scholarly journals Estimating a Nucleotide Substitution Rate for Maize from Polymorphism at a Major Domestication Locus

2005 ◽  
Vol 22 (11) ◽  
pp. 2304-2312 ◽  
Author(s):  
Richard M. Clark ◽  
Simon Tavaré ◽  
John Doebley
Keyword(s):  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Nucleotide Substitution Rate

scholarly journals Genomic diversity of SARS-CoV-2 can be accelerated by a mutation in the nsp14 gene

2020 ◽  
Author(s):  
Kosuke Takada ◽  
Mahoko Takahashi Ueda ◽  
Tokiko Watanabe ◽  
So Nakagawa
Keyword(s):  
Amino Acid ◽  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Acid Sites ◽  
Genomic Diversity ◽  
Nucleotide Substitution Rate ◽  
Structural Protein ◽  
Wild Type ◽  
Gamma Delta ◽  
Evolutionarily Conserved

AbstractNucleotide substitution rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is relatively low compared to the other RNA viruses because coronaviruses including SARS-CoV-2 encode non-structural protein 14 (nsp14) that is an error-correcting exonuclease protein. In this study, to understand genome evolution of SARS-CoV-2 in the current pandemic, we examined mutations of SARS-CoV-2 nsp14 which could inhibit its error-correcting function. First, to obtain functionally important sites of nsp14, we examined 62 representative coronaviruses belonging to alpha, beta, gamma, delta, and unclassified coronaviruses. As a result, 99 out of 527 amino acid sites of nsp14 were evolutionarily conserved. We then examined nsp14 sequences obtained from 28,082 SARS-CoV-2 genomes and identified 6 amino acid changes in nsp14 mutants that were not detected in the 62 representative coronaviruses. We examined genome substitution rates of these mutants and found that an nsp14 mutant with a proline to leucine change at position 203 (P203L) showed a higher substitution rate (35.9 substitutions/year) than SARS-CoV-2 possessing wild-type nsp14 (19.8 substitutions/year). We confirmed that the substitution rate of the P203L is significantly higher than those of other variants containing mutations in structural proteins. Although the number of SARS-CoV-2 variants containing P203L mutation of nsp14 is limited (26), these mutants appeared at least 10 times independently in the current pandemic. These results indicated that the molecular function of nsp14 is important for survival of various coronaviruses including SARS-CoV-2 and that some mutations such as P203L of nsp14 inhibiting its error-correcting function are removed rapidly due to their deleterious effects.

scholarly journals Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12106
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Nucleotide Substitution Rate ◽  
Genomic Comparison ◽  
Plant Family ◽  
Plastid Genomes ◽  
The Family ◽  
Unknown Reason ◽  
Order Of Magnitude ◽  
Insight Into

The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.

scholarly journals High nucleotide substitution rates associated with retrotransposon proliferation drive dynamic secretome evolution in smut pathogens

2021 ◽  
Author(s):  
JRL Depotter ◽  
B Ökmen ◽  
MK Ebert ◽  
J Beckers ◽  
J Kruse ◽  
...  
Keyword(s):  
Mating Type ◽  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Long Terminal Repeat Retrotransposons ◽  
Nucleotide Substitution Rate ◽  
Type Locus ◽  
Genome Expansion ◽  
Long Reads ◽  
Genes Encoding ◽  
Flanking Regions

AbstractTransposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to long terminal repeat retrotransposons (LTR-RTs) of the Copia and Gypsy superfamilies. From the studied smuts, LTR-RTs proliferated the most recently and to the furthest extent in the U. hordei genome, in which they make up for 19.5% of the genome. Interestingly, the extent of TE proliferation in different smut species is positively correlated to the mating-type locus size, which is largest in U. hordei with up to ~560 kb. TE transposition within the mating-type loci and their flanking regions are mating-type specific, which is likely due to the very low recombination activity in this region. Furthermore, LTR-RT proliferation was found to be associated with higher nucleotide substitution levels, as genes in genome regions that are rich in dynamic LTR-RTs display higher nucleotide substitution levels. The high nucleotide substitution rate particularly affected the evolution of genes encoding secreted proteins as substitutions more frequently led to amino acid alterations. The mechanism behind this increase in nucleotide substitution rate remains elusive, but seems not to be a consequence of the repeat-induced point mutation (RIP) mechanism, as genes and LTR-RTs did not display typical RIP substitutions.

scholarly journals KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences

2021 ◽  
Author(s):  
Zhang Zhang
Keyword(s):  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Selective Pressure ◽  
Synonymous Substitution ◽  
Nucleotide Substitution Rate ◽  
Synonymous Substitution Rate ◽  
Coding Sequences ◽  
Genome Wide ◽  
Genome Scale ◽  
Genome Wide Scan

KaKs_Calculator 3.0 is an updated toolkit that is capable for calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as non-coding nucleotide substitution rate normalized by synonymous substitution rate of adjacent coding sequences. As testified on empirical data, it shows effectiveness to detect the strength and mode of selection operated on molecular sequences, accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at whole genome scale. The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.

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