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Analysis of genome survey sequences and SSR marker development for Siamese Mud Carp, Henicorhynchus siamensis, using 454 pyrosequencing.

Iranawati F, Jung H, Chand V, Hurwood DA, Mather PB - Int J Mol Sci (2012)

Bottom Line: Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value < 10(-5)) with the majority matching well to reported fish sequences.One thousand eight hundred and thirty seven sequences containing SSR motifs were identified, of which 422 qualified for primer design and eight polymorphic loci have been tested with average observed and expected heterozygosity estimated at 0.75 and 0.83, respectively.Regardless of their relative levels of polymorphism and heterozygosity, microsatellite loci developed here are suitable for further population genetic studies in H. siamensis and may also be applicable to other related taxa.

View Article: PubMed Central - PubMed

Affiliation: Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Queensland 4000, Australia; E-Mails: v.chand@qut.edu.au (V.C.); d.hurwood@qut.edu.au (D.A.H.); p.mather@qut.edu.au (P.B.M.).

ABSTRACT
Siamese mud carp (Henichorynchus siamensis) is a freshwater teleost of high economic importance in the Mekong River Basin. However, genetic data relevant for delineating wild stocks for management purposes currently are limited for this species. Here, we used 454 pyrosequencing to generate a partial genome survey sequence (GSS) dataset to develop simple sequence repeat (SSR) markers from H. siamensis genomic DNA. Data generated included a total of 65,954 sequence reads with average length of 264 nucleotides, of which 2.79% contain SSR motifs. Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value < 10(-5)) with the majority matching well to reported fish sequences. KEGG analysis identified several metabolic pathways that provide insights into specific potential roles and functions of sequences involved in molecular processes in H. siamensis. Top protein domains detected included reverse transcriptase and the top putative functional transcript identified was an ORF2-encoded protein. One thousand eight hundred and thirty seven sequences containing SSR motifs were identified, of which 422 qualified for primer design and eight polymorphic loci have been tested with average observed and expected heterozygosity estimated at 0.75 and 0.83, respectively. Regardless of their relative levels of polymorphism and heterozygosity, microsatellite loci developed here are suitable for further population genetic studies in H. siamensis and may also be applicable to other related taxa.

No MeSH data available.


Related in: MedlinePlus

Gene Ontology (GO) terms for contig and singleton sequences in H. siamensis.
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f3-ijms-13-10807: Gene Ontology (GO) terms for contig and singleton sequences in H. siamensis.

Mentions: Gene Ontology (GO) terms could be assigned to 47,250 H. siamensis contigs (857) and singletons (46,393) based on BLAST matches to proteins with known functions (Figure 3, Table S1). GSS coding sequences were assigned to cellular components (4004 sequences), molecular function (4790 sequences) and biological processes (8313 sequences) (Figure 3). Among the H. siamensis GSSs assigned molecular functions, many were assigned to binding or catalytic functions, predominantly either enzyme regulators or molecular transducers (Figure 3). Cellular component assignments showed many GSS coding sequences were likely to possess cell and cell part functions, while those assigned biological process were mostly predicted to be involved in cellular or metabolic processes. Analyses of sequences in other fish species have identified transcripts possessing a similar range of potential metabolic functions [20,30,31].


Analysis of genome survey sequences and SSR marker development for Siamese Mud Carp, Henicorhynchus siamensis, using 454 pyrosequencing.

Iranawati F, Jung H, Chand V, Hurwood DA, Mather PB - Int J Mol Sci (2012)

Gene Ontology (GO) terms for contig and singleton sequences in H. siamensis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3472715&req=5

f3-ijms-13-10807: Gene Ontology (GO) terms for contig and singleton sequences in H. siamensis.
Mentions: Gene Ontology (GO) terms could be assigned to 47,250 H. siamensis contigs (857) and singletons (46,393) based on BLAST matches to proteins with known functions (Figure 3, Table S1). GSS coding sequences were assigned to cellular components (4004 sequences), molecular function (4790 sequences) and biological processes (8313 sequences) (Figure 3). Among the H. siamensis GSSs assigned molecular functions, many were assigned to binding or catalytic functions, predominantly either enzyme regulators or molecular transducers (Figure 3). Cellular component assignments showed many GSS coding sequences were likely to possess cell and cell part functions, while those assigned biological process were mostly predicted to be involved in cellular or metabolic processes. Analyses of sequences in other fish species have identified transcripts possessing a similar range of potential metabolic functions [20,30,31].

Bottom Line: Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value < 10(-5)) with the majority matching well to reported fish sequences.One thousand eight hundred and thirty seven sequences containing SSR motifs were identified, of which 422 qualified for primer design and eight polymorphic loci have been tested with average observed and expected heterozygosity estimated at 0.75 and 0.83, respectively.Regardless of their relative levels of polymorphism and heterozygosity, microsatellite loci developed here are suitable for further population genetic studies in H. siamensis and may also be applicable to other related taxa.

View Article: PubMed Central - PubMed

Affiliation: Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Queensland 4000, Australia; E-Mails: v.chand@qut.edu.au (V.C.); d.hurwood@qut.edu.au (D.A.H.); p.mather@qut.edu.au (P.B.M.).

ABSTRACT
Siamese mud carp (Henichorynchus siamensis) is a freshwater teleost of high economic importance in the Mekong River Basin. However, genetic data relevant for delineating wild stocks for management purposes currently are limited for this species. Here, we used 454 pyrosequencing to generate a partial genome survey sequence (GSS) dataset to develop simple sequence repeat (SSR) markers from H. siamensis genomic DNA. Data generated included a total of 65,954 sequence reads with average length of 264 nucleotides, of which 2.79% contain SSR motifs. Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value < 10(-5)) with the majority matching well to reported fish sequences. KEGG analysis identified several metabolic pathways that provide insights into specific potential roles and functions of sequences involved in molecular processes in H. siamensis. Top protein domains detected included reverse transcriptase and the top putative functional transcript identified was an ORF2-encoded protein. One thousand eight hundred and thirty seven sequences containing SSR motifs were identified, of which 422 qualified for primer design and eight polymorphic loci have been tested with average observed and expected heterozygosity estimated at 0.75 and 0.83, respectively. Regardless of their relative levels of polymorphism and heterozygosity, microsatellite loci developed here are suitable for further population genetic studies in H. siamensis and may also be applicable to other related taxa.

No MeSH data available.


Related in: MedlinePlus