Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming

The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described, but genetic diversity at a global scale within and amongst oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada and compared its sequence with those available from other main taxonomic groups in Quercus. We quantify genomic divergence amongst oaks and performed a sliding window analysis to detect the most variable regions amongst members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs amongst oaks species and sections and stress the need for a large global assessment of genetic diversity in this economically and ecologically important genus.

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Evolution of the U.S. Biological Select AgentRathayibacter toxicus

mBio ◽

10.1128/mbio.01280-18 ◽

2018 ◽

Vol 9 (4) ◽

Cited By ~ 6

Author(s):

Edward W. Davis ◽

Javier F. Tabima ◽

Alexandra J. Weisberg ◽

Lucas Dantas Lopes ◽

Michele S. Wiseman ◽

...

Keyword(s):

Genetic Diversity ◽

Adaptive Immune System ◽

The United States ◽

Genomic Diversity ◽

Data Set ◽

Important Species ◽

Content Type ◽

Low Genetic Diversity ◽

History Of ◽

Short Palindromic Repeat

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.

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Extensive Copy Number Variation in Fermentation-Related Genes amongSaccharomyces cerevisiaeWine Strains

10.1101/105502 ◽

2017 ◽

Author(s):

Jacob Steenwyk ◽

Antonis Rokas

Keyword(s):

Genetic Diversity ◽

Copy Number ◽

Wine Yeast ◽

Gene Families ◽

Genomic Variation ◽

Genomic Diversity ◽

Major Type ◽

Diauxic Shift ◽

Variable Regions ◽

Yeast Strains

AbstractDue to the importance ofSaccharomyces cerevisiaein wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences ofS. cerevisiaewine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ~4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance (CUP), flocculation (FLO), and glucose metabolism (HXT), as well as theSNOgene family whose members are expressed before or during the diauxic shift showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation.

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Phylogeographic Genetic Diversity in the White Sucker Hepatitis B Virus across the Great Lakes Region and Alberta, Canada

Viruses ◽

10.3390/v13020285 ◽

2021 ◽

Vol 13 (2) ◽

pp. 285

Author(s):

Cynthia R. Adams ◽

Vicki S. Blazer ◽

Jim Sherry ◽

Robert Scott Cornman ◽

Luke R. Iwanowicz

Keyword(s):

Genetic Diversity ◽

Hepatitis B Virus ◽

Hepatitis B ◽

Lake Michigan ◽

Illumina Miseq ◽

Genomic Variation ◽

Genomic Diversity ◽

White Sucker ◽

Fish Health ◽

B Virus

Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (Catostomus commersonii), a freshwater teleost, and belongs to the genus Parahepadnavirus. At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Given the relevance of genomic diversity to disease outcome for the orthohepadnaviruses, we sought to characterize genomic variation in WSHBV and determine how it is structured among watersheds. We identified WSHBV-positive white sucker inhabiting tributaries of Lake Michigan, Lake Superior, Lake Erie (USA), and Lake Athabasca (Canada). Copy number in plasma and in liver tissue was estimated via qPCR. Templates from 27 virus-positive fish were amplified and sequenced using a primer-specific, circular long-range amplification method coupled with amplicon sequencing on the Illumina MiSeq. Phylogenetic analysis of the WSHBV genome identified phylogeographical clustering reminiscent of that observed with human hepatitis B virus genotypes. Notably, most non-synonymous substitutions were found to cluster in the pre-S/spacer overlap region, which is relevant for both viral entry and replication. The observed predominance of p1/s3 mutations in this region is indicative of adaptive change in the polymerase open reading frame (ORF), while, at the same time, the surface ORF is under purifying selection. Although the levels of variation we observed do not meet the criteria used to define sub/genotypes of human and avian hepadnaviruses, we identified geographically associated genome variation in the pre-S and spacer domain sufficient to define five WSHBV haplotypes. This study of WSHBV genetic diversity should facilitate the development of molecular markers for future identification of genotypes and provide evidence in future investigations of possible differential disease outcomes.

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Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

Microorganisms ◽

10.3390/microorganisms9081612 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1612

Author(s):

Werner Ruppitsch ◽

Andjela Nisic ◽

Patrick Hyden ◽

Adriana Cabal ◽

Jasmin Sucher ◽

...

Keyword(s):

Genetic Diversity ◽

Safety Evaluation ◽

Gene Clusters ◽

Northern Region ◽

Genomic Diversity ◽

High Genetic Diversity ◽

Pathogenic Factors ◽

Flavor Development ◽

Genomic Characterization

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

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Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.1989 ◽

2019 ◽

Vol 286 (1916) ◽

pp. 20191989 ◽

Cited By ~ 1

Author(s):

M. C. Yates ◽

E. Bowles ◽

D. J. Fraser

Keyword(s):

Genetic Diversity ◽

Body Size ◽

Population Size ◽

Brook Trout ◽

Habitat Degradation ◽

Species Conservation ◽

Empirical Work ◽

Genomic Diversity ◽

Effective Population ◽

Isolated Populations

Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size ( N e ), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had no effect on either fitness correlate, which was determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low N e , and long-term isolation can represent important sources of variation and are capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.

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All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Diversity ◽

10.3390/d13040139 ◽

2021 ◽

Vol 13 (4) ◽

pp. 139

Author(s):

Marlien M. van der Merwe ◽

Jia-Yee S. Yap ◽

Peter D. Wilson ◽

Helen T. Murphy ◽

Andrew Ford

Keyword(s):

Genetic Diversity ◽

Allelic Variation ◽

Germplasm Conservation ◽

Snp Markers ◽

Genomic Diversity ◽

Ex Situ ◽

Spatial Distance ◽

Genetic Connectivity ◽

Conservation Genomics ◽

Modelling Framework

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

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Genetic diversity of small-ruminant lentiviruses: characterization of Norwegian isolates of Caprine arthritis encephalitis virus

Journal of General Virology ◽

10.1099/vir.0.81201-0 ◽

2006 ◽

Vol 87 (3) ◽

pp. 573-580 ◽

Cited By ~ 37

Author(s):

Britt Gjerset ◽

Anne K. Storset ◽

Espen Rimstad

Keyword(s):

Genetic Diversity ◽

Small Ruminant ◽

Genomic Sequence ◽

Sequence Divergence ◽

Encephalitis Virus ◽

Surface Glycoprotein ◽

Group Designation ◽

Variable Regions ◽

Caprine Arthritis Encephalitis Virus ◽

Small Ruminant Lentiviruses

Small-ruminant lentiviruses (SRLVs), including Caprine arthritis encephalitis virus (CAEV) in goats and maedi-visna virus (MVV) in sheep, are lentiviruses that, despite overall similarities, show considerable genetic variation in regions of the SRLV genome. To gain further knowledge about the genetic diversity and phylogenetic relationships among field isolates of SRLVs occurring in geographically distinct areas, the full-length genomic sequence of a CAEV isolate (CAEV-1GA) and partial env sequences obtained from Norwegian CAEV-infected goats were determined. The genome of CAEV-1GA consisted of 8919 bp. Alignment studies indicated significant diversity from published SRLV sequences. Deletions and hypervariability in the 5′ part of the env gene have implications for the size of the proposed CAEV-1GA Rev protein and the encoded surface glycoprotein (SU). The variable regions in the C-terminal part of SU obtained from Norwegian CAEV isolates demonstrate higher sequence divergence than has been described previously for SRLVs. Phylogenetic analysis based on SU sequences gives further support for a unique group designation. The results described here reveal a distant genetic relationship between Norwegian CAEV and other SRLVs and demonstrate that there is more geographical heterogeneity among SRLVs than reported previously.

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Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0009665 ◽

2021 ◽

Vol 15 (8) ◽

pp. e0009665

Author(s):

Shuai Xu ◽

Zhenpeng Li ◽

Yuanming Huang ◽

Lichao Han ◽

Yanlin Che ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Trees ◽

Gene Families ◽

Single Copy ◽

Taxonomic Classification ◽

Genomic Diversity ◽

Evolutionary Relationships ◽

Taxonomic Structure ◽

Pan Genome ◽

Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

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Genomic and demographic processes differentially influence genetic variation across the X chromosome

10.1101/2021.01.31.429027 ◽

2021 ◽

Author(s):

Daniel J. Cotter ◽

Timothy H. Webster ◽

Melissa A. Wilson

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Linkage Disequilibrium ◽

X Chromosome ◽

Global Scale ◽

Careful Consideration ◽

Human Populations ◽

Evolutionary Forces ◽

Ideal System ◽

Demographic Patterns

AbstractMutation, recombination, selection, and demography affect genetic variation across the genome. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. The X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these processes, notably the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. Here we investigate diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. We find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1 and highest on the non-recombining X chromosome, with the XTR falling in between, suggesting that the XTR (usually included in the non-recombining X) may need to be considered separately in future studies. We also observed strong population-specific effects on genetic diversity; not only does genetic variation differ on the X and autosomes among populations, but the effects of linked selection on the X relative to autosomes have been shaped by population-specific history. The substantial variation in patterns of variation across these regions provides insight into the unique evolutionary history contained within the X chromosome.Significance StatementDemography and selection affect the X chromosome differently from non-sex chromosomes. However, the X chromosome can be subdivided into multiple distinct regions that facilitate even more fine-scaled assessment of these processes. Here we study regions of the human X chromosome in 26 populations to find evidence that recombination may be mutagenic in humans and that the X-transposed region may undergo recombination. Further we observe that the effects of selection and demography act differently on the X chromosome relative to the autosomes across human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.

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Oxythermal habitat as a primary driver of ecological niche and genetic diversity in cisco (Coregonus artedi)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2021-0059 ◽

2021 ◽

Author(s):

Ryan C Grow ◽

Kyle D Zimmer ◽

Jennifer L Cruise ◽

Simon K Emms ◽

Loren M Miller ◽

...

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Dissolved Oxygen ◽

Cold Water ◽

Global Scale ◽

Isotopic Niche ◽

Coregonus Artedi ◽

Primary Driver ◽

Water Species ◽

Cold Water Species

Cisco (Coregonus artedi) are threatened by climate change and lake eutrophication, and their oxythermal habitat can be assessed with TDO3, the water temperature at which dissolved oxygen equals 3 mg L-1. We assessed the influence of TDO3 on cisco habitat use, genetic diversity, diets, and isotopic niche in 32 lakes ranging from oligotrophic to eutrophic. Results showed that as TDO3 increased cisco were captured higher in the water column, in a narrower band, with higher minimum temperatures and lower minimum dissolved oxygen. TDO3 was also negatively related to cisco allelic richness and expected heterozygosity, likely driven by summer kill events. Moreover, TDO3 influenced the isotopic niche of cisco, as fish captured deeper were more depleted in δ13C and more enriched in δ15N compared to epilimnetic baselines. Lastly, cisco in high TDO3 lakes consumed more Daphnia, had fewer empty stomachs, and achieved larger body size. Our work identifies specific characteristics of cisco populations that respond to climate change and eutrophication effects, and provides a framework for understanding responses of other cold-water species at the global scale.

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