scholarly journals Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum

2021 ◽  
Author(s):  
Benjamin Dauphin ◽  
Maira de Freitas Pereira ◽  
Annegret Kohler ◽  
Igor Grigoriev ◽  
Kerrie Barry ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Morphological Differentiation ◽  
Nucleotide Polymorphisms ◽  
Cenococcum Geophilum ◽  
Functional Variation ◽  
Symbiotic Fungus ◽  
Genome Variability ◽  
Lineage Differentiation ◽  
Number Variation

Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho-species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability and ecological functioning is poorly known. Here, we analysed 16 European isolates of the ascomycete Cenococcum geophilum, an extremely ubiquitous forest symbiotic fungus with no known sexual or asexual spore forming structures but with a massively enlarged genome. We carried out whole-genome sequencing to identify single-nucleotide polymorphisms. We found no geographic structure at the European scale but divergent lineages within sampling sites. Evidence for recombination was restricted to specific cryptic lineages. Lineage differentiation was supported by extensive copy-number variation. Finally, we confirmed heterothallism with a single MAT1 idiomorph per genome. Synteny analyses of the MAT1 locus revealed substantial rearrangements and a pseudogene of the opposite MAT1 idiomorph. Our study provides the first evidence for substantial genome-wide structural variation, lineage-specific recombination and low continent-wide genetic differentiation in C. geophilum. Our study provides a foundation for targeted analyses of intra-specific functional variation in this major symbiosis.

scholarly journals Cryptic genetic structure and copy‐number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum

2021 ◽  
Author(s):  
Benjamin Dauphin ◽  
Maíra Freitas Pereira ◽  
Annegret Kohler ◽  
Igor V. Grigoriev ◽  
Kerrie Barry ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Copy Number Variation ◽  
Copy Number ◽  
Cenococcum Geophilum ◽  
Symbiotic Fungus ◽  
Number Variation

scholarly journals Population genetics of immune-related multilocus copy number variation in Native Americans

2017 ◽  
Vol 14 (128) ◽  
pp. 20170057 ◽  
Author(s):  
Luciana W. Zuccherato ◽  
Silvana Schneider ◽  
Eduardo Tarazona-Santos ◽  
Robert J. Hardwick ◽  
Douglas E. Berg ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Native American ◽  
Native Americans ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genomic Variation ◽  
Population Subdivision ◽  
Nucleotide Polymorphisms ◽  
Number Variation

While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy–Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f , which quantifies the departure of homozygosity from the Hardy–Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1 , FCGR3A , FCGR3B and FCGR2C ) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.

X-linked inhibitor of apoptosis single nucleotide polymorphisms and copy number variation are not risk factors for asthma

Respirology ◽  
2013 ◽  
Vol 18 (4) ◽  
pp. 697-703 ◽  
Author(s):  
Eugene Roscioli ◽  
Rhys Hamon ◽  
Richard E. Ruffin ◽  
Peter Zalewski ◽  
Janet Grant ◽  
...  
Keyword(s):  
Risk Factors ◽  
Single Nucleotide Polymorphisms ◽  
Copy Number Variation ◽  
Copy Number ◽  
Inhibitor Of Apoptosis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Number Variation

Fungal heavy metal adaptation through single nucleotide polymorphisms and copy‐number variation

2020 ◽  
Vol 29 (21) ◽  
pp. 4157-4169
Author(s):  
Anna L. Bazzicalupo ◽  
Joske Ruytinx ◽  
Yi‐Hong Ke ◽  
Laura Coninx ◽  
Jan V. Colpaert ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Single Nucleotide Polymorphisms ◽  
Copy Number Variation ◽  
Copy Number ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Number Variation

scholarly journals Association Analysis to Copy Number Variation (CNV) of Opn4 Gene with Growth Traits of Goats

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 441
Author(s):  
LiJuan Li ◽  
Peng Yang ◽  
ShuYue Shi ◽  
ZiJing Zhang ◽  
QiaoTing Shi ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Growth Traits ◽  
Molecular Genetic ◽  
Copy Number Variant ◽  
Copy Number Variations ◽  
Individual Growth ◽  
Nucleotide Polymorphisms ◽  
Number Variation ◽  
Normal Copy Number

Extensive research has been carried out regarding the correlation between the growth traits of livestock and genetic polymorphisms, including single nucleotide polymorphisms and copy number variations (CNV). The purpose of this study was to analyze the CNV and its genetic effects of the Opn4 gene in 284 Guizhou goats (Guizhou black goat: n = 186, Guizhou white goat: n = 98). We used qPCR to detect the CNV of the Opn4 gene in Guizhou goats, and the classification results were correlated with the corresponding individual growth traits by SPSS software. The results showed that the Opn4 gene had a superior effect on growth traits with multiple copy variants in Guizhou black goats, and there was a significant correlation between copy number variation sites and body length traits. Contrary to the former conclusion, in Guizhou white goats, individuals with the Normal copy number type showed superior growth traits and copy number variant sites were significantly associated with body weight traits. Therefore, the CNV of the Opn4 gene can be used as a candidate molecular genetic marker to improve goat growth traits, speeding up the breeding process of goat elite varieties.

scholarly journals GSTM1 copy number variation in the context of single nucleotide polymorphisms in the human GSTM cluster

2016 ◽  
Vol 9 (1) ◽  
Author(s):  
Andrey V. Khrunin ◽  
Irina N. Filippova ◽  
Aydar M. Aliev ◽  
Tat’yana V. Tupitsina ◽  
Petr A. Slominsky ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Copy Number Variation ◽  
Copy Number ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Number Variation
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