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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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Short GBS sequences identify syntenic stretches between two Ostariophysian freshwater fish species. To reveal syntenic regions between Astyanax mexicanus and Danio rerio, we first identified stretches of the Danio genome harboring homologous sequences to our anonymous GBS marker sequences (A). Individual 64-bp sequences for the 2235 GBS markers in our linkage map were compared with the Danio genome both directly and by first aligning to larger Astyanax genomic scaffolds and predicted gene transcripts (B), followed by alignment of some or all of the larger sequence to the Danio genome based on BLAST sequence analysis (C). This resulted in identification of homologous sequences for 784 Astyanax GBS markers within the Danio genome. The markers shared between Danio chromosomes and Astyanax linkage groups are represented using an Oxford plot (D).
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fig2: Short GBS sequences identify syntenic stretches between two Ostariophysian freshwater fish species. To reveal syntenic regions between Astyanax mexicanus and Danio rerio, we first identified stretches of the Danio genome harboring homologous sequences to our anonymous GBS marker sequences (A). Individual 64-bp sequences for the 2235 GBS markers in our linkage map were compared with the Danio genome both directly and by first aligning to larger Astyanax genomic scaffolds and predicted gene transcripts (B), followed by alignment of some or all of the larger sequence to the Danio genome based on BLAST sequence analysis (C). This resulted in identification of homologous sequences for 784 Astyanax GBS markers within the Danio genome. The markers shared between Danio chromosomes and Astyanax linkage groups are represented using an Oxford plot (D).

Mentions: Cross-genera marker identification was greatly facilitated by alignment first to draft Astyanax genomic and transcriptomic resources, followed by searches of the homologous sequences in Danio (Figure 2, A–C). Although direct BLAST searches of our 64-bp GBS marker sequences returned results for few of the markers in our map (1.2%), success rates were much higher when using Astyanax genomic (26.5%) or transcriptomic (13.3%) sequences as an intermediary (Table 1). Each Danio rerio chromosome was represented in our comparative genomic analysis, with Astyanax linkage groups containing 14–52 markers (average = 30.84) comprising ancient syntenic blocks shared with each of 25 zebrafish chromosomes (Figure 2D). Of the 2235 GBS markers that constitute our linkage map, 784 marker sequences (35.1%) were successfully identified in the Danio rerio genome (Figure 3A).


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

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

Short GBS sequences identify syntenic stretches between two Ostariophysian freshwater fish species. To reveal syntenic regions between Astyanax mexicanus and Danio rerio, we first identified stretches of the Danio genome harboring homologous sequences to our anonymous GBS marker sequences (A). Individual 64-bp sequences for the 2235 GBS markers in our linkage map were compared with the Danio genome both directly and by first aligning to larger Astyanax genomic scaffolds and predicted gene transcripts (B), followed by alignment of some or all of the larger sequence to the Danio genome based on BLAST sequence analysis (C). This resulted in identification of homologous sequences for 784 Astyanax GBS markers within the Danio genome. The markers shared between Danio chromosomes and Astyanax linkage groups are represented using an Oxford plot (D).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Short GBS sequences identify syntenic stretches between two Ostariophysian freshwater fish species. To reveal syntenic regions between Astyanax mexicanus and Danio rerio, we first identified stretches of the Danio genome harboring homologous sequences to our anonymous GBS marker sequences (A). Individual 64-bp sequences for the 2235 GBS markers in our linkage map were compared with the Danio genome both directly and by first aligning to larger Astyanax genomic scaffolds and predicted gene transcripts (B), followed by alignment of some or all of the larger sequence to the Danio genome based on BLAST sequence analysis (C). This resulted in identification of homologous sequences for 784 Astyanax GBS markers within the Danio genome. The markers shared between Danio chromosomes and Astyanax linkage groups are represented using an Oxford plot (D).
Mentions: Cross-genera marker identification was greatly facilitated by alignment first to draft Astyanax genomic and transcriptomic resources, followed by searches of the homologous sequences in Danio (Figure 2, A–C). Although direct BLAST searches of our 64-bp GBS marker sequences returned results for few of the markers in our map (1.2%), success rates were much higher when using Astyanax genomic (26.5%) or transcriptomic (13.3%) sequences as an intermediary (Table 1). Each Danio rerio chromosome was represented in our comparative genomic analysis, with Astyanax linkage groups containing 14–52 markers (average = 30.84) comprising ancient syntenic blocks shared with each of 25 zebrafish chromosomes (Figure 2D). Of the 2235 GBS markers that constitute our linkage map, 784 marker sequences (35.1%) were successfully identified in the Danio rerio genome (Figure 3A).

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