Dataset Information

Development of nuclear microsatellites for the Arcto-Tertiary tree Zelkova carpinifolia (Ulmaceae) using 454 pyrosequencing.

ABSTRACT: UNLABELLED: PREMISE OF THE STUDY:The current study aimed at developing nuclear microsatellite markers for the relict tree species Zelkova carpinifolia, which is threatened in its natural range in the South Caucasus. • METHODS AND RESULTS:Pyrosequencing of an enriched microsatellite library on the Roche FLX platform using the 454 Titanium kit produced 86,058 sequence reads, most of which contained short tandem repeats. Eighty microsatellite loci identified using the software package QDD version 1 were selected and tested for proper PCR amplification. Of these, 13 allowed proper amplification and were shown to be polymorphic among a sample of 25 Z. carpinifolia specimens from various geographic origins. • CONCLUSIONS:The set of microsatellite markers will be suitable for the assessment of genetic diversity in Z. carpinifolia. They will allow for an examination of phylogeographic patterns as well as of population structure and gene flow within this species.

SUBMITTER: Maharramova EH

PROVIDER: S-EPMC4103100 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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Development of nuclear microsatellites for the Arcto-Tertiary tree Zelkova carpinifolia (Ulmaceae) using 454 pyrosequencing.

Maharramova Elmira H EH Muller Ludo A LA Korotkova Nadja N Borsch Thomas T

Applications in plant sciences 20140211 3

<h4>Unlabelled</h4><h4>Premise of the study</h4>The current study aimed at developing nuclear microsatellite markers for the relict tree species Zelkova carpinifolia, which is threatened in its natural range in the South Caucasus. •<h4>Methods and results</h4>Pyrosequencing of an enriched microsatellite library on the Roche FLX platform using the 454 Titanium kit produced 86,058 sequence reads, most of which contained short tandem repeats. Eighty microsatellite loci identified using the software ...[more]

PMID: 25202606

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Project description:BackgroundRNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies is a subject of great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software was originally designed for single genome assembly and cannot be used to simultaneously assemble and estimate the abundance of multiple closely related quasispecies sequences.ResultsIn this paper, we introduce a new Viral Spectrum Assembler (ViSpA) method for quasispecies spectrum reconstruction and compare it with the state-of-the-art ShoRAH tool on both simulated and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. Experimental results show that ViSpA outperforms ShoRAH on simulated error-free reads, correctly assembling 10 out of 10 quasispecies and 29 sequences out of 40 quasispecies. While ShoRAH has a significant advantage over ViSpA on reads simulated with sequencing errors due to its advanced error correction algorithm, ViSpA is better at assembling the simulated reads after they have been corrected by ShoRAH. ViSpA also outperforms ShoRAH on real 454 reads. Indeed, 7 most frequent sequences reconstructed by ViSpA from a real HCV dataset are viable (do not contain internal stop codons), and the most frequent sequence was within 1% of the actual open reading frame obtained by cloning and Sanger sequencing. In contrast, only one of the sequences reconstructed by ShoRAH is viable. On a real HIV dataset, ShoRAH correctly inferred only 2 quasispecies sequences with at most 4 mismatches whereas ViSpA correctly reconstructed 5 quasispecies with at most 2 mismatches, and 2 out of 5 sequences were inferred without any mismatches. ViSpA source code is available at http://alla.cs.gsu.edu/~software/VISPA/vispa.html.ConclusionsViSpA enables accurate viral quasispecies spectrum reconstruction from 454 pyrosequencing reads. We are currently exploring extensions applicable to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations.

Dataset Information

Development of nuclear microsatellites for the Arcto-Tertiary tree Zelkova carpinifolia (Ulmaceae) using 454 pyrosequencing.

Publications

Development of nuclear microsatellites for the Arcto-Tertiary tree Zelkova carpinifolia (Ulmaceae) using 454 pyrosequencing.

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