scholarly journals Population genomics reveal distinct and diverging populations of An. minimus in Cambodia - a widespread malaria vector in Southeast Asia

2021 ◽  
Author(s):  
Brandyce St. Laurent ◽  
Nick Harding ◽  
Nick Deason ◽  
Kolthida Oy ◽  
Chea Sok Loeun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southeast Asia ◽  
Genome Sequencing ◽  
Malaria Vector ◽  
Population Genomics ◽  
Sequence Data ◽  
Malaria Vectors ◽  
Open Access Resource ◽  
Two Populations ◽  
Access Resource

Anopheles minimus is an important malaria vector throughout its wide geographic range across Southeast Asia. Genome sequencing could provide important insights into the unique malaria transmission dynamics in this region, where many vector species feed and rest outdoors. We describe results from a study using Illumina deep whole-genome sequencing of 302 wild-caught An. minimus collected from three Cambodian provinces over several years (2010, 2014-2016) and seasons to examine the level of population structure and genetic diversity within this species. These specimens cluster into four distinct populations of An. minimus s.s., with two populations overlapping geographically. We describe the underlying genetic diversity and divergence of these populations and investigated the genetic variation in genes known to be involved in insecticide resistance. We found strong signals of selection within these An. minimus populations, most of which were present in the two Northeastern Cambodian populations and differ from those previously described in African malaria vectors. Cambodia is the focus of the emergence and spread of drug-resistant malaria parasites, so understanding the underlying genetic diversity and resilience of the vectors of these parasites is key to implementing effective malaria control and elimination strategies. These data are publicly available as part of the MalariaGEN Vector Observatory, an open access resource of genome sequence data.

scholarly journals Population genomics of East Asian ethnic groups

Hereditas ◽  
2020 ◽  
Vol 157 (1) ◽  
Author(s):  
Ziqing Pan ◽  
Shuhua Xu
Keyword(s):  
Genetic Diversity ◽  
East Asia ◽  
Ethnic Groups ◽  
Population Genomics ◽  
Sequence Data ◽  
East Asian ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Evolutionary Forces ◽  
Asian Populations

AbstractEast Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.

scholarly journals The population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen

2020 ◽  
Author(s):  
Danilo Pereira ◽  
Ursula Oggenfuss ◽  
Bruce A. McDonald ◽  
Daniel Croll
Keyword(s):  
Genetic Diversity ◽  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Sequence Data ◽  
Demographic History ◽  
Purifying Selection ◽  
Population Level ◽  
Wide Range ◽  
Genome Analyses

AbstractThe activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point (RIP) mutations is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIP mutations is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyze 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.Data SummaryAll Illumina sequence data is available from the NCBI SRA BioProject numbers PRJNA606320, PRJNA398070 and PRJNA476481 (https://www.ncbi.nlm.nih.gov/bioproject). The Methods and Supplementary Figures S1-S11 and Supplementary Tables S1-S4 provide all information on strain locations and outcomes of genome analyses.

scholarly journals Extensive genetic diversity among populations of the malaria mosquito Anopheles moucheti revealed by population genomics

2016 ◽  
Author(s):  
Caroline Fouet ◽  
Colince Kamdem ◽  
Stephanie Gamez ◽  
Bradley J. White
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Large Scale ◽  
Environmental Changes ◽  
Population Genomics ◽  
Demographic History ◽  
Control Measures ◽  
Malaria Vectors ◽  
African Countries ◽  
Population Size Estimates

AbstractMalaria vectors are exposed to intense selective pressures due to large-scale intervention programs that are underway in most African countries. One of the current priorities is therefore to clearly assess the adaptive potential of Anopheline populations, which is critical to understand and anticipate the response mosquitoes can elicit against such adaptive challenges. The development of genomic resources that will empower robust examinations of evolutionary changes in all vectors including currently understudied species is an inevitable step toward this goal. Here we constructed double-digest Restriction Associated DNA (ddRAD) libraries and generated 6461 Single Nucleotide Polymorphisms (SNPs) that we used to explore the population structure and demographic history of wild-caught Anopheles moucheti from Cameroon. The genome-wide distribution of allelic frequencies among samples best fitted that of an old population at equilibrium, characterized by a weak genetic structure and extensive genetic diversity, presumably due to a large long term effective population size. Estimates of FST and Linkage Disequilibrium (LD) across SNPs reveal a very low genetic differentiation throughout the genome and the absence of segregating LD blocks among populations, suggesting an overall lack of local adaptation. Our study provides the first investigation of the genetic structure and diversity in An. moucheti at the genomic scale. We conclude that, despite a weak genetic structure, this species has the potential to challenge current vector control measures and other rapid anthropogenic and environmental changes thanks to its great genetic diversity.

Allozyme Variation and Population Substructuring in the Caucasian Ground Lizards Lacerta derjugini and Lacerta praticola

2011 ◽  
Vol 4 (2) ◽  
pp. 115-119 ◽  
Author(s):  
Ross D. MacCulloch ◽  
Ilya S. Darevsky ◽  
Robert W. Murphy ◽  
Jinzhong Fu
Keyword(s):  
Genetic Diversity ◽  
Allozyme Variation ◽  
Close Proximity ◽  
Geographic Separation ◽  
Population Substructuring ◽  
Allozyme Loci ◽  
Two Populations

Genetic diversity at 35 allozyme loci was surveyed in Lacerta derjugini (3 populations) and L. praticola (2 populations). Indices of variability were consistent with those found in other Caucasian Lacerta. There was little genetic substructuring between two populations of L. praticola despite considerable geographic separation. Conversely, populations of L. derjugini in close proximity to one another exhibited considerable substructuring.

scholarly journals Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

2021 ◽  
Author(s):  
Zhilin Yuan ◽  
Irina S. Druzhinina ◽  
John G. Gibbons ◽  
Zhenhui Zhong ◽  
Yves Van de Peer ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Genomic Island ◽  
Population Genomics ◽  
Growth Yield ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Mechanisms ◽  
Melanin Biosynthesis ◽  
Two Populations

AbstractUnderstanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila–S. salsa symbiosis.

scholarly journals nPhase: an accurate and contiguous phasing method for polyploids

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Omar Abou Saada ◽  
Andreas Tsouris ◽  
Chris Eberlein ◽  
Anne Friedrich ◽  
Joseph Schacherer
Keyword(s):  
Genome Sequencing ◽  
Population Genomics ◽  
Short Reads ◽  
Link Type ◽  
Long Reads

AbstractWhile genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy (https://github.com/OmarOakheart/nPhase). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids.

Genetic diversity of Amomum xanthioides and its related species from Southeast Asia and China

2021 ◽  
Author(s):  
Mikako Sone ◽  
Shu Zhu ◽  
Xiao Cheng ◽  
Sounthone Ketphanh ◽  
Swe Swe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southeast Asia ◽  
Related Species

scholarly journals Malaria vector species composition and entomological indices following indoor residual spraying in regions bordering Lake Victoria, Tanzania

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Charles Kakilla ◽  
Alphaxard Manjurano ◽  
Karen Nelwin ◽  
Jackline Martin ◽  
Fabian Mashauri ◽  
...  
Keyword(s):  
Species Composition ◽  
Vector Control ◽  
Malaria Vector ◽  
Lake Victoria ◽  
Indoor Residual Spraying ◽  
Transmission Risk ◽  
Malaria Vectors ◽  
Vector Species ◽  
Sporozoite Rate ◽  
Pirimiphos Methyl

Abstract Background Vector control through long-lasting insecticidal nets (LLINs) and focal indoor residual spraying (IRS) is a major component of the Tanzania national malaria control strategy. In mainland Tanzania, IRS has been conducted annually around Lake Victoria basin since 2007. Due to pyrethroid resistance in malaria vectors, use of pyrethroids for IRS was phased out and from 2014 to 2017 pirimiphos-methyl (Actellic® 300CS) was sprayed in regions of Kagera, Geita, Mwanza, and Mara. Entomological surveillance was conducted in 10 sprayed and 4 unsprayed sites to determine the impact of IRS on entomological indices related to malaria transmission risk. Methods WHO cone bioassays were conducted monthly on interior house walls to determine residual efficacy of pirimiphos-methyl CS. Indoor CDC light traps with or without bottle rotator were hung next to protected sleepers indoors and also set outdoors (unbaited) as a proxy measure for indoor and outdoor biting rate and time of biting. Prokopack aspirators were used indoors to capture resting malaria vectors. A sub-sample of Anopheles was tested by PCR to determine species identity and ELISA for sporozoite rate. Results Annual IRS with Actellic® 300CS from 2015 to 2017 was effective on sprayed walls for a mean of 7 months in cone bioassay. PCR of 2016 and 2017 samples showed vector populations were predominantly Anopheles arabiensis (58.1%, n = 4,403 IRS sites, 58%, n = 2,441 unsprayed sites). There was a greater proportion of Anopheles funestus sensu stricto in unsprayed sites (20.4%, n = 858) than in sprayed sites (7.9%, n = 595) and fewer Anopheles parensis (2%, n = 85 unsprayed, 7.8%, n = 591 sprayed). Biting peaks of Anopheles gambiae sensu lato (s.l.) followed periods of rainfall occurring between October and April, but were generally lower in sprayed sites than unsprayed. In most sprayed sites, An. gambiae s.l. indoor densities increased between January and February, i.e., 10–12 months after IRS. The predominant species An. arabiensis had a sporozoite rate in 2017 of 2.0% (95% CI 1.4–2.9) in unsprayed sites compared to 0.8% (95% CI 0.5–1.3) in sprayed sites (p = 0.003). Sporozoite rates were also lower for An. funestus collected in sprayed sites. Conclusion This study contributes to the understanding of malaria vector species composition, behaviour and transmission risk following IRS around Lake Victoria and can be used to guide malaria vector control strategies in Tanzania.

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