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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

Distribution of simple sequence repeat (SSR) nucleotide classes among different nucleotide types in H. siamensis.
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f4-ijms-13-10807: Distribution of simple sequence repeat (SSR) nucleotide classes among different nucleotide types in H. siamensis.

Mentions: A total 1837 simple sequence repeats (SSRs) or microsatellites comprising 74.41% dinucleotide repeats, 9.53% trinucleotide repeats and 16.06% tetra/penta/hextanucleotide repeats were detected (Figure 4) among the H. siamensis GSS sequences. Recognition of a high number of dinucleotide repeats in H. siamensis is consistent with previous studies in fish and other aquatic organisms [21,14]. From 1837 detected SSRs, a total of 422 SSR primer sets comprising 78% dinucleotide repeat primers, 8.3% trinucleotide repeat primers, and 13.7% tetra/penta/hextanucleotide repeat primers were designed successfully (Table S2). The majority of SSRs detected and primers designed for their amplification in H. siamensis were singletons. A large number of SSRs were detected in H. siamensis contig sequences but primers were not designed successfully in these sequences. This result suggests that the GSSs in H. siamensis mostly consisted of non-coding regions which have high polymorphic sites, or alternatively this could be a common homopolymer problem with 454 sequencing.


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)

Distribution of simple sequence repeat (SSR) nucleotide classes among different nucleotide types in H. siamensis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4-ijms-13-10807: Distribution of simple sequence repeat (SSR) nucleotide classes among different nucleotide types in H. siamensis.
Mentions: A total 1837 simple sequence repeats (SSRs) or microsatellites comprising 74.41% dinucleotide repeats, 9.53% trinucleotide repeats and 16.06% tetra/penta/hextanucleotide repeats were detected (Figure 4) among the H. siamensis GSS sequences. Recognition of a high number of dinucleotide repeats in H. siamensis is consistent with previous studies in fish and other aquatic organisms [21,14]. From 1837 detected SSRs, a total of 422 SSR primer sets comprising 78% dinucleotide repeat primers, 8.3% trinucleotide repeat primers, and 13.7% tetra/penta/hextanucleotide repeat primers were designed successfully (Table S2). The majority of SSRs detected and primers designed for their amplification in H. siamensis were singletons. A large number of SSRs were detected in H. siamensis contig sequences but primers were not designed successfully in these sequences. This result suggests that the GSSs in H. siamensis mostly consisted of non-coding regions which have high polymorphic sites, or alternatively this could be a common homopolymer problem with 454 sequencing.

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