Temporal diversification and no geographic population structure in the most abundant European ectomycorrhizal fungus Russula ochroleuca

2021 ◽  
Vol 51 ◽  
pp. 101061
Author(s):  
Petra Veselá ◽  
Martina Vašutová ◽  
Daniel Volařík ◽  
Pavel Cudlín
Keyword(s):  
Population Structure ◽  
Ectomycorrhizal Fungus ◽  
Geographic Population

scholarly journals A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Eugenie C Yen ◽  
Shane A McCarthy ◽  
Juan A Galarza ◽  
Tomas N Generalovic ◽  
Sarah Pelan ◽  
...  
Keyword(s):  
Population Structure ◽  
Genome Assembly ◽  
De Novo ◽  
Consensus Sequence ◽  
Parental Origin ◽  
De Novo Genome Assembly ◽  
Geographic Population ◽  
Long Reads ◽  
Tiger Moth ◽  
Innovative Solution

ABSTRACT Background Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. Findings We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. Conclusions We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.

Genetic Diversity and Population Structure of Phyllosticta citriasiana in China

2020 ◽  
Author(s):  
Yibing Zeng ◽  
Tao Xiong ◽  
Bei Liu ◽  
Elma Carstens ◽  
Xiangling Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Mating Type ◽  
Tan Spot ◽  
Long Distance ◽  
High Genetic Diversity ◽  
Geographic Population ◽  
Sexual And Asexual Reproduction ◽  
Geographic Populations ◽  
Genetic Clusters

Phyllosticta citriasiana is the causal agent of citrus tan spot, an important pomelo disease in Asia. At present, there is little or no information on the epidemiology or population structure of P. citriasiana. Using simple sequence repeat (SSR) markers, 94 isolates obtained from three pomelo production regions in southern/southeastern China were analyzed. The analyses showed high genetic diversity in each of the three geographic populations. A STRUCTURE analysis revealed two genetic clusters among the 94 isolates, one geographic population was dominated by genotypes in one cluster while the other two geographic populations were dominated by genotypes of the second cluster. P. citriasiana has a heterothallic mating system with two idiomorphs, MAT1-1 and MAT1-2. Analyses using mating type-specific primers revealed that both mating types were present in all three geographic populations, and in all three populations the mating type ratios were in equilibrium. Although the sexual stage of the fungus has not been discovered yet, analyses of allelic associations indicated evidence for sexual and asexual reproduction within and among populations. Despite the observed genetic differentiation among the three geographic populations, evidence for long-distance gene flow was found.

Multilocus sequence typing using mitochondrial genes (mtMLST) reveals geographic population structure of Ixodes ricinus ticks

2014 ◽  
Vol 5 (2) ◽  
pp. 152-160 ◽  
Author(s):  
Ruth E. Dinnis ◽  
Frederik Seelig ◽  
Antra Bormane ◽  
Michael Donaghy ◽  
Stephanie A. Vollmer ◽  
...  
Keyword(s):  
Population Structure ◽  
Ixodes Ricinus ◽  
Multilocus Sequence Typing ◽  
Mitochondrial Genes ◽  
Geographic Population ◽  
Ixodes Ricinus Ticks

scholarly journals Geographic population structure analysis of worldwide human populations infers their biogeographical origins

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Eran Elhaik ◽  
◽  
Tatiana Tatarinova ◽  
Dmitri Chebotarev ◽  
Ignazio S. Piras ◽  
...  
Keyword(s):  
Population Structure ◽  
Structure Analysis ◽  
Human Populations ◽  
Geographic Population ◽  
Population Structure Analysis

scholarly journals Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009269
Author(s):  
Gerry Tonkin-Hill ◽  
Shazia Ruybal-Pesántez ◽  
Kathryn E. Tiedje ◽  
Virginie Rougeron ◽  
Michael F. Duffy ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Population Structure ◽  
Surface Antigen ◽  
Local Population ◽  
Biological Significance ◽  
Public Health Problem ◽  
Major Public Health Problem ◽  
Malaria Surveillance ◽  
Geographic Population ◽  
Variant Surface Antigen

Malaria remains a major public health problem in many countries. Unlike influenza and HIV, where diversity in immunodominant surface antigens is understood geographically to inform disease surveillance, relatively little is known about the global population structure of PfEMP1, the major variant surface antigen of the malaria parasite Plasmodium falciparum. The complexity of the var multigene family that encodes PfEMP1 and that diversifies by recombination, has so far precluded its use in malaria surveillance. Recent studies have demonstrated that cost-effective deep sequencing of the region of var genes encoding the PfEMP1 DBLα domain and subsequent classification of within host sequences at 96% identity to define unique DBLα types, can reveal structure and strain dynamics within countries. However, to date there has not been a comprehensive comparison of these DBLα types between countries. By leveraging a bioinformatic approach (jumping hidden Markov model) designed specifically for the analysis of recombination within var genes and applying it to a dataset of DBLα types from 10 countries, we are able to describe population structure of DBLα types at the global scale. The sensitivity of the approach allows for the comparison of the global dataset to ape samples of Plasmodium Laverania species. Our analyses show that the evolution of the parasite population emerging out of Africa underlies current patterns of DBLα type diversity. Most importantly, we can distinguish geographic population structure within Africa between Gabon and Ghana in West Africa and Uganda in East Africa. Our evolutionary findings have translational implications in the context of globalization. Firstly, DBLα type diversity can provide a simple diagnostic framework for geographic surveillance of the rapidly evolving transmission dynamics of P. falciparum. It can also inform efforts to understand the presence or absence of global, regional and local population immunity to major surface antigen variants. Additionally, we identify a number of highly conserved DBLα types that are present globally that may be of biological significance and warrant further characterization.

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