scholarly journals Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0154722 ◽  
Author(s):  
Polina B. Drozdova ◽  
Oleg V. Tarasov ◽  
Andrew G. Matveenko ◽  
Elina A. Radchenko ◽  
Julia V. Sopova ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Comparative Analysis ◽  
Genome Sequencing

scholarly journals Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

2007 ◽  
Vol 104 (31) ◽  
pp. 12825-12830 ◽  
Author(s):  
W. Wei ◽  
J. H. McCusker ◽  
R. W. Hyman ◽  
T. Jones ◽  
Y. Ning ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Comparative Analysis ◽  
Genome Sequencing

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 Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8251 ◽  
Author(s):  
Zhanjun Wang ◽  
Beibei Xu ◽  
Bao Li ◽  
Qingqing Zhou ◽  
Guiyi Wang ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Comparative Analysis ◽  
Codon Usage ◽  
Plant Species ◽  
Populus Trichocarpa ◽  
Model Organisms ◽  
Mutation Pressure ◽  
Chloroplast Genomes ◽  
Usage Patterns ◽  
Exogenous Expression

Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.

scholarly journals Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

2018 ◽  
Vol 12 (6) ◽  
pp. e0006566 ◽  
Author(s):  
Elizabeth M. Batty ◽  
Suwittra Chaemchuen ◽  
Stuart Blacksell ◽  
Allen L. Richards ◽  
Daniel Paris ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Orientia Tsutsugamushi ◽  
Human Pathogen ◽  
Long Read
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