scholarly journals Corrigendum to: Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2021 ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Whole Genome

scholarly journals Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Copy Number ◽  
Small Scale ◽  
Whole Genome ◽  
Copy Number Changes ◽  
The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

scholarly journals Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Joseph Crispell ◽  
Ruth N. Zadoks ◽  
Simon R. Harris ◽  
Brent Paterson ◽  
Desmond M. Collins ◽  
...  
Keyword(s):  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bovine Tuberculosis ◽  
Whole Genome ◽  
Host System

scholarly journals Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand

2018 ◽  
Vol 5 ◽  
Author(s):  
Marian Price-Carter ◽  
Rudiger Brauning ◽  
Geoffrey W. de Lisle ◽  
Paul Livingstone ◽  
Mark Neill ◽  
...  
Keyword(s):  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Mycobacterium Bovis ◽  
Whole Genome

scholarly journals Whole-Genome Sequencing ofSalmonellaMississippi and Typhimurium Definitive Type 160, Australia and New Zealand

2019 ◽  
Vol 25 (9) ◽  
pp. 1690-1697
Author(s):  
Laura Ford ◽  
Danielle Ingle ◽  
Kathryn Glass ◽  
Mark Veitch ◽  
Deborah A. Williamson ◽  
...  
Keyword(s):  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome

scholarly journals MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations

2020 ◽  
Vol 10 (9) ◽  
pp. 3009-3014 ◽  
Author(s):  
Mitchell A Ellison ◽  
Jennifer L Walker ◽  
Patrick J Ropp ◽  
Jacob D Durrant ◽  
Karen M Arndt
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Sequence Alignments ◽  
Causal Variants ◽  
User Friendly ◽  
Analyze Data

Abstract MutantHuntWGS is a user-friendly pipeline for analyzing Saccharomyces cerevisiae whole-genome sequencing data. It uses available open-source programs to: (1) perform sequence alignments for paired and single-end reads, (2) call variants, and (3) predict variant effect and severity. MutantHuntWGS outputs a shortlist of variants while also enabling access to all intermediate files. To demonstrate its utility, we use MutantHuntWGS to assess multiple published datasets; in all cases, it detects the same causal variants reported in the literature. To encourage broad adoption and promote reproducibility, we distribute a containerized version of the MutantHuntWGS pipeline that allows users to install and analyze data with only two commands. The MutantHuntWGS software and documentation can be downloaded free of charge from https://github.com/mae92/MutantHuntWGS.

Introgression v1

2021 ◽  
Author(s):  
Graham Etherington
Keyword(s):  
Great Britain ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Legal Protection ◽  
Population Level ◽  
Population Increase ◽  
Whole Genome ◽  
Mustela Putorius ◽  
Mammalian Predator

The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as ‘pure’ polecats.

scholarly journals Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 475 ◽  
Author(s):  
Ji Qi ◽  
Asela J Wijeratne ◽  
Lynn P Tomsho ◽  
Yi Hu ◽  
Stephan C Schuster ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Whole Genome Sequencing ◽  
Gene Conversion ◽  
Genome Sequencing ◽  
Whole Genome
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