Limits...
A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology.

Carlson BM, Onusko SW, Gross JB - G3 (Bethesda) (2014)

Bottom Line: We leveraged emergent genomic and transcriptomic resources to anchor hundreds of anonymous Astyanax markers to the genome of the zebrafish (Danio rerio), the most closely related model organism to our study species.Further, our map successfully informed the positions of unplaced Astyanax genomic scaffolds within particular linkage groups.This ability to identify the relative location, orientation, and linear order of unaligned genomic scaffolds will facilitate ongoing efforts to improve on the current early draft and assemble future versions of the Astyanax physical genome.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221.

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Related in: MedlinePlus

Colinearity between Astyanax linkage groups and genome scaffolds. We visualized the “anchoring” of seven unplaced Astyanax genome scaffolds (various colors) to linkage group 23 (black) in our Astyanax linkage map. For clarity, only scaffolds harboring four or more GBS markers were included. Scaffolds correspond to discrete, colinear sections of the linkage group with minimal overlap. The linear arrangement of markers is largely preserved between the scaffold and the linkage group. The scale for Astyanax scaffolds is in Mb; the scale for linkage group 23 is shown in cM.
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fig4: Colinearity between Astyanax linkage groups and genome scaffolds. We visualized the “anchoring” of seven unplaced Astyanax genome scaffolds (various colors) to linkage group 23 (black) in our Astyanax linkage map. For clarity, only scaffolds harboring four or more GBS markers were included. Scaffolds correspond to discrete, colinear sections of the linkage group with minimal overlap. The linear arrangement of markers is largely preserved between the scaffold and the linkage group. The scale for Astyanax scaffolds is in Mb; the scale for linkage group 23 is shown in cM.

Mentions: In many cases, markers present on the same scaffold clustered together over a portion of a linkage group with little or no interruption from unplaced markers or markers from other scaffolds (Figure 4). We expect these results will help inform chromosomal positions of scaffolds, given that linkage maps have been successfully used to augment genomic resources in other fish species, including several species of catfish (Liu 2011; Ninwichian et al. 2012), rainbow trout (Palti et al. 2011; Palti et al. 2012), and Atlantic salmon (Lorenz et al. 2010). We believe our high-density GBS-based map resources will both provide a resource for more refined QTL analyses and inform the genomic architecture of the Astyanax genome sequencing project.


A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology.

Carlson BM, Onusko SW, Gross JB - G3 (Bethesda) (2014)

Colinearity between Astyanax linkage groups and genome scaffolds. We visualized the “anchoring” of seven unplaced Astyanax genome scaffolds (various colors) to linkage group 23 (black) in our Astyanax linkage map. For clarity, only scaffolds harboring four or more GBS markers were included. Scaffolds correspond to discrete, colinear sections of the linkage group with minimal overlap. The linear arrangement of markers is largely preserved between the scaffold and the linkage group. The scale for Astyanax scaffolds is in Mb; the scale for linkage group 23 is shown in cM.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4321032&req=5

fig4: Colinearity between Astyanax linkage groups and genome scaffolds. We visualized the “anchoring” of seven unplaced Astyanax genome scaffolds (various colors) to linkage group 23 (black) in our Astyanax linkage map. For clarity, only scaffolds harboring four or more GBS markers were included. Scaffolds correspond to discrete, colinear sections of the linkage group with minimal overlap. The linear arrangement of markers is largely preserved between the scaffold and the linkage group. The scale for Astyanax scaffolds is in Mb; the scale for linkage group 23 is shown in cM.
Mentions: In many cases, markers present on the same scaffold clustered together over a portion of a linkage group with little or no interruption from unplaced markers or markers from other scaffolds (Figure 4). We expect these results will help inform chromosomal positions of scaffolds, given that linkage maps have been successfully used to augment genomic resources in other fish species, including several species of catfish (Liu 2011; Ninwichian et al. 2012), rainbow trout (Palti et al. 2011; Palti et al. 2012), and Atlantic salmon (Lorenz et al. 2010). We believe our high-density GBS-based map resources will both provide a resource for more refined QTL analyses and inform the genomic architecture of the Astyanax genome sequencing project.

Bottom Line: We leveraged emergent genomic and transcriptomic resources to anchor hundreds of anonymous Astyanax markers to the genome of the zebrafish (Danio rerio), the most closely related model organism to our study species.Further, our map successfully informed the positions of unplaced Astyanax genomic scaffolds within particular linkage groups.This ability to identify the relative location, orientation, and linear order of unaligned genomic scaffolds will facilitate ongoing efforts to improve on the current early draft and assemble future versions of the Astyanax physical genome.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221.

Show MeSH
Related in: MedlinePlus