scholarly journals Gene conversion facilitates the adaptive evolution of self-resistance in highly toxic newts

2021 ◽  
Author(s):  
Kerry L Gendreau ◽  
Angela D Hornsby ◽  
Michael TJ Hague ◽  
Joel W McGlothlin
Keyword(s):  
Gene Conversion ◽  
Gene Families ◽  
Nonsynonymous Substitution ◽  
Extreme Resistance ◽  
Antipredator Defense ◽  
Exon Duplication ◽  
Nonsynonymous Substitution Rate ◽  
Evolution Of Gene Families ◽  
High Concentrations ◽  
Novel Exon

AbstractTarichanewts contain high concentrations of the deadly toxin TTX as an antipredator defense, requiring them to be physiologically resistant to their own toxin. Here, we reconstruct the origins of TTX self-resistance by sequencing the voltage-gated sodium channel (SCNA) gene family, the target of TTX, in newts and related salamanders. We show that extreme resistance in newts consists of a mixture of ancient changes and lineage-specific substitutions and that the nonsynonymous substitution rate is elevated in newts, suggesting positive selection. We also identify a novel exon duplication withinSCN4Aencoding an expressed TTX-binding site. Two resistance-conferring changes within newts appear to have spread via nonallelic gene conversion: in one case, one codon was copied between paralogs, and in the second, multiple substitutions were homogenized between the duplicate exons ofSCN4A. Our results demonstrate that gene conversion can accelerate the coordinated evolution of gene families in response to selection.

scholarly journals Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates

2017 ◽  
Vol 114 (48) ◽  
pp. 12779-12784 ◽  
Author(s):  
Arbel Harpak ◽  
Xun Lan ◽  
Ziyue Gao ◽  
Jonathan K. Pritchard
Keyword(s):  
Gene Conversion ◽  
Genetic Diseases ◽  
Sequence Divergence ◽  
Duplicate Gene ◽  
Gene Families ◽  
Sequence Evolution ◽  
Donor Region ◽  
Order Of Magnitude ◽  
Evolution Of Gene Families ◽  
Gene Duplicates

Gene conversion is the copying of a genetic sequence from a “donor” region to an “acceptor.” In nonallelic gene conversion (NAGC), the donor and the acceptor are at distinct genetic loci. Despite the role NAGC plays in various genetic diseases and the concerted evolution of gene families, the parameters that govern NAGC are not well characterized. Here, we survey duplicate gene families and identify converted tracts in 46% of them. These conversions reflect a large GC bias of NAGC. We develop a sequence evolution model that leverages substantially more information in duplicate sequences than used by previous methods and use it to estimate the parameters that govern NAGC in humans: a mean converted tract length of 250 bp and a probability of 2.5×10−7 per generation for a nucleotide to be converted (an order of magnitude higher than the point mutation rate). Despite this high baseline rate, we show that NAGC slows down as duplicate sequences diverge—until an eventual “escape” of the sequences from its influence. As a result, NAGC has a small average effect on the sequence divergence of duplicates. This work improves our understanding of the NAGC mechanism and the role that it plays in the evolution of gene duplicates.

scholarly journals Sequence identity in an early chorion multigene family is the result of localized gene conversion.

Genetics ◽  
1991 ◽  
Vol 128 (3) ◽  
pp. 595-606
Author(s):  
B L Hibner ◽  
W D Burke ◽  
T H Eickbush
Keyword(s):  
Nucleotide Sequence ◽  
Gene Conversion ◽  
Nucleotide Sequence Identity ◽  
Early Period ◽  
Gene Families ◽  
Multigene Families ◽  
Coding Regions ◽  
Sequence Identity ◽  
Isolation And Characterization ◽  
Sequence Exchange

Abstract The multigene families that encode the chorion (eggshell) of the silk moth, Bombyx mori, are closely linked on one chromosome. We report here the isolation and characterization of two segments, totaling 102 kb of genomic DNA, containing the genes expressed during the early period of choriogenesis. Most of these early genes can be divided into two multigene families, ErA and ErB, organized into five divergently transcribed ErA/ErB gene pairs. Nucleotide sequence identity in the major coding regions of the ErA genes was 96%, while nucleotide sequence identity for the ErB major coding regions was only 63%. Selection pressure on the encoded proteins cannot explain this difference in the level of sequence conservation between the ErA and ErB gene families, since when only fourfold redundant codon positions are considered, the divergence within the ErA genes is 8%, while the divergence within the ErB genes (corrected for multiple substitutions at the same site) is 110%. The high sequence identity of the ErA major exons can be explained by sequence exchange events similar to gene conversion localized to the major exon of the ErA genes. These gene conversions are correlated with the presence of clustered copies of the nucleotide sequence GGXGGX, encoding paired glycine residues. This sequence has previously been correlated with gradients of gene conversion that extend throughout the coding and noncoding regions of the High-cysteine (Hc) chorion genes of B. mori. We suggest that the difference in the extent of the conversion tracts in these gene families reflects a tendency for these recombination events to become localized over time to the protein encoding regions of the major exons.

High-frequency germ line gene conversion in transgenic mice

1992 ◽  
Vol 12 (6) ◽  
pp. 2545-2552
Author(s):  
J R Murti ◽  
M Bumbulis ◽  
J C Schimenti
Keyword(s):  
Gene Conversion ◽  
Dna Sequences ◽  
High Frequency ◽  
Germ Line ◽  
Gene Families ◽  
Histochemical Staining ◽  
Evolutionary Significance ◽  
Evolutionary Divergence ◽  
Lacz Gene ◽  
Male Gametes

Gene conversion is the nonreciprocal transfer of genetic information between two related genes or DNA sequences. It can influence the evolution of gene families, having the capacity to generate both diversity and homogeneity. The potential evolutionary significance of this process is directly related to its frequency in the germ line. While measurement of meiotic inter- and intrachromosomal gene conversion frequency is routine in fungal systems, it has hitherto been impractical in mammals. We have designed a system for identifying and quantitating germ line gene conversion in mice by analyzing transgenic male gametes for a contrived recombination event. Spermatids which undergo the designed intrachromosomal gene conversion produce functional beta-galactosidase (encoded by the lacZ gene), which is visualized by histochemical staining. We observed a high incidence of lacZ-positive spermatids (approximately 2%), which were produced by a combination of meiotic and mitotic conversion events. These results demonstrate that gene conversion in mice is an active recombinational process leading to nonparental gametic haplotypes. This high frequency of intrachromosomal gene conversion seems incompatible with the evolutionary divergence of newly duplicated genes. Hence, a process may exist to uncouple gene pairs from frequent conversion-mediated homogenization.

scholarly journals treeWidget: a BioJS component to visualise phylogenetic trees

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 49 ◽  
Author(s):  
Fabian Schreiber
Keyword(s):  
Phylogenetic Trees ◽  
Protein Domains ◽  
Gene Families ◽  
Sequence Information ◽  
Gene Duplications ◽  
Link Type ◽  
History Of ◽  
Conservation Patterns ◽  
Evolution Of Gene Families ◽  
The Web

Summary: Phylogenetic trees are widely used to represent the evolution of gene families. As the history of gene families can be complex (including lots of gene duplications), its visualisation can become a difficult task. A good/accurate visualisation of phylogenetic trees - especially on the web - allows easier understanding and interpretation of trees to help to reveal the mechanisms that shape the evolution of a specific set of gene/species. Here, I present treeWidget, a modular BioJS component to visualise phylogenetic trees on the web. Through its modularity, treeWidget can be easily customized to allow the display of sequence information, e.g. protein domains and alignment conservation patterns.Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7707

scholarly journals Long-Term Persistence of Infection in Chimpanzees Inoculated with an Infectious Hepatitis C Virus Clone Is Associated with a Decrease in the Viral Amino Acid Substitution Rate and Low Levels of Heterogeneity

2004 ◽  
Vol 78 (18) ◽  
pp. 9782-9789 ◽  
Author(s):  
Javier Fernandez ◽  
Deborah Taylor ◽  
Duncan R. Morhardt ◽  
Kathleen Mihalik ◽  
Montserrat Puig ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Substitution Rate ◽  
Selective Pressure ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Nonsynonymous Substitution Rate ◽  
Over Time

ABSTRACT Two chimpanzees, 1535 and 1536, became persistently infected following inoculation with RNA transcripts from cDNA clones of hepatitis C virus (HCV). Analysis of the HCV genomes from both animals showed an accumulation of amino acid substitutions over time. The appearance of substitutions in the envelope genes was associated with increased antienvelope antibody titers. However, extensive mutations were not incorporated into hypervariable region 1 (HVR1). A comparison of the nonsynonymous substitution rate/synonymous substitution rate was made at various time points to analyze selective pressure. The highest level of selective pressure occurred during the acute phase and decreased as the infection continued. The nonsynonymous substitution rate was initially higher than the synonymous substitution rate but decreased over time from 3.3 × 10−3 (chimpanzee 1535) and 3.2 × 10−3 (chimpanzee 1536) substitutions/site/year at week 26 to 1.4 × 10−3 (chimpanzee 1535) and 1.7 × 10−3 (chimpanzee 1536) at week 216, while the synonymous substitution rate remained steady at ∼1 × 10−3 substitutions/site/year. Analysis of PCR products using single-stranded conformational polymorphism indicated a low level of heterogeneity in the viral genome. The results of these studies confirm that the persistence of infection is not solely due to changes in HVR1 or heterogeneity and that the majority of variants observed in natural infections could not arise simply through mutation during the time period most humans and chimpanzees are observed. These data also indicate that immune pressure and selection continue throughout the chronic phase.

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