Author Correction: Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

Abstract Objectives Pistacia genus belongs to the flowering plants in the cashew family and contains at least 11 species. The whole-genome resequencing data of different species from Pistacia genus are described herein. The data reported here will be useful for better understand the adaptive evolution, demographic history, genetic diversity, population structure, and domestication of pistachio. Data description Genomic DNA was isolated from fresh leaves and used to construct libraries with insert size of 350 bp. Sequence libraries were made and sequenced on the Illumina Hiseq 4000 platform to produce 150 bp paired-end reads. A total number of 4,851,118,730 billion reads (ranging from 33,305,900 to 34,990,618 reads per sample) were created across all samples. We produced a total of 727.67 Gbp data which have been deposited in the Genome Sequence Archive (GSA) database with the Accession of CRA000978. All of the data are also available as the sequence read archive (SRA) format in the National Center for Biotechnology Information (NCBI) with identifier of SRP189222, mirroring our deposited data in GSA.

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

10.22541/au.164190604.45542461/v1 ◽

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.

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Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing

Tropical Animal Health and Production ◽

10.1007/s11250-021-02605-6 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Lei-Lei Li ◽

Shi-Ke Ma ◽

Wei Peng ◽

You-Gui Fang ◽

Hai-Rui Duo ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Whole Genome ◽

Genome Resequencing ◽

Sheep Breeds ◽

Tibetan Sheep ◽

Whole Genome Resequencing

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

Scientific Reports ◽

10.1038/s41598-021-87445-y ◽

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.

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