scholarly journals Two-speed genome expansion drives the evolution of pathogenicity in animal fungal pathogens

2021 ◽  
Author(s):  
Theresa Wacker ◽  
Nicolas Helmstetter ◽  
Duncan Wilson ◽  
Matthew C Fisher ◽  
David John Studholme ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Fungal Pathogens ◽  
Batrachochytrium Dendrobatidis ◽  
Gene Copy Number ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Batrachochytrium Salamandrivorans ◽  
Conserved Genes ◽  
Genome Assemblies ◽  
High Quality Genome

The origins of virulence in amphibian-infecting chytrids Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are largely unknown. Here, we use deep nanopore sequencing of Bsal and comparative genomics against 21 high quality genome assemblies that span the fungal Chytridiomycota. Bsal has the most repeat-rich genome, comprising 40.9% repetitive elements, which has expanded to more than 3X the length of its conspecific Bd. M36 metalloprotease virulence factors are highly expanded in Bsal and 53% of the 177 unique genes are flanked by transposable elements, suggesting a repeat-driven expansion. Genes of the largest M36 sub-family of are mostly (84%) flanked upstream by a novel LINE element, a repeat superfamily implicated with gene copy number variations. We find that Bsal has a highly compartmentalized genome architecture, with these virulence factors enriched in gene-sparse/repeat-rich genome compartments, while core conserved genes occur in gene-rich/repeat-poor compartments; this is a hallmark of two-speed genome evolution. Furthermore, genes with signatures of positive selection in Bd are enriched in repeat-rich regions, suggesting they are a cradle for the evolution of chytrid pathogenicity, and also has a two-speed genome. This is the first evidence of two-speed genomes in any animal pathogen, and sheds new light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.

scholarly journals Genomic Instability in Fungal Plant Pathogens

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 421 ◽  
Author(s):  
Shay Covo
Keyword(s):  
Chromosomal Aberrations ◽  
Plant Pathogens ◽  
Gene Copy Number ◽  
Copy Number Variations ◽  
Plant Diseases ◽  
Gene Copy ◽  
Modern Agriculture ◽  
Fungal Plant Pathogens ◽  
Conserved Genes ◽  
Dna Replication Stress

Fungi and fungal-like organisms (oomycetes) that cause diseases in plants have impacted human communities for centuries and probably from the dawn of agriculture. In modern agriculture, there is a constant race between new strategies to manage fungal plant pathogens and their ability to adapt. An important component in this race is fungal genetic diversity. Mechanisms such as sexual and parasexual recombination that contribute to the creation of novel allele combinations in fungal plant pathogens are briefly discussed in the first part of this review. Advances in genomics have enabled the investigation of chromosomal aberrations of agriculturally important fungal isolates at the nucleotide level. Some of these cases are summarized in the second part of this review; it is claimed that the effect of chromosomal aberrations on pathogenicity should be studied mechanistically. More data on the effect of gene copy number variations on phenotypes that are relevant to agriculture are especially needed. Genome rearrangements through translocations have shaped the genome of fungal plant pathogens by creating lineage-specific chromosome territories encoding for genes participating in plant diseases. Pathogenicity chromosomes are unique cases of such lineage-specific genetic elements, interestingly these chromosomes can be transferred horizontally and thus transforming a non-pathogenic strain to a pathogenic one. The third part of this review describes our attempts to reveal mutators in fungal plant pathogens by identifying fungi that lack important DNA repair genes or respond to DNA damage in an unconventional way. We found that a group of fungal plant pathogens lack conserved genes that are needed for an important Holliday junction resolution pathway. In addition, in Fusarium oxysporum, the rate-limiting step in dNTP production is not induced under DNA replication stress. This is very different from organisms from bacteria to humans. It remains to be seen if these mechanisms promote genetic instability in fungal plant pathogens.

Abstract 3098: ERCC1 gene copy number variations in resected non-small cell lung cancer

2012 ◽  
Author(s):  
Luc Friboulet ◽  
Ken A. Olaussen ◽  
Alexander Valent ◽  
Ximing Tang ◽  
Tao Tang ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Copy Number ◽  
Gene Copy Number ◽  
Copy Number Variations ◽  
Small Cell ◽  
Gene Copy ◽  
Small Cell Lung

scholarly journals Impact of Endogenous Intronic Retroviruses on Major Histocompatibility Complex Class II Diversity and Stability

2008 ◽  
Vol 82 (13) ◽  
pp. 6667-6677 ◽  
Author(s):  
Gaby G. M. Doxiadis ◽  
Nanine de Groot ◽  
Ronald E. Bontrop
Keyword(s):  
Major Histocompatibility Complex ◽  
Rhesus Macaques ◽  
Gene Copy Number ◽  
Population Level ◽  
Endogenous Retrovirus ◽  
Copy Number Variations ◽  
Primate Species ◽  
Gene Copy ◽  
Major Histocompatibility ◽  
Histocompatibility Complex

ABSTRACT The major histocompatibility complex (MHC) represents a multigene family that is known to display allelic and gene copy number variations. Primate species such as humans, chimpanzees (Pan troglodytes), and rhesus macaques (Macaca mulatta) show DRB region configuration polymorphism at the population level, meaning that the number and content of DRB loci may vary per haplotype. Introns of primate DRB alleles differ significantly in length due to insertions of transposable elements as long endogenous retrovirus (ERV) and human ERV (HERV) sequences in the DRB2, DRB6, and DRB7 pseudogenes. Although the integration of intronic HERVs resulted sooner or later in the inactivation of the targeted genes, the fixation of these endogenous retroviral segments over long time spans seems to have provided evolutionary advantage. Intronic HERVs may have integrated in a sense or an antisense manner. On the one hand, antisense-oriented retroelements such as HERV-K14I, observed in intron 2 of the DRB7 genes in humans and chimpanzees, seem to promote stability, as configurations/alleles containing these hits have experienced strong conservative selection during primate evolution. On the other hand, the HERVK3I present in intron 1 of all DRB2 and/or DRB6 alleles tested so far integrated in a sense orientation. The data suggest that multigenic regions in particular may benefit from sense introgressions by HERVs, as these elements seem to promote and maintain the generation of diversity, whereas these types of integrations may be lethal in monogenic systems, since they are known to influence transcript regulation negatively.

Associations of MYH3 gene copy number variations with transcriptional expression and growth traits in Chinese cattle

Gene ◽  
2014 ◽  
Vol 535 (2) ◽  
pp. 106-111 ◽  
Author(s):  
Yao Xu ◽  
Tao Shi ◽  
Hanfang Cai ◽  
Yang Zhou ◽  
Xianyong Lan ◽  
...  
Keyword(s):  
Copy Number ◽  
Growth Traits ◽  
Gene Copy Number ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Transcriptional Expression ◽  
Chinese Cattle ◽  
Myh3 Gene
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