scholarly journals Population Genetics and a Study of Speciation Using Next-Generation Sequencing: An Educational Primer for Use with “Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets”

Genetics ◽  
2013 ◽  
Vol 193 (3) ◽  
pp. 671-675 ◽  
Author(s):  
Patricia J. Wittkopp
Keyword(s):  
Population Genetics ◽  
Next Generation Sequencing ◽  
Related Species ◽  
Accessory Gland ◽  
Next Generation ◽  
Male Accessory Gland ◽  
Closely Related Species ◽  
Field Crickets ◽  
Generation Sequencing

scholarly journals Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

Genetics ◽  
2012 ◽  
Vol 193 (2) ◽  
pp. 501-513 ◽  
Author(s):  
Jose A. Andrés ◽  
Erica L. Larson ◽  
Steven M. Bogdanowicz ◽  
Richard G. Harrison
Keyword(s):  
Related Species ◽  
Accessory Gland ◽  
Male Accessory Gland ◽  
Closely Related Species ◽  
Field Crickets

scholarly journals Characterization of 23 Polymorphic SSR Markers in Salix humboldtiana (Salicaceae) Using Next-Generation Sequencing and Cross-Amplification from Related Species

2015 ◽  
Vol 3 (4) ◽  
pp. 1400120 ◽  
Author(s):  
Jorge A. Bozzi ◽  
Sascha Liepelt ◽  
Sebastian Ohneiser ◽  
Leonardo A. Gallo ◽  
Paula Marchelli ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ssr Markers ◽  
Related Species ◽  
Next Generation ◽  
Cross Amplification ◽  
Generation Sequencing

scholarly journals ngsTools: methods for population genetics analyses from next-generation sequencing data

2014 ◽  
Vol 30 (10) ◽  
pp. 1486-1487 ◽  
Author(s):  
Matteo Fumagalli ◽  
Filipe G. Vieira ◽  
Tyler Linderoth ◽  
Rasmus Nielsen
Keyword(s):  
Population Genetics ◽  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals SNP Development in Penaeus vannamei via Next-Generation Sequencing and DNA Pool Sequencing

Fishes ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 36
Author(s):  
Yongyu Huang ◽  
Lili Zhang ◽  
Hui Ge ◽  
Guodong Wang ◽  
Shiyu Huang ◽  
...  
Keyword(s):  
Population Genetics ◽  
Next Generation Sequencing ◽  
Allele Frequency ◽  
Minor Allele Frequency ◽  
Penaeus Vannamei ◽  
Next Generation ◽  
High Quality ◽  
High Quality Snps ◽  
Dna Pool ◽  
Generation Sequencing

Next-generation sequencing and pool sequencing have been widely used in SNP (single-nucleotide polymorphism) detection and population genetics research; however, there are few reports on SNPs related to the growth of Penaeus vannamei. The purpose of this study was to call SNPs from rapid-growing (RG) and slow-growing (SG) individuals’ transcriptomes and use DNA pool sequencing to assess the reliability of SNPs. Two parameters were applied to detect SNPs. One parameter was the p-values generated using Fisher’s exact test, which were used to calculate the significance of allele frequency differences between RG and SG. The other one was the AFI (minor allele frequency imbalance), which was defined to highlight the fold changes in MAF (minor allele frequency) values between RG and SG. There were 216,015 hypothetical SNPs, which were obtained based on the transcriptome data. Finally, 104 high-quality SNPs and 96,819 low-quality SNPs were predicted. Then, 18 high-quality SNPs and 17 low-quality SNPs were selected to assess the reliability of the detection process. Here, 72.22% (13/18) accuracy was achieved for high-quality SNPs, while only 52.94% (9/17) accuracy was achieved for low-quality SNPs. These SNPs enrich the data for population genetics studies of P. vannamei and may play a role in the development of SNP markers for future breeding studies.

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