Association of sequence variation in Brassica GLABRA1 orthologs with leaf hairiness

AbstractThe HFE locus encodes an HLA class-I-type protein important in iron regulation and segregates replacement mutations that give rise to the most common form of genetic hemochromatosis. The high frequency of one disease-associated mutation, C282Y, and the nature of this disease have led some to suggest a selective advantage for this mutation. To investigate the context in which this mutation arose and gain a better understanding of HFE genetic variation, we surveyed nucleotide variability in 11.2 kb encompassing the HFE locus and experimentally determined haplotypes. We fully resequenced 60 chromosomes of African, Asian, or European ancestry as well as one chimpanzee, revealing 41 variable sites and a nucleotide diversity of 0.08%. This indicates that linkage to the HLA region has not substantially increased the level of HFE variation. Although several haplotypes are shared between populations, one haplotype predominates in Asia but is nearly absent elsewhere, causing higher than average genetic differentiation among the three major populations. Our samples show evidence of intragenic recombination, so the scarcity of recombination events within the C282Y allele class is consistent with selection increasing the frequency of a young allele. Otherwise, the pattern of variability in this region does not clearly indicate the action of positive selection at this or linked loci.

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Synonymous single nucleotide polymorphism in arsenic (+3) methyltransferase of the Western mosquitofish (Gambusia affinis) and its gene expression among field populations

Ecotoxicology ◽

10.1007/s10646-021-02376-8 ◽

2021 ◽

Author(s):

Daesik Park ◽

Catherine R. Propper ◽

Guangning Wang ◽

Matthew C. Salanga

Keyword(s):

Gene Expression ◽

Sequence Variation ◽

Allelic Variation ◽

Arsenic Concentration ◽

Gambusia Affinis ◽

Contamination Level ◽

Water Medium ◽

Single Nucleotide ◽

Wide Range ◽

High Arsenic

AbstractNaturally occurring arsenic is toxic at extremely low concentrations, yet some species persist even in high arsenic environments. We wanted to test if these species show evidence of evolution associated with arsenic exposure. To do this, we compared allelic variation across 872 coding nucleotides of arsenic (+3) methyltransferase (as3mt) and whole fish as3mt gene expression from three field populations of Gambusia affinis, from water sources containing low (1.9 ppb), medium-low (3.3 ppb), and high (15.7 ppb) levels of arsenic. The high arsenic site exceeds the US EPA’s Maximum Contamination Level for drinking water. Medium-low and high populations exhibited homozygosity, and no sequence variation across all animals sampled. Eleven of 24 fish examined (45.8%) in the low arsenic population harbored synonymous single nucleotide polymorphisms (SNPs) in exons 4 and/or 10. SNP presence in the low arsenic population was not associated with differences in as3mt transcript levels compared to fish from the medium-low site, where SNPs were noted; however, as3mt expression in fish from the high arsenic concentration site was significantly lower than the other two sites. Low sequence variation in fish populations from sites with medium-low and high arsenic concentrations suggests greater selective pressure on this allele, while higher variation in the low population suggests a relaxed selection. Our results suggest gene regulation associated with arsenic detoxification may play a more crucial role in influencing responses to arsenic than polymorphic gene sequence. Understanding microevolutionary processes to various contaminants require the evaluation of multiple populations across a wide range of pollution exposures.

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Distinguishing the Effects of Mutational Biases and Natural Selection on DNA Sequence Variation

Genetics ◽

10.1093/genetics/147.4.1989 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1989-1991

Author(s):

Hiroshi Akashi

Keyword(s):

Natural Selection ◽

Dna Sequence ◽

Sequence Variation ◽

Dna Sequence Variation

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The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species

Molecular Ecology Resources ◽

10.1111/1755-0998.13329 ◽

2021 ◽

Author(s):

Eva Lena F. Estensmo ◽

Sundy Maurice ◽

Luis Morgado ◽

Pedro M. Martin‐Sanchez ◽

Inger Skrede ◽

...

Keyword(s):

Sequence Variation ◽

Fungal Species ◽

Dna Metabarcoding

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Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley

International Journal of Molecular Sciences ◽

10.3390/ijms22136783 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6783

Author(s):

Renata Orłowska ◽

Katarzyna A. Pachota ◽

Wioletta M. Dynkowska ◽

Agnieszka Niedziela ◽

Piotr T. Bednarek

Keyword(s):

Dna Methylation ◽

Transposable Elements ◽

Dna Sequence ◽

Sequence Variation ◽

Nuclear Dna ◽

Point Mutations ◽

Mobile Elements ◽

Dna Demethylation ◽

Plant Genome

A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.

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