Level Of Nucleotide Substitutions Research Articles

Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow

BackgroundThe genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.ResultsFractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.ConclusionsMembers of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.

Nonprotein-Coding RNAs as Regulators of Development in Tunicates.

Tunicates, or urochordates, are a group of small marine organisms that are found widely throughout the seas of the world. As most plausible sister group of the vertebrates, they are of utmost importance for a comprehensive understanding of chordate evolution; hence, they have served as model organisms for many aspects of the developmental biology. Current genomic analysis of tunicates indicates that their genomes evolved with a fast rate not only at the level of nucleotide substitutions but also in terms of genomic organization. The latter involves genome reduction, rearrangements, as well as the loss of some important coding and noncoding RNA (ncRNAs) elements and even entire genomic regions that are otherwise well conserved. These observations are largely based on evidence from comparative genomics resulting from the analysis of well-studied gene families such as the Hox genes and their noncoding elements. In this chapter, the focus lies on the ncRNA complement of tunicates, with a particular emphasis on microRNAs, which have already been studied extensively for other animal clades. MicroRNAs are known as important regulators of key genes in animal development, and they are intimately related to the increase morphological complexity in higher metazoans. Here we review the discovery, evolution, and genome organization of the miRNA repertoire, which has been drastically reduced and restructured in tunicates compared to the chordate ancestor. Known functions of microRNAs as regulators of development in tunicates are a central topic. For instance, we consider the role of miRNAs as regulators of the muscle development and their importance in the regulation of the differential expression during the oral siphon regeneration. Beyond microRNAs, we touch upon the functions of some other ncRNAs such as yellow crescent RNA, moRNAs, RMST lncRNAs, or spliced-leader (SL) RNAs, which have diverse functions associated with the embryonic development, neurogenesis, and mediation of mRNA stability in general.

Selective Constraint on Copy Number Variation in Human Piwi-Interacting RNA Loci

Piwi-interacting RNAs (piRNAs) are a recently discovered class of small non-coding RNA found in animals. PiRNAs are primarily expressed in the germline where their best understood function is to repress transposable elements. Unlike previous studies that investigated the evolution of piRNA-generating loci at the level of nucleotide substitutions, here we studied the evolution of piRNA-generating loci at the level of copy number variation (i.e. duplications and deletions) using genome-wide copy number variation data from three human populations. Our analysis shows that at the level of copy number variation there is strong selective constraint and a very high mutation rate in human piRNA-generating loci. Our results differ from a model of positive selection on copy number variation in piRNA-generating loci previously proposed in rodents. We discuss possible reasons for this difference based on the transposable element insertion histories in the rodent and primate lineages.

Similar Relative Mutation Rates in the Three Genetic Compartments of Mesostigma and Chlamydomonas

Levels of nucleotide substitution at silent sites in organelle versus nuclear DNAs have been used to estimate relative mutation rates among these compartments and explain lineage-specific features of genome evolution. Synonymous substitution divergence values in animals suggest that the rate of mutation in the mitochondrial DNA is 10-50 times higher than that of the nuclear DNA, whereas overall data for most seed plants support relative mutation rates in mitochondrial, plastid, and nuclear DNAs of 1:3:10. Little is known about relative mutation rates in green algae, as substitution rate data is limited to only the mitochondrial and nuclear genomes of the chlorophyte Chlamydomonas. Here, we measure silent-site substitution rates in the plastid DNA of Chlamydomonas and the three genetic compartments of the streptophyte green alga Mesostigma. In contrast to the situation in animals and land plants, our results support similar relative mutation rates among the three genetic compartments of both Chlamydomonas and Mesostigma. These data are discussed in relation to published intra-species genetic diversity data for the three genetic compartments of Chlamydomonas and are ultimately used to address contemporary hypotheses on the organelle genome evolution. To guide future work, we describe evolutionary divergence data of all publically available Mesostigma viride strains and identify, for the first time, three distinct lineages of Mesostigma.

Candida asiatica sp. nov., an anamorphic ascomycetous yeast species isolated from natural samples from Thailand, Taiwan, and Japan

Six yeast strains of a novel anamorphic yeast species were isolated from natural samples collected in Thailand (RV60(T) and LYSM9), Taiwan (SC5L04 and GE19S05), and Japan (JCM 11058 and JCM 11059). Analysis of the D1/D2 domain of the large subunit rRNA gene sequences revealed that the sequences of five strains (LYSM9, SC5L04, GE19S05, JCM 11058, and JCM 11059) were identical and differed from the sequence of strain RV60(T) by only one nucleotide substitution. The closest recognized species in terms of pairwise sequence similarity was Candida abiesophila, but the level of nucleotide substitution (14.2-14.3%) was sufficient to justify the description of a separate species. Phenotypic characteristics of the six strains were almost the same except for two strains from Japan, which showed the ability to ferment glucose and grew in the presence of 10% NaCl and 5% glucose while the others did not. The phenotypic characteristics of the six strains included proliferation by multilateral budding, absence of ascospores, arthrospores, and ballistospores, and negative Diazonium blueB and urease tests. The major ubiquinone was Q-7. On the basis of the above findings, the six strains were assigned to a single novel species of Candida, for which the name Candida asiatica sp. nov. is proposed. The type strain is RV60(T) (BCC 25966(T)=NBRC 103863(T)=CBS 10863(T)).

Kluyveromyces siamensissp. nov., an ascomycetous yeast isolated from water in a mangrove forest in Ranong Province, Thailand

Seven strains of a novel Kluyveromyces species were isolated from seven water samples collected from a mangrove forest. Analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene sequences revealed that the sequences of five strains (RS8(T), RS20, RS54, RV42 and RV89) were identical and differed from the other two strains (RS65 and RV153) by only one nucleotide substitution in 544 nucleotides (nt). The closest species in terms of pairwise sequences similarity was Kluyveromyces aestuarii, but the level of nucleotide substitution (six to seven nucleotide substitutions in 544 nt) was sufficient to justify the description of a separate species. The phylogenetic tree based on the sequence of the D1/D2 domain of the LSU rRNA gene rather suggested that the new species is a sister species of K. aestuarii and forms a clade with the other six recognized species of Kluyveromyces. Sequence analysis of the internal transcribed spacer (ITS1-5.8S rRNA gene-ITS2) region supported their distinct status as a species. The phenotypic characteristics of the seven strains were typical of the genus Kluyveromyces. On this basis, the seven strains were assigned to a single novel species of the genus Kluyveromyces, for which the name Kluyveromyces siamensis sp. nov. is proposed. The type strain is RS8(T) (BCC 25962(T)=NBRC 103859(T)=CBS 10860(T)).

Candida phangngensis sp. nov., an anamorphic yeast species in the Yarrowia clade, isolated from water in mangrove forests in Phang-Nga Province, Thailand

Two yeast strains (TM2-16 and PT1-17(T)) were isolated by membrane filtration from samples of estuarine water collected from two mangrove forests, in Khao Lumpee-Haad Thaimueang National Park and Mu Ko Ra-Ko Prathong National Park, Phang-Nga Province, Thailand. Analysis of the D1/D2 domain of the large-subunit rDNA sequences revealed that the sequences of the two strains were identical. The closest species in terms of pairwise sequence similarity was Candida galli, but the level of nucleotide substitutions (13.2 %) was sufficient to justify the description of a separate species. Phylogenetic analysis demonstrated that the two strains occupy a basal position with respect to Yarrowia lipolytica and C. galli of the Yarrowia clade, supported by a high bootstrap value. The two strains showed identical phenotypic characteristics, including proliferation by multilateral budding, absence of ascospores and ballistoconidia and negative Diazonium blue B and urease reactions. The major ubiquinone was Q-9. On the basis of the above findings, these two strains were assigned to a single novel species of the genus Candida, for which the name Candida phangngensis sp. nov. is proposed. The type strain is PT1-17(T) (=BCC 21306(T) =NBRC 101970(T) [corrected] =CBS 10407(T)).

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage

Current models of codon substitution are formulated at the levels of nucleotide substitution and do not explicitly consider the separate effects of mutation and selection. They are thus incapable of inferring whether mutation or selection is responsible for evolution at silent sites. Here we implement a few population genetics models of codon substitution that explicitly consider mutation bias and natural selection at the DNA level. Selection on codon usage is modeled by introducing codon-fitness parameters, which together with mutation-bias parameters, predict optimal codon frequencies for the gene. The selective pressure may be for translational efficiency and accuracy or for fine-tuning translational kinetics to produce correct protein folding. We apply the models to compare mitochondrial and nuclear genes from several mammalian species. Model assumptions concerning codon usage are found to affect the estimation of sequence distances (such as the synonymous rate d(S), the nonsynonymous rate d(N), and the rate at the 4-fold degenerate sites d(4)), as found in previous studies, but the new models produced very similar estimates to some old ones. We also develop a likelihood ratio test to examine the null hypothesis that codon usage is due to mutation bias alone, not influenced by natural selection. Application of the test to the mammalian data led to rejection of the null hypothesis in most genes, suggesting that natural selection may be a driving force in the evolution of synonymous codon usage in mammals. Estimates of selection coefficients nevertheless suggest that selection on codon usage is weak and most mutations are nearly neutral. The sensitivity of the analysis on the assumed mutation model is discussed.

Candida thaimueangensis sp. nov., an anamorphic yeast species from estuarine water in a mangrove forest in Thailand

Four yeast strains (TM1-01(T), TM1-07, TM3-47 and TM3-49) were isolated by membrane filtration from estuarine water collected from a mangrove forest in Phang-Nga province, southern Thailand. Analysis of the D1/D2 domains of the large-subunit rDNA sequence revealed that the sequences of the four strains were identical. The closest recognized species in terms of pairwise sequence similarity was Pichia deserticola, but the level of nucleotide substitution (4.8 %) was sufficient to justify the description of a separate species. Phylogenetic analysis demonstrated that the four strains occupy a basal position with respect to Pichia membranifaciens and close relatives. The four strains showed identical phenotypic characteristics, including proliferation by multilateral budding, absence of ascospores, arthrospores and ballistospores and negative reactions for Diazonium blue B and urease. The major ubiquinone was Q-7. On the basis of the above findings, these four strains were assigned to a single novel species of the genus Candida, for which the name Candida thaimueangensis sp. nov. is proposed. The type strain is TM1-01(T) (=CBS 10360(T)=NBRC 101967(T)=BCC 21229(T)).

A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates

Short interspersed nuclear elements (SINEs) provide a near homoplasy free and copious source of molecular evolutionary markers with precisely defined character polarity. Used as molecular cladistic markers in presence/absence analyses, they represent a powerful complement to phylogenetic reconstructions that are based on sequence comparisons on the level of nucleotide substitutions. Recent sequence comparisons of large data sets incorporating a broad eutherian taxonomic sample have led to considerations of the different primate infraorders to constitute a paraphyletic group. Statistically significant support against the monophyly of primates has been obtained by clustering the flying lemur—also termed colugo—( Cynocephalus, Dermoptera) amidst the primates as the sister group to anthropoid primates (New World monkeys, Old World monkeys, and hominoids). We discovered retrotransposed markers that clearly favor the monophyly of primates, with the markers specific to all extant primates but definitively absent at the orthologous loci in the flying lemur and other non-primates. By screening the colugo genome for phylogenetic informative SINEs, we also recovered a novel family of dermopteran specific SINE elements that we call CYN. This element is probably derived from the isoleucine tRNA and appears in monomeric, dimeric, and trimeric forms. It has no long tRNA unrelated region and no poly(A) linker between the monomeric subunits. The characteristics of the novel CYN-SINE family indicate a relatively recent history. Therefore, this SINE family is not suitable to solve the phylogenetic affiliation between dermopterans and primates. Nevertheless it is a valuable device to reconstruct the evolutionary steps from a functional tRNA to an interspersed SINE element.

Mitochondrial DNA restriction site variation in the Townsend's vole, Microtus townsendii

The mitochondrial DNA (mtDNA) from the Townsend's vole, Microtus townsendii, was compared with mouse mtDNA by positioning vole restriction enzyme fragments on the known laboratory mouse mtDNA molecule by homology hybridization. The vole mitochondrial genome is conserved in general sequence organization and size but does contain a nonhomologous region of more than 600 base pairs not found in the mouse sequence. Thirty-five voles were collected from seven different localities throughout the range of the species, including insular populations on Bowen and Vancouver islands. The variation of vole mtDNA sequences within this species was assayed with six hexameric and four tetrameric type II restriction endonucleases. These individuals can be divided into seven distinct maternal lines. The level of nucleotide substitution between populations is shown to be as high as 0.896 ± 0.350%. The voles from Bowen Island showed no detectable variation within their population, or divergence from a mainland population on the adjacent coast. This fact suggests a recent colonization of Bowen Island. The samples from Vancouver Island fall into two major maternal lines, which show 0.453 ± 0.240% divergence. These insular maternal lines are 0.677 ± 0.257% divergent from the most closely related mainland population. These results suggest that the voles on Vancouver Island represent long-established maternal lines, and are not derived by a recent colonization from a mainland source population. Based on conservative estimates for rates of nucleotide substitution, Vancouver Island has been inhabited by the Townsend's vole since at least the Olympic interglacial.

THE NATURE OF NUCLEOTIDE SEQUENCE DIVERGENCE BETWEEN BARLEY AND MAIZE CHLOROPLAST DNA

Analysis of a 2175-base pair (bp) SmaI-HindIII fragment of barley chloroplast DNA revealed that rbcL (the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase) and atpB (the gene for the beta subunit of ATPase) are transcribed divergently and are separated by an untranscribed region of 155-166 bp. The rbcL mRNA has a 320-residue untranslated leader region, whereas the atpB mRNA has a 296- to 309-residue leader region. The sequence of these regions, together with the initial 113 bp of the atpB-coding region and the initial 1279 bp of the rbcL-coding region, is compared with the analogous maize chloroplast DNA sequences. Two classes of nucleotide differences are present, substitutions and insertions/deletions. Nucleotide substitutions show a 1.9-fold bias toward transitions in the rbcL-coding region and a 1.5-fold bias toward transitions in the noncoding region. The level of nucleotide substitutions between the barley and maize sequences is about 0.065/bp. Seventy-one percent of the substitutions in the rbcL-coding region are at the third codon position, and 95% of these are synonymous changes. Insertion/deletion events, which are confined to the noncoding regions, are not randomly distributed in these regions and are often associated with short repeated sequences. The extent of change for the noncoding regions (about 0.093 events/bp) is less than the extent of change at the third codon positions in the rbcL-coding region (about 0.135 events/bp), including insertion/delection events. Limited sequence analysis of the analogous DNA from a wild line ( Hordeum spontaneum) and a primitive Iranian barley (H. vulgare) suggested a low rate of chloroplast DNA evolution. Compared to spinach chloroplast DNA, the barley rbcL-atpB untranslated region is extremely diverged, with only the putative rbcL promoters and ribosome-binding site being extensively conserved.