scholarly journals Requirement of Whole-Genome Sequencing and Background History of the National and International Genome Initiatives

2017 ◽  
pp. 107-115
Author(s):  
Mahendar Thudi ◽  
Rajeev K. Varshney
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
History Of ◽  
Background History

scholarly journals Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Thomas R Connor ◽  
Clare R Barker ◽  
Kate S Baker ◽  
François-Xavier Weill ◽  
Kaisar Ali Talukder ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Low Income ◽  
Shigella Flexneri ◽  
Virulence Gene ◽  
Low Income Countries ◽  
Whole Genome ◽  
Phylogenetic Groups ◽  
Gene Acquisition ◽  
History Of

Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.

scholarly journals Evolutionary history of Tibetans inferred from whole-genome sequencing

PLoS Genetics ◽  
2017 ◽  
Vol 13 (4) ◽  
pp. e1006675 ◽  
Author(s):  
Hao Hu ◽  
Nayia Petousi ◽  
Gustavo Glusman ◽  
Yao Yu ◽  
Ryan Bohlender ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Evolutionary History ◽  
Whole Genome ◽  
History Of

Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7)

2020 ◽  
Vol 142 ◽  
pp. 203-211
Author(s):  
AJ Tighe ◽  
MD Gallagher ◽  
J Carlsson ◽  
I Matejusova ◽  
F Swords ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Whole Genome ◽  
Pancreas Disease ◽  
Codon Positions ◽  
History Of ◽  
Unique Strain ◽  
Salmon Pancreas Disease Virus

Salmon pancreas disease virus, more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain of SAV previously isolated from ballan wrasse was subjected to whole genome sequencing using nanopore sequencing. In order to accurately examine the evolutionary history of this strain in comparison to other SAV strains, a partitioned phylogenetic analysis was performed to account for variation in the rate of evolution for both individual genes and codon positions. Partitioning the genome alignments almost doubled the observed branch lengths in the phylogenetic tree when compared to the more common approach of applying one model of substitution across the genome and significantly increased the statistical fit of the best-fitting models of nucleotide substitution. Based on the genomic data, a valid case can be made for the viral strain examined in this study to be considered a new SAV genotype. In addition, this study adds to a growing number of studies in which SAV has been found to infect non-salmonid fish, and as such we have suggested that the viral species name be amended to the more inclusive ‘piscine alphavirus’.

Investigation of a possible outbreak of NDM-5-producing ST16 Klebsiella pneumoniae among patients in Denmark with no history of recent travel using whole-genome sequencing

2015 ◽  
Vol 3 (3) ◽  
pp. 219-221 ◽  
Author(s):  
Anette M. Hammerum ◽  
Frank Hansen ◽  
Bente Olesen ◽  
Carsten Struve ◽  
Barbara J. Holzknecht ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
History Of

scholarly journals Whole-genome sequencing reveals a deeper history of dynamic biotic complexity along North America's North Pacific Coast

Authorea ◽  
2020 ◽  
Author(s):  
Jocelyn Colella ◽  
Tianying Lan ◽  
Sandra Talbot ◽  
Charlotte Lindqvist ◽  
Joseph Cook
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
North Pacific ◽  
Pacific Coast ◽  
Whole Genome ◽  
History Of

scholarly journals Speciation in sympatry with ongoing secondary gene flow and an olfactory trigger in a radiation of Cameroon cichlids

2017 ◽  
Author(s):  
Jelmer W. Poelstra ◽  
Emilie J. Richards ◽  
Christopher H. Martin
Keyword(s):  
Gene Flow ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Olfactory Receptor ◽  
Sexual Isolation ◽  
Sympatric Speciation ◽  
Whole Genome ◽  
Speciation Event ◽  
History Of ◽  
Olfactory Receptor Genes

AbstractWhether speciation can happen in the absence of geographical barriers and if so, under which conditions, is a fundamental question in our understanding of the evolution of new species. Among candidates for sympatric speciation, Cameroon crater lake cichlid radiations have been considered the most compelling. However, it was recently shown that a more complex scenario than a single colonization followed by isolation underlies these radiations. Here, we perform a detailed investigation of the speciation history of a radiation of Coptodon cichlids from Lake Ejagham using whole-genome sequencing data. The existence of the Lake Ejagham Coptodon radiation is remarkable since this 0.5 km2 lake offers limited scope for divergence across a shallow depth gradient, disruptive selection is weak, the species are sexually monochromatic, yet assortative mating is strong. We infer that Lake Ejagham was colonized by Coptodon cichlids almost as soon as it came into existence 9,000 years ago, yet speciation events occurred only in the last 1,000-2,000 years. We show that secondary gene flow from a nearby riverine species has been ongoing, into ancestral as well as extant Lake Ejagham lineages, and we identify and date river-to-lake admixture blocks. One of these contains a cluster of olfactory receptor genes that introgressed close to the time of the first speciation event and coincides with a higher overall rate of admixture into the recipient lineages. Olfactory signaling is a key component of mate choice and species recognition in cichlids. A functional role for this introgression event is consistent with previous findings that assortative mating appears much stronger than ecological divergence in Ejagham Coptodon. We conclude that speciation in this radiation took place in sympatry, yet may have benefited from ongoing riverine gene flow.Author SummaryDespite an active search for empirical examples and much theoretical work, sympatric speciation remains one of the most controversial ideas in evolutionary biology. While a host of examples have been described in the last few decades, more recent results have shown that several of the most convincing systems have not evolved in complete isolation from allopatric populations after all. By itself, documenting the occurrence of secondary gene flow is not sufficient to reject the hypothesis of sympatric speciation, since speciation can still be considered sympatric if gene flow did not contribute significantly to the build-up of reproductive isolation. One way forward is to use genomic data to infer where, when and into which lineages gene flow occurred, and identify the regions of the genome that experienced admixture. In this study, we use whole-genome sequencing to examine one of the cichlid radiations from a small isolated Cameroon lake, which have long been the flagship example of sympatric speciation. We show that gene flow from a riverine species into the lake has been ongoing during the history of the radiation. In line with this, we infer that the lake was colonized very soon after it was formed, and argue that Lake Ejagham is not as isolated as previously assumed. The magnitude of secondary gene flow was relatively even across Lake Ejagham lineages, yet with some evidence for differential admixture, most notably before the first speciation event into the C. deckerti and C. ejagham lineage. Among the sequences that were introgressed into this lineage is a cluster of olfactory receptor genes, which may have facilitated speciation by promoting sexual isolation between incipient species, consistent with previous findings that sexual isolation appears to be stronger than ecological isolation in Ejagham Coptodon. We conclude that speciation in this radiation took place in sympatry, yet may have benefited from ongoing riverine gene flow.

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