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Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.

Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, Bryan GJ - G3 (Bethesda) (2013)

Bottom Line: These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes.Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion.The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

View Article: PubMed Central - PubMed

Affiliation: Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom.

ABSTRACT
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

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Summary of DM genome assembly anchoring using three different map resources. The number of uniquely and jointly anchored superscaffolds for each resource is given in the appropriate intersection. Cumulative size (Mb) of superscaffolds anchored in each category is shown in parenthesis. The total number of 649 anchored superscaffolds represents 623 Mb of the assembled DM potato genome. Figure updated from the Potato Genome Sequencing Consortium (2011).
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fig3: Summary of DM genome assembly anchoring using three different map resources. The number of uniquely and jointly anchored superscaffolds for each resource is given in the appropriate intersection. Cumulative size (Mb) of superscaffolds anchored in each category is shown in parenthesis. The total number of 649 anchored superscaffolds represents 623 Mb of the assembled DM potato genome. Figure updated from the Potato Genome Sequencing Consortium (2011).

Mentions: The RH- and tomato-based in silico anchoring strategies independently anchored 470 (527 Mb, 72.5%) and 402 (417 Mb, 57.4%) superscaffolds, respectively (Table 2). Figure 3 shows the superscaffold anchoring summary for both the linkage (DM map) and the two in silico (RH and tomato maps) approaches. The total set of 649 superscaffolds anchored in at least one map was integrated hierarchically, starting with the DMDD-based framework map, placing additional superscaffolds using first the RH and then tomato assignment. The hierarchical ‘alignment’ of the maps is described below.


Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.

Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, Bryan GJ - G3 (Bethesda) (2013)

Summary of DM genome assembly anchoring using three different map resources. The number of uniquely and jointly anchored superscaffolds for each resource is given in the appropriate intersection. Cumulative size (Mb) of superscaffolds anchored in each category is shown in parenthesis. The total number of 649 anchored superscaffolds represents 623 Mb of the assembled DM potato genome. Figure updated from the Potato Genome Sequencing Consortium (2011).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815063&req=5

fig3: Summary of DM genome assembly anchoring using three different map resources. The number of uniquely and jointly anchored superscaffolds for each resource is given in the appropriate intersection. Cumulative size (Mb) of superscaffolds anchored in each category is shown in parenthesis. The total number of 649 anchored superscaffolds represents 623 Mb of the assembled DM potato genome. Figure updated from the Potato Genome Sequencing Consortium (2011).
Mentions: The RH- and tomato-based in silico anchoring strategies independently anchored 470 (527 Mb, 72.5%) and 402 (417 Mb, 57.4%) superscaffolds, respectively (Table 2). Figure 3 shows the superscaffold anchoring summary for both the linkage (DM map) and the two in silico (RH and tomato maps) approaches. The total set of 649 superscaffolds anchored in at least one map was integrated hierarchically, starting with the DMDD-based framework map, placing additional superscaffolds using first the RH and then tomato assignment. The hierarchical ‘alignment’ of the maps is described below.

Bottom Line: These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes.Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion.The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

View Article: PubMed Central - PubMed

Affiliation: Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom.

ABSTRACT
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

Show MeSH
Related in: MedlinePlus