Evolution of Microsatellite Loci of Tropical and Temperate Anguilla Eels

Tseng, Mei‐Chun

doi:10.3390/ijms13044281

Cited by 7 publications

(2 citation statements)

References 44 publications

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“…The SNP frequency was moderately higher in the reported species. The transition/transversion ratio (2.0) was also higher than Pacific oyster (1.3) [43] and Drosophila(1.5) [44] .…”

Section: Discussionmentioning

confidence: 85%

SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing

Wei

Zhang

et al. 2014

PLoS ONE

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The application of next generation sequencing technology has greatly facilitated high throughput single nucleotide polymorphism (SNP) discovery and genotyping in genetic research. In the present study, SNPs were discovered based on two transcriptomes of Litopenaeus vannamei (L. vannamei) generated from Illumina sequencing platform HiSeq 2000. One transcriptome of L. vannamei was obtained through sequencing on the RNA from larvae at mysis stage and its reference sequence was de novo assembled. The data from another transcriptome were downloaded from NCBI and the reads of the two transcriptomes were mapped separately to the assembled reference by BWA. SNP calling was performed using SAMtools. A total of 58,717 and 36,277 SNPs with high quality were predicted from the two transcriptomes, respectively. SNP calling was also performed using the reads of two transcriptomes together, and a total of 96,040 SNPs with high quality were predicted. Among these 96,040 SNPs, 5,242 and 29,129 were predicted as non-synonymous and synonymous SNPs respectively. Characterization analysis of the predicted SNPs in L. vannamei showed that the estimated SNP frequency was 0.21% (one SNP per 476 bp) and the estimated ratio for transition to transversion was 2.0. Fifty SNPs were randomly selected for validation by Sanger sequencing after PCR amplification and 76% of SNPs were confirmed, which indicated that the SNPs predicted in this study were reliable. These SNPs will be very useful for genetic study in L. vannamei, especially for the high density linkage map construction and genome-wide association studies.

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“…The SNP frequency was moderately higher in the reported species. The transition/transversion ratio (2.0) was also higher than Pacific oyster (1.3) [43] and Drosophila(1.5) [44] .…”

Section: Discussionmentioning

confidence: 85%

SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing

Wei

Zhang

et al. 2014

PLoS ONE

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“…; Pilot et al . ; Tseng ). Microsatellites allow for detailed analyses of interactions among environmental and ecological factors and their influence on population genetic variability (Messier et al .…”

Section: Introductionmentioning

confidence: 99%

‘True’ null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements

Dabrowski

Bornelöv

Kruczyk

et al. 2014

Molecular Ecology Resources

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Null alleles are alleles that for various reasons fail to amplify in a PCR assay. The presence of null alleles in microsatellite data is known to bias the genetic parameter estimates. Thus, efficient detection of null alleles is crucial, but the methods available for indirect null allele detection return inconsistent results. Here, our aim was to compare different methods for null allele detection, to explain their respective performance and to provide improvements. We applied several approaches to identify the 'true' null alleles based on the predictions made by five different methods, used either individually or in combination. First, we introduced simulated 'true' null alleles into 240 population data sets and applied the methods to measure their success in detecting the simulated null alleles. The single best-performing method was ML-NullFreq_frequency. Furthermore, we applied different noise reduction approaches to improve the results. For instance, by combining the results of several methods, we obtained more reliable results than using a single one. Rule-based classification was applied to identify population properties linked to the false discovery rate. Rules obtained from the classifier described which population genetic estimates and loci characteristics were linked to the success of each method. We have shown that by simulating 'true' null alleles into a population data set, we may define a null allele frequency threshold, related to a desired true or false discovery rate. Moreover, using such simulated data sets, the expected null allele homozygote frequency may be estimated independently of the equilibrium state of the population.

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