生马铃薯物种是将重要农艺性状渗入栽培马铃薯的宝贵资源，其中关键物种为Solanum chacoense及其二倍体自交系克隆M6——该克隆具有自交亲和性，且具备理想的块茎商品品质与抗病性状。对S. chacoense M6克隆的基因组进行测序与组装，获得的基因组组装大小为825,767,562 bp，包含8260个支架（scaffold），支架N50长度为713,602 bp；通过假分子（pseudomolecule）构建，将508 Mb的基因组序列锚定至12条染色体上；基因组注释得到49,124个高置信度基因模型，代表37,740个基因。将M6基因组与其他6个茄科物种进行比较分析，发现由158,367个基因组成的茄科核心基因集，以及3个马铃薯物种特有的1,897个基因。相关文件包括：Readme.txt；523_3_assembly_ALLPATHS_v4.1.fasta（S. chacoense M6的基因组组装文件，含8260个支架序列）；M6_v4.1_PM.fa（S. chacoense M6的假分子文件，含12条染色体序列）；M6_v4.1_masked_PM.fa（S. chacoense M6的masked假分子文件，含12条染色体序列）；M6_v4.1_scaffold.agp（描述S. chacoense M6支架组装成假分子的AGP文件）；M6_v4.1_PM_plus_chrUn.fa（S. chacoense M6的假分子文件，含12条染色体序列及未锚定的chrUn序列）；short_summary_BUSCO_output.txt（基因组组装结果的BUSCO（Benchmarking Universal Single-Copy Orthologs）运行摘要输出文件）；full_table_BUSCO_output.tsv（基因组组装结果的BUSCO运行完整表格输出文件）；m6.hc.gene_models.chr_corrected.gff3（S. chacoense M6高置信度基因模型的通用特征格式文件（GFF3，Generic Feature Format version 3），2018年6月修正版）；m6.hc.gene_models.all_chrs_corrected.gff3（S. chacoense M6高置信度基因模型的通用特征格式文件（GFF3），含chrUn序列）；pasa_m6.hc.gene_models.cdna.fa（转录本序列...）