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Front Genet
2021 Jan 01;12:717764. doi: 10.3389/fgene.2021.717764.
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Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas.
Wang Q
,
Liu Y
,
Yan L
,
Chen L
,
Li B
.
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Mesocentrotus nudus is an important commercially aquatic species because of its high edible and medicinal values. However, wild stocks have dramatically decreased in recent decades. Understanding the population structure and genetic diversity can provide vital information for genetic conservation and improvement. In the present study, the genotyping-by-sequencing (GBS) approach was adopted to identify the genome-wide single-nucleotide polymorphisms (SNPs) from a collection of 80 individuals consisting of five geographical populations (16 individuals from each population), covering the natural habitats of M. nudus in China seas. An average of 0.96-Gb clean reads per sample were sequenced, and a total of 51,738 biallelic SNPs were identified. Based on these SNPs, diversity index analysis showed that all populations have a similar pattern with positive Fis (0.136) and low Ne (724.3). Low genetic differentiation and high genetic connectivity among five geographical populations were detected by pairwise Fst, principal component analysis (PCA), admixture, and phylogenetic analysis. Besides, two YWL individuals originating from an isolated ancestor may imply that there is a genetically differentiated population in the adjacent sea. Overall, the results showed that GBS is an effective method to detect genome-wide SNPs for M. nudus and suggested that the protective measures and the investigation with larger spatial scale and sample size for M. nudus should be carried out in the future.
FIGURE 1. Map for sample locations of Mesocentrotus nudus in China.
FIGURE 2. Principal components analysis (PCA) 3D plot of the 80 individuals using genome-wide single-nucleotide polymorphisms (SNPs).
FIGURE 3. Admixture analyses of 80 individuals based on the genome-wide single-nucleotide polymorphisms (SNPs). (A) Cross-validation plot for the number of ancestral populations (k). (B) Stacked bar plot for the k = 2. (C) Stacked bar plot for the k = 3. Each column represents an individual, and the length of colored segments denotes the proportion of an individual’s genome inherited from one of k ancestral populations.
FIGURE 4. Individual-level phylogeny constructed using SNPhylo.
FIGURE 5. Population-level phylogeny with migration edges constructed using TreeMix.
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