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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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Assembled BAC sequence for LuSP197F07. Each scaffold assembly is derived from PE sequences of a combined pool of 82 DM BACs (spanning scaffolding gaps on chromosome 4) and single end sequence at greater read depth from one of the six subpools derived from the same BACs. The assemblies show a direct sequence running from PGSC0003DMB000000278 (− orientation, full length, cyan) through into PGSC0003DMB000000051 (+ orientation, blue) in accordance with the AGP and fully validating the decision to split PGSC00003DMB0000000278 at position 824768 and to split PGSC0003DMB000000051 at position 1859342 as indicated in the AGP file. Regions of good alignment (>98% identity, >1000 bases) are indicated as thick lines. Thin lines indicate no good alignment between the superscaffold and BAC sequences. The BAC end sequences are labeled with their Genbank IDs and are indicated at each end of the plot by black arrows. Breakpoints in the BAC sequences are indicated by orange diagonal lines and annotated with the assigned breakpoints coordinate from the AGP.
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fig5: Assembled BAC sequence for LuSP197F07. Each scaffold assembly is derived from PE sequences of a combined pool of 82 DM BACs (spanning scaffolding gaps on chromosome 4) and single end sequence at greater read depth from one of the six subpools derived from the same BACs. The assemblies show a direct sequence running from PGSC0003DMB000000278 (− orientation, full length, cyan) through into PGSC0003DMB000000051 (+ orientation, blue) in accordance with the AGP and fully validating the decision to split PGSC00003DMB0000000278 at position 824768 and to split PGSC0003DMB000000051 at position 1859342 as indicated in the AGP file. Regions of good alignment (>98% identity, >1000 bases) are indicated as thick lines. Thin lines indicate no good alignment between the superscaffold and BAC sequences. The BAC end sequences are labeled with their Genbank IDs and are indicated at each end of the plot by black arrows. Breakpoints in the BAC sequences are indicated by orange diagonal lines and annotated with the assigned breakpoints coordinate from the AGP.

Mentions: In addition to the complete assemblies described previously, most other clones could be assembled to a series of contigs which did not span multiple superscaffolds and which have not been included in the BAC pool assembly summary (Table S6). Details of the BAC analysis are given in the Materials and Methods section and a representative example validating a potential break-point in Chromosome 4 is illustrated in Figure 5. A list of putative erroneous superscaffold assembly locations (breakpoints), and the BACs which provide validation for them are given in Table S7.


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)

Assembled BAC sequence for LuSP197F07. Each scaffold assembly is derived from PE sequences of a combined pool of 82 DM BACs (spanning scaffolding gaps on chromosome 4) and single end sequence at greater read depth from one of the six subpools derived from the same BACs. The assemblies show a direct sequence running from PGSC0003DMB000000278 (− orientation, full length, cyan) through into PGSC0003DMB000000051 (+ orientation, blue) in accordance with the AGP and fully validating the decision to split PGSC00003DMB0000000278 at position 824768 and to split PGSC0003DMB000000051 at position 1859342 as indicated in the AGP file. Regions of good alignment (>98% identity, >1000 bases) are indicated as thick lines. Thin lines indicate no good alignment between the superscaffold and BAC sequences. The BAC end sequences are labeled with their Genbank IDs and are indicated at each end of the plot by black arrows. Breakpoints in the BAC sequences are indicated by orange diagonal lines and annotated with the assigned breakpoints coordinate from the AGP.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: Assembled BAC sequence for LuSP197F07. Each scaffold assembly is derived from PE sequences of a combined pool of 82 DM BACs (spanning scaffolding gaps on chromosome 4) and single end sequence at greater read depth from one of the six subpools derived from the same BACs. The assemblies show a direct sequence running from PGSC0003DMB000000278 (− orientation, full length, cyan) through into PGSC0003DMB000000051 (+ orientation, blue) in accordance with the AGP and fully validating the decision to split PGSC00003DMB0000000278 at position 824768 and to split PGSC0003DMB000000051 at position 1859342 as indicated in the AGP file. Regions of good alignment (>98% identity, >1000 bases) are indicated as thick lines. Thin lines indicate no good alignment between the superscaffold and BAC sequences. The BAC end sequences are labeled with their Genbank IDs and are indicated at each end of the plot by black arrows. Breakpoints in the BAC sequences are indicated by orange diagonal lines and annotated with the assigned breakpoints coordinate from the AGP.
Mentions: In addition to the complete assemblies described previously, most other clones could be assembled to a series of contigs which did not span multiple superscaffolds and which have not been included in the BAC pool assembly summary (Table S6). Details of the BAC analysis are given in the Materials and Methods section and a representative example validating a potential break-point in Chromosome 4 is illustrated in Figure 5. A list of putative erroneous superscaffold assembly locations (breakpoints), and the BACs which provide validation for them are given in Table S7.

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