scholarly journals Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tetsuo Kon ◽  
Liyi Pei ◽  
Ryota Ichikawa ◽  
Chunyan Chen ◽  
Ping Wang ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Genomics ◽  
Living Environment ◽  
Large Yellow Croaker ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Resequencing ◽  
Genetic Population ◽  
Whole Genome Resequencing ◽  
Sea Area

AbstractLarge yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.

scholarly journals Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

2021 ◽  
Vol 17 (3) ◽  
Author(s):  
Xiao Wei ◽  
Fei Shen ◽  
Qiuping Zhang ◽  
Ning Liu ◽  
Yuping Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Principal Component ◽  
Private Allele ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genome Resequencing ◽  
Cultivar Group ◽  
Prunus Salicina ◽  
Whole Genome Resequencing

AbstractChinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance because of its extensive genetic diversity and nutritional attributes that are beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. In this study, we constructed high-quality SNPs through whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. Phylogenetic analysis, principal component analysis, and population structure profiling indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China clustered with the other three groups. The genetic diversity indices including private allele number, observed heterozygosity, expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. Gene flow from the SCG to FG was also detected. Based on the distribution of wild resources, we concluded that the domestication center of origin of the Chinese plum was southwestern China. This study also provided genetic variation features and the population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants to improve Chinese plum varieties.

scholarly journals The population genomics of invasive species

2021 ◽  
Author(s):  
Henry North ◽  
Angela McGaughran ◽  
Chris Jiggins
Keyword(s):  
Invasive Species ◽  
New Technologies ◽  
Population Genomics ◽  
Balancing Selection ◽  
Rapid Evolution ◽  
Invasion Biology ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Wide Range ◽  
Whole Genome Resequencing

By studying invasive species, evolutionary geneticists have been able to simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole-genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole-genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many individuals simply increases the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies to be applied. To date whole-genome resequencing has only been applied to a handful of invasive systems, but these studies have highlighted important roles for processes such as balancing selection and hybridization that allow invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.

scholarly journals Contrasting whole-genome and reduced representation sequencing for population demographic inference: an alpine mammal example

2022 ◽  
Author(s):  
Daria Martchenko ◽  
Aaron Shafer
Keyword(s):  
Isolation By Distance ◽  
Demographic History ◽  
Genomic Region ◽  
Whole Genome ◽  
Summary Statistics ◽  
Effective Population ◽  
Genome Resequencing ◽  
Reduced Representation ◽  
Whole Genome Resequencing ◽  
Population Demographic

Genomic approaches to the study of population demography rely on accurate SNP calling and by-proxy the site frequency spectrum (SFS). Two main questions for the design of such studies remain poorly investigated: do reduced genomic sequencing summary statistics reflect that of whole genome, and how do sequencing strategies and derived summary statistics impact demographic inferences? To address those questions, we applied the ddRAD sequencing approach to 254 individuals and whole genome resequencing approach to 35 mountain goat (Oreamnos americanus) individuals across the species range with a known demographic history. We identified SNPs with 5 different variant callers and used ANGSD to estimate the genotype likelihoods (GLs). We tested combinations of SNP filtering by linkage disequilibrium (LD), minor allele frequency (MAF) and the genomic region. We compared the resulting suite of summary statistics reflective of the SFS and quantified the relationship to demographic inferences by estimating the contemporary effective population size (Ne), isolation-by-distance and population structure, FST, and explicit modelling of the demographic history with δaδi. Filtering had a larger effect than sequencing strategy, with the former strongly influencing summary statistics. Estimates of contemporary Ne and isolation-by-distance patterns were largely robust to the choice of sequencing, pipeline, and filtering. Despite the high variance in summary statistics, whole genome and reduced representation approaches were overall similar in supporting a glacial induced vicariance and low Ne in mountain goats. We discuss why whole genome resequencing data is preferable, and reiterate support the use of GLs, in part because it limits user-determined filters.

scholarly journals Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

2020 ◽  
Author(s):  
Xiao Wei ◽  
Fei Shen ◽  
Qiuping Zhang ◽  
Ning Liu ◽  
Yuping Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
South China ◽  
Yangtze River Basin ◽  
Private Allele ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Cultivar Group ◽  
Prunus Salicina ◽  
Whole Genome Resequencing

AbstractChinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance due to their extensive genetic diversity and nutritional attributes beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. Here, we construed high-density haplotype map by whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. The phylogenetic analysis, the principal component analysis, and the population structure profiling, indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China were clustered with the other three groups. The genetic diversity indices including the private allele number, the observed heterozygosity, the expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. The gene flow from the SCG to the FG was detected as well. We concluded that the origin center of Chinese plum was at the Yangtze River Basin in South China. This study provided genetic variation features and population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants for improving Chinese plum varieties.

scholarly journals Recent Secondary Contacts, Linked Selection, and Variable Recombination Rates Shape Genomic Diversity in the Model Species Anolis carolinensis

2019 ◽  
Vol 11 (7) ◽  
pp. 2009-2022 ◽  
Author(s):  
Yann Bourgeois ◽  
Robert P Ruggiero ◽  
Joseph D Manthey ◽  
Stéphane Boissinot
Keyword(s):  
Population Genomics ◽  
Anolis Carolinensis ◽  
South Florida ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Green Anole ◽  
Genetic Clusters ◽  
Whole Genome Resequencing ◽  
Linked Selection

AbstractGaining a better understanding on how selection and neutral processes affect genomic diversity is essential to gain better insights into the mechanisms driving adaptation and speciation. However, the evolutionary processes affecting variation at a genomic scale have not been investigated in most vertebrate lineages. Here, we present the first population genomics survey using whole genome resequencing in the green anole (Anolis carolinensis). Anoles have been intensively studied to understand mechanisms underlying adaptation and speciation. The green anole in particular is an important model to study genome evolution. We quantified how demography, recombination, and selection have led to the current genetic diversity of the green anole by using whole-genome resequencing of five genetic clusters covering the entire species range. The differentiation of green anole’s populations is consistent with a northward expansion from South Florida followed by genetic isolation and subsequent gene flow among adjacent genetic clusters. Dispersal out-of-Florida was accompanied by a drastic population bottleneck followed by a rapid population expansion. This event was accompanied by male-biased dispersal and/or selective sweeps on the X chromosome. We show that the interaction between linked selection and recombination is the main contributor to the genomic landscape of differentiation in the anole genome.

scholarly journals The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

2019 ◽  
Vol 144 (5) ◽  
pp. 321-328
Author(s):  
Shuang Jiang ◽  
Haishan An ◽  
Xiaoqing Wang ◽  
Chunhui Shi ◽  
Jun Luo ◽  
...  
Keyword(s):  
Population Structure ◽  
Molecular Marker ◽  
Whole Genome ◽  
Marker Assisted Breeding ◽  
Genome Resequencing ◽  
Polymorphic Ssrs ◽  
Ssr Loci ◽  
Whole Genome Resequencing ◽  
Wild Accessions ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in cultivar identification, genetic relationship analysis, and quantitative trait locus mapping. Currently, the selection of hybrid progeny plants in molecular marker-assisted breeding mostly relies on SSR markers because of their ease of operation. In Pyrus, a large number of SSR markers have been developed previously. The method to identify polymorphic SSRs quickly is still lacking in cultivated as well as wild pear species. We present a large number of polymorphic SSRs identified using a quick in silico approach applied across 30 cultivated and wild accessions from Pyrus species. A total of 49,147 SSR loci were identified in Pyrus, and their genotypes were evaluated by whole-genome resequencing data of 30 Pyrus accessions. The results show that most SSR loci were dinucleotide repeat motifs located in intergenic regions. The genotypes of all SSR loci were revealed in all accessions. A total of 23,209 loci were detected, with more than one genotype in all Pyrus accessions. We selected 702 highly polymorphic SSR loci to characterize the pear accessions with an average polymorphism information content value of 0.67, suggesting that these SSR loci were highly polymorphic. The genetic relationship of Pyrus species in the neighbor-joining (NJ) tree and population structure showed a clear division between the oriental and occidental accessions. The population structure split all oriental pears into two groups: cultivars and wild accessions. These new findings of the polymorphic SSR loci in this study are valuable for selecting appropriate markers in molecular marker-assisted breeding in Pyrus.

scholarly journals Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Somatic Mutations ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Genome Resequencing ◽  
Diversity Pattern ◽  
Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

scholarly journals Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 258
Author(s):  
Karim Karimi ◽  
Duy Ngoc Do ◽  
Mehdi Sargolzaei ◽  
Younes Miar
Keyword(s):  
Population Genomics ◽  
Association Studies ◽  
American Mink ◽  
Population History ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Effective Population ◽  
Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

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