scholarly journals Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome

2018 ◽  
Vol 20 (3) ◽  
pp. 423-431 ◽  
Author(s):  
David J. Studholme ◽  
Preeti Panda ◽  
Eugenio Sanfuentes Von Stowasser ◽  
Mariela González ◽  
Rowena Hill ◽  
...  
Keyword(s):  
New Zealand ◽  
Genome Sequencing ◽  
Phytophthora Kernoviae

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 An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

2020 ◽  
Author(s):  
John-Sebastian Eden ◽  
Rebecca Rockett ◽  
Ian Carter ◽  
Hossinur Rahman ◽  
Joep de Ligt ◽  
...  
Keyword(s):  
New Zealand ◽  
Infectious Diseases ◽  
Genome Sequencing ◽  
Phylogenetic Analyses ◽  
Emerging Infectious Diseases ◽  
Whole Genome Sequencing Data ◽  
Viral Diversity ◽  
Whole Genome ◽  
Sequencing Data ◽  
Public Data

AbstractThe SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.

Phytophthora kernoviae. [Distribution map].

2017 ◽  
Author(s):  
Keyword(s):  
New Zealand ◽  
South America ◽  
Geographical Distribution ◽  
Fagus Sylvatica ◽  
Distribution Map ◽  
Annona Cherimola ◽  
Phytophthora Kernoviae ◽  
New Distribution ◽  
Distribution In Europe ◽  
Drimys Winteri

Abstract A new distribution map is provided for Phytophthora kernoviae Beales & S. A. Kirk. Oomycetes: Peronosporales: Peronosporaceae. Hosts: mainly Rhododendron spp. and beech (Fagus sylvatica), but also Annona cherimola, Magnolia spp., Quercus spp. and Drimys winteri. Information is given on the geographical distribution in Europe (Irish Republic, UK, England, Wales and Scotland), South AMerica (Chile) and Oceania (New Zealand).

scholarly journals An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
John-Sebastian Eden ◽  
Rebecca Rockett ◽  
Ian Carter ◽  
Hossinur Rahman ◽  
Joep de Ligt ◽  
...  
Keyword(s):  
New Zealand ◽  
Infectious Diseases ◽  
Genome Sequencing ◽  
Phylogenetic Analyses ◽  
Emerging Infectious Diseases ◽  
Whole Genome Sequencing Data ◽  
Viral Diversity ◽  
Whole Genome ◽  
Sequencing Data ◽  
Public Data

Abstract The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.

scholarly journals Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pippa Scott ◽  
Ji Zhang ◽  
Trevor Anderson ◽  
Patricia C. Priest ◽  
Stephen Chambers ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
New Zealand ◽  
Primary School ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Ad Hoc ◽  
Epidemiological Studies ◽  
Whole Genome ◽  
Typing Method ◽  
Allelic Differences

AbstractEpidemiological studies of communicable diseases increasingly use large whole-genome sequencing (WGS) datasets to explore the transmission of pathogens. It is important to obtain an initial overview of datasets and identify closely related isolates, but this can be challenging with large numbers of isolates and imperfect sequencing. We used an ad hoc whole-genome multi locus sequence typing method to summarise data from a longitudinal study of Staphylococcus aureus in a primary school in New Zealand. Each pair of isolates was compared and the number of genes where alleles differed between isolates was tallied to produce a matrix of “allelic differences”. We plotted histograms of the number of allelic differences between isolates for: all isolate pairs; pairs of isolates from different individuals; and pairs of isolates from the same individual. 340 sequenced isolates were included, and the ad hoc shared genome contained 445 genes. There were between 0 and 420 allelic differences between isolate pairs and the majority of pairs had more than 260 allelic differences. We found many genetically closely related S. aureus isolates from single individuals and a smaller number of closely-related isolates from separate individuals. Multiple S. aureus isolates from the same individual were usually very closely related or identical over the ad hoc shared genome. Siblings carried genetically similar, but not identical isolates. An ad hoc shared genome approach to WGS analysis can accommodate imperfect sequencing of the included isolates, and can provide insights into relationships between isolates in epidemiological studies with large WGS datasets containing diverse isolates.

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