Comparative population genomics confirms little population structure in two commercially targeted carcharhinid sharks

The genomics era has ushered in exciting possibilities to examine the genetic bases that undergird the characteristic features of Verticillium dahliae and other plant pathogens. In this review, we provide historical perspectives on some of the salient biological characteristics of V. dahliae, including its morphology, microsclerotia formation, host range, disease symptoms, vascular niche, reproduction, and population structure. The kaleidoscopic population structure of this pathogen is summarized, including different races of the pathogen, defoliating and nondefoliating phenotypes, vegetative compatibility groupings, and clonal populations. Where possible, we place the characteristic differences in the context of comparative and functional genomics analyses that have offered insights into population divergence within V. dahliae and the related species. Current challenges are highlighted along with some suggested future population genomics studies that will contribute to advancing our understanding of the population divergence in V. dahliae. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Genome-wide characterization of genetic diversity and population structure of Valeriana officinalis L.

10.21203/rs.2.10069/v1 ◽

2019 ◽

Author(s):

Maja Boczkowska ◽

Katarzyna Bączek ◽

Olga Kosakowska ◽

Anna Rucińska ◽

Wiesław Podyma ◽

...

Keyword(s):

Population Structure ◽

Population Genomics ◽

Natural Populations ◽

Valeriana Officinalis ◽

Wild Populations ◽

Genetic Fingerprint ◽

Genome Wide ◽

Species Population ◽

Outcrossing Species

Abstract Background: Valeriana officinalis L. is one of the most important medicinal plant with a mild sedative, nervine, antispasmodic and relaxant effect. Despite a substantial number of studies on this species, population genomics has not yet been analyzed. The main aim of this study was: characterization of genetic variation of natural populations of V. officinalis in Poland and comparison of variation of wild populations and the cultivated form using Next Generation Sequencing based DArTseq technique. We also would like to establish foundations for genetic monitoring of the species in the future and to develop genetic fingerprint profile for samples deposited in gene bank and in natural sites in order to assess the degree of their genetic integrity and population structure preservation in the future.Results: The major and also the most astounding result of our work is the low level of observed heterozygosity of individual plants from natural populations despite the fact that the species is widespread in the studied area. Inbreeding, in naturally outcrossing species such as valerian, decreases the reproductive success. The analysis of the population structure indicated the potential presence of metapopulation in a broad area of Poland and the formation of a distinct gene pool in Bieszczady Mountains. The results also indicate the presence of individuals of the cultivated form in natural populations in the region where the species is cultivated for the needs of the pharmaceutical industry and this could lead to structural and genetic imbalance in wild populations.Conclusions: The DArTseq technology can be applied effectively in genetic studies of V. officinalis. The genetic variability of wild populations is in fact significantly lower than assumed. Individuals from the cultivated population are found in the natural environment and their impact on wild populations should be monitored.

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Little hope for the polyploid endemic Pyrenean Larkspur (Delphinium montanum): evidences from population genomics and Ecological Niche Modelling

10.1101/2021.09.15.460086 ◽

2021 ◽

Author(s):

Pascaline Salvado ◽

Pere Aymerich Boixader ◽

Josep Parera ◽

Albert Vila Bonfill ◽

Maria Martin ◽

...

Keyword(s):

Population Structure ◽

Ecological Niche ◽

Population Genomics ◽

Diploid Species ◽

Ecological Niche Modelling ◽

High Mountain ◽

Suitable Habitat ◽

Sky Islands ◽

Niche Modelling ◽

Ecological Requirements

Species endemic to restricted geographical ranges represent a particular conservation issue, be it for their heritage interest. In a context of global change, this is particularly the case for plants which belong to high-mountain ecosystems and, because of their ecological requirements, are doomed to survive or disappear on their "sky islands". The Pyrenean Larkspur (Delphinium montanum, Ranunculaceae) is endemic to the Eastern part of the Pyrenees (France and Spain). It is now only observable at a dozen of localities and some populations show signs of decline, such as a recurrent lack of flowering. Implementing population genomic approach (e.g. RAD-seq like) is particularly useful to understand genomic patterns of diversity and differentiation in order to provide recommendations in term of conservation. However, it remains challenging for species such as D. montanum that are autotetraploid with a large genome size (1C-value > 10 pg) as most methods currently available were developed for diploid species. A Bayesian framework able to call genotypes with uncertainty allowed us to assess genetic diversity and population structure in this system. Our results show evidence for inbreeding (mean GIS = 0.361) within all the populations and substantial population structure (mean GST = 0.403) at the metapopulation level. In addition to a lack of connectivity between populations, spatial projections of Ecological Niche Modelling analyses under different climatic scenarios predict a dramatic decrease of suitable habitat for D. montanum in the future. Based on these results, we discuss the relevance and feasibility of different conservation measures.

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Comparative population structure of two edible Indo-Pacific coral reef sea cucumbers (Echinodermata: Holothuroidea)

Bulletin of Marine Science ◽

10.5343/bms.2013.1001 ◽

2014 ◽

Vol 90 (1) ◽

pp. 359-378 ◽

Cited By ~ 4

Author(s):

Derek J Skillings ◽

Christopher E Bird ◽

Robert J Toonen

Keyword(s):

Population Structure ◽

Coral Reef ◽

Sea Cucumbers ◽

Comparative Population

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Geography Shapes the Population Genomics of Salmonella enterica Dublin

Genome Biology and Evolution ◽

10.1093/gbe/evz158 ◽

2019 ◽

Vol 11 (8) ◽

pp. 2220-2231 ◽

Cited By ~ 3

Author(s):

Gavin J Fenske ◽

Anil Thachil ◽

Patrick L McDonough ◽

Amy Glaser ◽

Joy Scaria

Keyword(s):

Population Structure ◽

Salmonella Enterica ◽

Core Genome ◽

Population Genomics ◽

Negative Impact ◽

Antibiotic Resistance Genes ◽

Virulence Plasmid ◽

Ancestral State ◽

Secretion Systems ◽

Data Set

Abstract Salmonella enterica serotype Dublin (S. Dublin) is a bovine-adapted serotype that can cause serious systemic infections in humans. Despite the increasing prevalence of human infections and the negative impact on agricultural processes, little is known about the population structure of the serotype. To this end, we compiled a manually curated data set comprising of 880 S. Dublin genomes. Core genome phylogeny and ancestral state reconstruction revealed that region-specific clades dominate the global population structure of S. Dublin. Strains of S. Dublin in the UK are genomically distinct from US, Brazilian, and African strains. The geographical partitioning impacts the composition of the core genome as well as the ancillary genome. Antibiotic resistance genes are almost exclusively found in US genomes and are mediated by an IncA/C2 plasmid. Phage content and the S. Dublin virulence plasmid were strongly conserved in the serotype. Comparison of S. Dublin to a closely related serotype, S. enterica serotype Enteritidis, revealed that S. Dublin contains 82 serotype specific genes that are not found in S. Enteritidis. Said genes encode metabolic functions involved in the uptake and catabolism of carbohydrates and virulence genes associated with type VI secretion systems and fimbria assembly respectively.

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