Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity
Data files
Feb 13, 2018 version files 2.25 GB
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523_3_assembly_ALLPATHS_v4.1.fasta
834.15 MB
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523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff
77.65 MB
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full_table_BUSCO_output.tsv
86.69 KB
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M6_gene_expression_matrix.xlsx
5.59 MB
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m6_gene_models.func_anno.txt
2.59 MB
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M6_v4.1_masked_PM.fa
511.89 MB
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M6_v4.1_PM.fa
511.89 MB
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pasa_m6.hc.gene_models.cdna.fa
79.01 MB
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pasa_m6.hc.gene_models.cds.fa
60.77 MB
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pasa_m6.hc.gene_models.gff3
52.73 MB
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pasa_m6.hc.gene_models.pep.fa
20.70 MB
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pasa_m6.hc.gene_models.repr.pep.fa
14.74 MB
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README.txt
1.60 KB
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short_summary_BUSCO_output.txt
708 B
Feb 16, 2018 version files 2.29 GB
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523_3_assembly_ALLPATHS_v4.1.fasta
834.15 MB
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523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff
77.65 MB
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full_table_BUSCO_output.tsv
86.69 KB
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M6_gene_expression_matrix.xlsx
5.59 MB
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m6_gene_models.func_anno.txt
2.59 MB
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M6_v4.1_masked_PM.fa
511.89 MB
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M6_v4.1_PM.fa
511.89 MB
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pasa_m6.hc.gene_models.cdna.fa
79.01 MB
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pasa_m6.hc.gene_models.cds.fa
60.77 MB
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pasa_m6.hc.gene_models.gff3
52.73 MB
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pasa_m6.hc.gene_models.pep.fa
20.70 MB
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pasa_m6.hc.gene_models.repr.pep.fa
14.74 MB
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README.txt
1.60 KB
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short_summary_BUSCO_output.txt
708 B
Feb 28, 2018 version files 2.49 GB
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523_3_assembly_ALLPATHS_v4.1.fasta
834.15 MB
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523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff
77.65 MB
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full_table_BUSCO_output.tsv
86.69 KB
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M6_gene_expression_matrix.xlsx
5.59 MB
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m6_gene_models.func_anno.txt
2.59 MB
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M6_v4.1_masked_PM.fa
511.89 MB
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M6_v4.1_PM.fa
511.89 MB
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pasa_m6.hc.gene_models.cdna.fa
79.01 MB
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pasa_m6.hc.gene_models.cds.fa
60.77 MB
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pasa_m6.hc.gene_models.Chr.gff3
58.23 MB
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pasa_m6.hc.gene_models.gff3
52.73 MB
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pasa_m6.hc.gene_models.pep.fa
20.70 MB
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pasa_m6.hc.gene_models.repr.pep.fa
14.74 MB
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README.txt
1.59 KB
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short_summary_BUSCO_output.txt
708 B
Jul 02, 2018 version files 4.34 GB
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523_3_assembly_ALLPATHS_v4.1.fasta
834.15 MB
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523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff
77.65 MB
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full_table_BUSCO_output.tsv
86.69 KB
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M6_gene_expression_matrix.xlsx
5.59 MB
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m6_gene_models.func_anno.txt
2.59 MB
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M6_v4.1_masked_PM.fa
511.89 MB
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M6_v4.1_PM.fa
511.89 MB
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m6.hc.gene_models.chr.gff3
47.68 MB
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pasa_m6.hc.gene_models.cdna.fa
79.01 MB
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pasa_m6.hc.gene_models.cds.fa
60.77 MB
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pasa_m6.hc.gene_models.Chr.gff3
58.23 MB
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pasa_m6.hc.gene_models.pep.fa
20.70 MB
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pasa_m6.hc.gene_models.repr.pep.fa
14.74 MB
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README.txt
1.62 KB
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short_summary_BUSCO_output.txt
708 B
Aug 30, 2018 version files 4.43 GB
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523_3_assembly_ALLPATHS_v4.1.fasta
834.15 MB
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523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff
77.65 MB
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full_table_BUSCO_output.tsv
86.69 KB
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M6_gene_expression_matrix.xlsx
5.59 MB
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m6_gene_models.func_anno.txt
2.59 MB
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M6_v4.1_masked_PM.fa
511.89 MB
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M6_v4.1_PM.fa
511.89 MB
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M6_v4.1_scaffold.agp
28 KB
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m6.hc.gene_models.chr.gff3
47.68 MB
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pasa_m6.hc.gene_models.cdna.fa
79.01 MB
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pasa_m6.hc.gene_models.cds.fa
60.77 MB
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pasa_m6.hc.gene_models.pep.fa
20.70 MB
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pasa_m6.hc.gene_models.repr.pep.fa
14.74 MB
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README.txt
1.73 KB
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short_summary_BUSCO_output.txt
708 B
Jan 08, 2019 version files 4.65 GB
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523_3_assembly_ALLPATHS_v4.1.fasta
834.15 MB
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523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff
77.65 MB
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full_table_BUSCO_output.tsv
86.69 KB
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M6_gene_expression_matrix.xlsx
5.59 MB
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m6_gene_models.func_anno.txt
2.59 MB
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M6_v4.1_masked_PM.fa
511.89 MB
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M6_v4.1_PM.fa
511.89 MB
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M6_v4.1_scaffold.agp
28 KB
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m6.hc.gene_models.all_chrs.gff3
56.18 MB
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m6.hc.gene_models.chr.gff3
47.68 MB
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pasa_m6.hc.gene_models.cdna.fa
79.01 MB
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pasa_m6.hc.gene_models.cds.fa
60.77 MB
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pasa_m6.hc.gene_models.pep.fa
20.70 MB
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pasa_m6.hc.gene_models.repr.pep.fa
14.74 MB
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README.txt
1.83 KB
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short_summary_BUSCO_output.txt
708 B
Apr 19, 2019 version files 6.13 GB
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523_3_assembly_ALLPATHS_v4.1.fasta
834.15 MB
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523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff
77.65 MB
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full_table_BUSCO_output.tsv
86.69 KB
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M6_gene_expression_matrix.xlsx
5.59 MB
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m6_gene_models.func_anno.txt
2.59 MB
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M6_v4.1_masked_PM.fa
511.89 MB
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M6_v4.1_PM_plus_chrUn.fa
867.08 MB
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M6_v4.1_PM.fa
511.89 MB
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M6_v4.1_scaffold.agp
28 KB
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m6.hc.gene_models.all_chrs_corrected.gff3
56.18 MB
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m6.hc.gene_models.all_chrs.gff3
56.18 MB
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m6.hc.gene_models.chr_corrected.gff3
47.68 MB
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m6.hc.gene_models.chr.gff3
47.68 MB
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pasa_m6.hc.gene_models.cdna.fa
79.01 MB
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pasa_m6.hc.gene_models.cds.fa
60.77 MB
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pasa_m6.hc.gene_models.pep.fa
20.70 MB
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pasa_m6.hc.gene_models.repr.pep.fa
14.74 MB
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README.txt
2 KB
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short_summary_BUSCO_output.txt
708 B
Nov 26, 2019 version files 5.98 GB
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523_3_assembly_ALLPATHS_v4.1.fasta
834.15 MB
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523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff
77.65 MB
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full_table_BUSCO_output.tsv
86.69 KB
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M6_gene_expression_matrix.xlsx
5.59 MB
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m6_gene_models.func_anno.txt
2.59 MB
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M6_v4.1_masked_PM.fa
511.89 MB
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M6_v4.1_PM_plus_chrUn.fa
867.08 MB
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M6_v4.1_PM.fa
511.89 MB
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M6_v4.1_scaffold.agp
28 KB
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m6.hc.gene_models.all_chrs_corrected.gff3
56.18 MB
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m6.hc.gene_models.chr_corrected.gff3
47.68 MB
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pasa_m6.hc.gene_models.cdna.fa
79.01 MB
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pasa_m6.hc.gene_models.cds.fa
60.77 MB
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pasa_m6.hc.gene_models.pep.fa
20.70 MB
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pasa_m6.hc.gene_models.repr.pep.fa
14.74 MB
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README.txt
2 KB
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short_summary_BUSCO_output.txt
708 B
Abstract
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 revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding.