SNP discovery in Mauremys reevesii and M. sinensis using restriction site-associated DNA sequence (RAD-seq)

Xie, Qiming; Rong, Chaozhen; Li, Xilei; Lai, Nianyue; Chen, Tiantian; Li, Qingqing; Su, Shiping

doi:10.1007/s12686-019-01126-7

Cited by 2 publications

(2 citation statements)

References 4 publications

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“…For example, SNP markers in eggplant (Solanum melongena) were developed based on RAD-seq and more than 2000 SNPs can be mapped according to Illumina GoldenGate analysis (Barchi et al 2011). Xie et al (2020) performed extensive RAD-seq of Mauremys reevesii and Mauremys sinensis and 144 new high-quality markers from four regions of China were developed. Studies have shown that RAD-seq can be used to discover a large number of SNP markers for population genetics.…”

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confidence: 99%

Identification of a large dataset of SNPs in hair‐fin anchovy (Setipinna tenuifilis) based on RAD‐seq

Peng

Zhang

et al. 2021

Animal Genetics

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Hair-fin anchovy (Setipinna tenuifilis) is an economically important fish distributed in the West Indian Ocean and the Northwest Pacific Ocean. In this study, 154 individuals in eight populations of S. tenuifilis were sequenced and 850 million raw reads were obtained using restriction site-associated DNA sequencing (RAD-seq). First, we identified 14 012 044 hypothetical SNP markers. A dataset of 199 903 high-quality SNPs was collected after further screening. These SNPs have a strong ability to test the genetic diversity between the eight populations. The differentiation and genetic law between samples were explored based on SNPs in populations of S. tenuifilis. The results of this study will provide data for protecting the genetic resources of the species.

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confidence: 99%

Identification of a large dataset of SNPs in hair‐fin anchovy (Setipinna tenuifilis) based on RAD‐seq

Peng

Zhang

et al. 2021

Animal Genetics

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“…Recent range-wide survey initiatives in the United States have yielded additional samples beyond the range examined by Bailey et al (2008) and genomic analyses have drastically improved. Restriction-site associated DNA sequencing (RADSeq) yielding single nucleotide polymorphisms (SNPs) have become the most economic and accessible genetic markers that offer enhanced resolution of genetic diversity and population structure compared to microsatellites ( Georges et al 2018 ; Xie et al 2019 ; Gallego-García et al 2021 ). Here, we sought to improve our understanding of P. gorzugi range-wide genetic diversity and population structure amid a rapidly changing environment and identify the most vulnerable populations.…”

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confidence: 99%

Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system

Vandewege,

Gutierrez,

Davis

et al. 2024

Journal of Heredity

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The lower Rio Grande and Pecos River of the southwest United States of America have been heavily modified by human activities, profoundly impacting the integrity of their aquatic wildlife. In this context, we focused our study on the population genomics of the Rio Grande Cooter (Pseudemys gorzugi), a freshwater turtle of increasing conservation concern, residing in these two rivers and their tributaries. The genetic data revealed two distinct populations: one in the Pecos and Black rivers of New Mexico, and another in the Rio Grande and Devils River of Texas, with admixed individuals identified at the confluence of the Rio Grande and Pecos River. In addition to having a smaller geographic range, we found lower observed heterozygosity, reduced nucleotide diversity, and a smaller effective population size (Ne) in New Mexico population. Our results depict a significant isolation-by-distance pattern across their distribution, with migration being notably infrequent at river confluences. These findings are pivotal for future conservation and restoration strategies, emphasizing the need to recognize the unique needs of each population.

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SNP discovery in Mauremys reevesii and M. sinensis using restriction site-associated DNA sequence (RAD-seq)

Cited by 2 publications

References 4 publications

Identification of a large dataset of SNPs in hair‐fin anchovy (Setipinna tenuifilis) based on RAD‐seq

Identification of a large dataset of SNPs in hair‐fin anchovy (Setipinna tenuifilis) based on RAD‐seq

Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system

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