2nd Codon Positions Research Articles

Morphometric and DNA-based identification of horseshoe crab Carcinoscorpius rotundicauda (Latreille, 1802) and Tachypleus gigas (Müller, 1785) from Bangladesh coast

Horseshoe crabs are the living fossils of xiphosurans that have survived for over 200 million years without morphological change and records fossil dating back 500 million years. A study was conducted on morphometric and molecular characterization of horseshoe crab Carcinoscorpius rotundicauda (Latreille, 1802) and Tachypleus gigas (Müller, 1785) from Bangladesh waters. A total of ten samples of C. rotundicauda and one sample of T. gigas were collected from Dublar Char, Sundarbans and Cox’s bazar from June 2016 to May 2017 and February 2024, respectively. Among them, four specimens were male and seven female. Morphometric measurements were taken from all the collected samples and differentiated male and female based on the second pair of legs, the pedipalps. The species were genetically identified using mitochondrial cytochrome c oxidase subunit I (COI) gene. An average length of about 670.5 bp nucleotide sequences were obtained. Average percentage of nucleotide frequencies were T (30.3), C (16.3), A (34.4) and G (19.0) for C. rotundicauda and T (34.45), C (22.01), A (27.91) and C (15.63) for T. gigas. GC content analysis showed that average GC 36.20% and AT 63.80%. The average GC content at the 1st, 2nd and 3rd codon position were 38.82%, 37.87% and 31.92% respectively. This is the first report of DNA barcoding of a living fossil C. rotundicauda and T. gigas from Bangladesh and will serve as baseline information for future research, conservation and management of this invaluable primitive creature. Bioresearch Commu. 10(2): 1489-1494, 2024 (July)

Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson's Disease.

Codon usage bias (CUB) is the phenomenon of non-uniform usage of synonymous codons in which some codons are more used than others and it helps in understanding the molecular organization of genome. Bioinformatic approach was used to analyze the protein-coding sequences of genes associated with Parkinson's disease (PD) to explore compositional features and codon usage pattern as no details work was reported yet. The average improved effective number of codons (Nc) and Nc prime were 42.74 and 44.26 respectively, indicated that CUB was low in these genes. In most of the genes, the overall GC content was almost 50% and GC content at the 1st codon position was the highest while GC content at the 2nd codon position was lowest. Relative synonymous codon usage (RSCU) analysis elucidated over-represented (p > 1.6) and under-represented codons (p < 0.6). The GTG (Val) is the only codon over-represented in all genes. Over-represented codons except (GTG) were A or T ending while under-represented codons (except ACT) were G or C ending. The codons namely TTA (Leu), CTA (Leu), ATC (Ile), ATA (Ile), AGT (Ser), AAC (Asn), TGT (Cys), TGC (Cys), CGC (Arg), AGA (Arg), and AGG (Arg) were absent in SNCA1 to SNCA8 genes. The codon TCG (Ser) was absent in all genes except UCHL1 and PINK1. Correspondence analysis (COA) revealed that the pattern of codon usage differs among genes associated with PD. Neutrality plot analysis indicated some of the points are diagonal distribution suggested that mutation pressure influenced the CUB in genes associated with PD.

Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships

Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.

Codon Directional Asymmetry Suggests Swapped Prebiotic 1st and 2nd Codon Positions.

Background: Codon directional asymmetry (CDA) classifies the 64 codons into palindromes (XYX, CDA = 0), and 5′- and 3′-dominant (YXX and XXY, CDA < 0 and CDA > 0, respectively). Previously, CDA was defined by the purine/pyrimidine divide (A,G/C,T), where X is either a purine or a pyrimidine. For the remaining codons with undefined CDA, CDA was defined by the 5′ or 3′ nucleotide complementary to Y. This CDA correlates with cognate amino acid tRNA synthetase classes, antiparallel beta sheet conformation index and the evolutionary order defined by the self-referential genetic code evolution model (CDA < 0: class I, high beta sheet index, late genetic code inclusion). Methods: We explore associations of CDAs defined by nucleotide classifications according to complementarity strengths (A:T, weak; C:G, strong) and keto-enol/amino-imino groupings (G,T/A,C), also after swapping 1st and 2nd codon positions with amino acid physicochemical and structural properties. Results: Here, analyses show that for the eight codons whose purine/pyrimidine-based CDA requires using the rule of complementarity with the midposition, using weak interactions to define CDA instead of complementarity increases associations with tRNA synthetase classes, antiparallel beta sheet index and genetic code evolutionary order. CDA defined by keto-enol/amino-imino groups, 1st and 2nd codon positions swapped, correlates with amino acid parallel beta sheet formation indices and Doolittle’s hydropathicities. Conclusions: Results suggest (a) prebiotic swaps from N2N1N3 to N1N2N3 codon structures, (b) that tRNA-mediated translation replaced direct codon-amino acid interactions, and (c) links between codon structures and cognate amino acid properties.

Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa.

All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st–2nd codon positions are more biased than those at the 2nd–3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.

Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous

The Cornales is a relatively small but morphologically diverse order in the basal position of the Asterids clade. Previous study hypothesized that the order might have undergone ancient rapid radiation during the Cretaceous when major angiosperm lineages were established. We conducted the phylogenomic analysis of Cornales using 81 plastid genome sequences with 67 newly generated in this study to test the hypothesis. This sampling represents all the families and 31 out of 48 genera in the order. Phylogenetic analyses were conducted using different datasets to examine the effects of different coding positions and character coding methods. We further conducted divergence time, diversification rate, and biogeographic analyses to understand the early evolutionary history of Cornales in space and time. Our phylogenetic analyses of four datasets (the amino acid characters, the 1st and 2nd codon positions of protein coding genes, nucleotide characters with degenerated coding method, and noncoding regions) resulted in a robust phylogeny congruent with results of previous studies, showing (((Cornaceae-Alangiaceae)-(Curtisiaceae-Grubbiaceae))-(((Nyssaceae-Davidiaceae)-Mastixiaceae)-((Hydrostachyaceae-(Hydrangeaceae-Loasaceae)))). Phylogenetic relationships within families were also well resolved. Conflicts in the placement of Hydrostachyaceae were found from analyses of two datasets, the nucleotide characters of all codon position and the 3rd codon positions, where the family was united with Loasaceae, but not strongly supported. Results from divergence time analyses suggested a mid-Cretaceous origin of Cornales followed by rapid early diversification into major clades/families within 10 million years. The early diversification of Cornales may have been facilitated by divergence in habitat and morphology following geographic dispersals. The ancestral distribution of the order was inferred as a widespread range covering Asia, Europe, North America, and Africa when including fossils in the analyses, suggesting an origin of the order likely along the Tethys Seaway where the areas were connected in the mid-Cretaceous. Inferred geographic origins of each family differed to some extent between analyses including fossils vs excluding fossils. In the analysis with extant and fossil species, the origins of the African Hydrostachyaceae and Grubbiaceae-Curtisiaceae clade were inferred to have involved two independent events, an intercontinental dispersal from the northern hemisphere to Africa and an intercontinental vicariance between the northern hemisphere and Africa, respectively. Other families were inferred to have evolved in the northern hemisphere with subsequent intercontinental dispersal(s) to other areas including to Central and South America, during their subsequent diversification. Net diversification rate analysis based on treePL dated phylogeny using MEDUSA detected a nearly 5-fold decrease in the African endemic Curtisiaceae-Grubbiaceae (CuG) clade and an increase of rate in the Hydrangeaceae-Loasaceae (HL) clade. Within HL, a decrease in the Fendlera-Jamesia clade and an increase in the Philadelphus clade were also detected. The findings are also consistent with the level of present species diversity in these lineages. Our study demonstrated the value of plastid genome in phylogenomic study, but posed an old challenge of biogeographic study with fossil data and raised caution for the synonymous substitution sites of plastid genome in phylogenomics studies.

&lt;p class="HeadingRunIn"&gt;&lt;strong&gt;Phylogenetics of a small caddisfly genus (Thremmatidae: &lt;em&gt;Oligophlebodes&lt;/em&gt;): comparison among multiple hypotheses from DNA barcode data&lt;/strong&gt;&lt;/p&gt;

Barcoding datasets can serve as a resource for species associations and delineations, but single-gene trees estimated by distance methods do not provide strong estimates of phylogeny. Using DNA data from the Barcode of Life Database (BOLD), we calculate a phylogenetic tree for Oligophlebodes (Trichoptera: Thremmatidae), a small genus of caddisfly endemic to the Western United States. Here we estimate a preliminary phylogeny for Oligophlebodes using Bayesian likelihood, and compare it to trees produced by distance and standard likelihood methods. Using the barcode region of the cytochrome oxidase 1 (COI) gene, we analyzed 44 individuals representing five species (and 2 unknowns) and a sister-genus outgroup (Neophylax) from locations ranging from Southern New Mexico northwest into British Columbia. Partitioned Bayesian likelihood analysis under the F81 (1st codon positions) and HKY80 + I + Γ (for both the 2nd and 3rd codon positions) model gave the consensus topology (Neophylax toshi, (O. sierra, (O. ruthae inc. spc. 1 &amp; 2, O. sigma, (spc. 3 &amp; 4, (O. ardis, O. minutus)))). Species identifications were supported by monophyly of most species-level taxa. However, confirmation of species identifications of unknowns was complicated by incomplete taxon sampling for spc. 1 &amp; 2. Placement of spc. 3 &amp; 4 may serve as support for taxonomic review of O. minutus. Compared with an existing published phylogeny of Oligophlebodes BOLD sequences constructed under RAxML, the Bayesian hypothesis had higher resolution at the basal node of Oligophlebodes. Because of their support values, both likelihood trees are recommended over the BOLD TaxonID tree (an unrooted neighbor joining tree using the Kimura 2-parameter model). The novel topology produced in the Bayesian tree supports further explorations by likelihood-based methods, including partitioned analyses, of our preliminary Oligophlebodes dataset that can be used as additional lines of evidence to support morphological work.

Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas.

The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.

Unique features of nucleotide and codon usage patterns in mycoplasmas revealed by information entropy

Currently, the comparison between GC usage pattern at the 3rd codon position and codon usage index is commonly used to estimate the roles of evolutionary forces in shaping synonymous codon usages, however, this kind of analysis often losses the information about the role of A/T usage bias in shaping synonymous codon usage bias. To overcome this limitation and better understand the interplay between nucleotide and codon usages for the evolution of bacteria at gene levels, in this study, we employed the information entropy method with some modification to estimate roles of nucleotide compositions in the overall codon usage bias for 18 mycoplasma species in combination with Davies-Bouldin index. At gene levels, the overall nucleotide usage bias represents A content as the highest, followed by T, G and C for mycoplasmas, resulting in a low GC content. This feature is universal across these species derived from different hosts, suggesting that the hosts have the limited impact on nucleotide usage bias of mycoplasmas. Information entropy and Davies-Bouldin index can better reveal that the nucleotide usage bias at the 3rd codon position is essential in shaping the overall nucleotide bias for all given mycoplasmas except M. pneumoniae M129. Davies-Bouldin index revealed that the 1st and 2nd codon position play more important role in synonymous codon usage bias than that of the 3rd position at gene levels. To our knowledge, this is the first comprehensive investigation into cooperation between nucleotide and codon usages for mycoplasma and extends our knowledge of the mechanisms that contribute to codon usage and evolution of this microorganism.

Dissimilar substitution rates between two strands of DNA influence codon usage pattern in some human genes

We illustrated the descriptive aspects of codon usage of some important human genes and their expression potential in E. coli. By comparing the results of various codon usage parameters, effects that are due to selection and mutational pressures have been deciphered. The variation in GC3s explains a significant proportion of the variation in codon usage patterns. The codons CGC, CGG, CTG and GCG showed strong positive correlation with GC3, which suggested that codon usage had been influenced by GC bias. We also found that ACC (Thr, RSCU-1.77), GCC (Ala, RSCU-1.67), CCC (Pro, RSCU-1.54), TCC (Ser, RSCU-1.47) were frequently used which signified that C was common at 2nd and 3rd codon positions. Correspondence analysis revealed that F1 axis had significant correlation with various GC contents suggesting that compositional properties under mutation pressure might affect codon usage bias. Nc-GC3 plot analysis suggested that both mutation pressure and natural selection might affect the codon usage bias which is also supported by neutrality plot analysis. The dinucleotide CT, TG and AG were significantly over-represented and CG, TA, AT, TT, and GT were underrepresented due to high rate of spontaneous mutation resulting from cytosine deamination.

Molecular phylogeny of the Achatinoidea (Mollusca: Gastropoda)

This study presents a multi-gene phylogenetic analysis of the Achatinoidea and provides an initial basis for a taxonomic re-evaluation of family level groups within the superfamily. A total of 5028 nucleotides from the nuclear rRNA, actin and histone 3 genes and the 1st and 2nd codon positions of the mitochondrial cytochrome c oxidase subunit I gene were sequenced from 24 species, representing six currently recognised families. Results from maximum likelihood, neighbour joining, maximum parsimony and Bayesian inference trees revealed that, of currently recognised families, only the Achatinidae are monophyletic. For the Ferussaciidae, Ferussacia folliculus fell separately to Cecilioides gokweanus and formed a sister taxon to the rest of the Achatinoidea. For the Coeliaxidae, Coeliaxis blandii and Pyrgina umbilicata did not group together. The Subulinidae was not resolved, with some subulinids clustering with the Coeliaxidae and Thyrophorellidae. Three subfamilies currently included within the Subulinidae based on current taxonomy likewise did not form monophyletic groups.

Origin and Evolution of Nitrogen Fixation Genes on Symbiosis Islands and Plasmid in Bradyrhizobium.

The nitrogen fixation (nif) genes of nodule-forming Bradyrhizobium strains are generally located on symbiosis islands or symbiosis plasmids, suggesting that these genes have been transferred laterally. The nif genes of rhizobial and non-rhizobial Bradyrhizobium strains were compared in order to infer the evolutionary histories of nif genes. Based on all codon positions, the phylogenetic tree of concatenated nifD and nifK sequences showed that nifDK on symbiosis islands formed a different clade from nifDK on non-symbiotic loci (located outside of symbiosis islands and plasmids) with elongated branches; however, these genes were located in close proximity, when only the 1st and 2nd codon positions were analyzed. The guanine (G) and cytosine (C) content of the 3rd codon position of nifDK on symbiosis islands was lower than that on non-symbiotic loci. These results suggest that nif genes on symbiosis islands were derived from the non-symbiotic loci of Bradyrhizobium or closely related strains and have evolved toward a lower GC content with a higher substitution rate than the ancestral state. Meanwhile, nifDK on symbiosis plasmids clustered with nifDK on non-symbiotic loci in the tree representing all codon positions, and the GC content of symbiotic and non-symbiotic loci were similar. These results suggest that nif genes on symbiosis plasmids were derived from the non-symbiotic loci of Bradyrhizobium and have evolved with a similar evolutionary pattern and rate as the ancestral state.

Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling

Previous analyses of single diatom chloroplast protein-encoded genes recovered results highly incongruent with both traditional phylogenies and phylogenies derived from the nuclear encoded small subunit (SSU) gene. Our analysis here of six individual chloroplast genes (atpB, psaA, psaB, psbA, psbC and rbcL) obtained similar anomalous results. However, phylogenetic noise in these genes did not appear to be correlated, and their concatenation appeared to effectively sum their collective signal. We empirically demonstrated the value of combining phylogenetic information profiling, partitioned Bremer support and entropy analysis in examining the utility of various partitions in phylogenetic analysis. Noise was low in the 1st and 2nd codon positions, but so was signal. Conversely, high noise levels in the 3rd codon position was accompanied by high signal. Perhaps counterintuitively, simple exclusion experiments demonstrated this was especially true at deeper nodes where the 3rd codon position contributed most to a result congruent with morphology and SSU (and the total evidence tree here). Correlated with our empirical findings, probability of correct signal (derived from information profiling) increased and the statistical significance of substitutional saturation decreased as data were aggregated. In this regard, the aggregated 3rd codon position performed as well or better than more slowly evolving sites. Simply put, direct methods of noise removal (elimination of fast-evolving sites) disproportionately removed signal. Information profiling and partitioned Bremer support suggest that addition of chloroplast data will rapidly improve our understanding of the diatom phylogeny, but conversely also illustrate that some parts of the diatom tree are likely to remain recalcitrant to addition of molecular data. The methods based on information profiling have been criticized for their numerous assumptions and parameter estimates and the fact that they are based on quartets of taxa. Our empirical results support theoretical arguments that the simplifying assumptions made in these methods are robust to “real-life” situations.

Constraint on di-nucleotides by codon usage bias in bacterial genomes

It has been reported earlier that the relative di-nucleotide frequency (RDF) in different parts of a genome is similar while the frequency is variable among different genomes. So RDF is termed as genome signature in bacteria. It is not known if the constancy in RDF is governed by genome wide mutational bias or by selection. Here we did comparative analysis of RDF between the inter-genic and the coding sequences in seventeen bacterial genomes, whose gene expression data was available. The constraint on di-nucleotides was found to be higher in the coding sequences than that in the inter-genic regions and the constraint at the 2nd codon position was more than that in the 3rd position within a genome. Further analysis revealed that the constraint on di-nucleotides at the 2nd codon position is greater in the high expression genes (HEG) than that in the whole genomes as well as in the low expression genes (LEG). We analyzed RDF at the 2nd and the 3rd codon positions in simulated coding sequences that were computationally generated by keeping the codon usage bias (CUB) according to genome G+C composition and the sequence of amino acids unaltered. In the simulated coding sequences, the constraint observed was significantly low and no significant difference was observed between the HEG and the LEG in terms of di-nucleotide constraint. This indicated that the greater constraint on di-nucleotides in the HEG was due to the stronger selection on CUB in these genes in comparison to the LEG within a genome. Further, we did comparative analyses of the RDF in the HEG rpoB and rpoC of 199 bacteria, which revealed a common pattern of constraints on di-nucleotides at the 2nd codon position across these bacteria. To validate the role of CUB on di-nucleotide constraint, we analyzed RDF at the 2nd and the 3rd codon positions in simulated rpoB/rpoC sequences. The analysis revealed that selection on CUB is an important attribute for the constraint on di-nucleotides at these positions in bacterial genomes. We believe that this study has come with major findings of the role of CUB on di-nucleotide constraint in bacterial genomes.

The hemagglutinin mutation E391K of pandemic 2009 influenza revisited

Phylogenetic analyses based on small to moderately sized sets of sequential data lead to overestimating mutation rates in influenza hemagglutinin (HA) by at least an order of magnitude. Two major underlying reasons are: the incomplete lineage sorting, and a possible absence in the analyzed sequences set some of key missing ancestors. Additionally, during neighbor joining tree reconstruction each mutation is considered equally important, regardless of its nature. Here we have implemented a heuristic method optimizing site dependent factors weighting differently 1st, 2nd, and 3rd codon position mutations, allowing to extricate incorrectly attributed sub-clades. The least squares regression analysis of distribution of frequencies for all mutations observed on a partially disentangled tree for a large set of unique 3243 HA sequences, along all nucleotide positions, was performed for all mutations as well as for non-equivalent amino acid mutations – in both cases demonstrating almost flat gradients, with a very slight downward slope towards the 3′-end positions. The mean mutation rates per sequence per year were 3.83×10−4 for the all mutations, and 9.64×10−5 for the non-equivalent ones.

Phylogenetic analysis of the angiosperm-floricolous insect–yeast association: Have yeast and angiosperm lineages co-diversified?

Metschnikowia (Saccharomycetales, Metschnikowiaceae/Metschnikowia clade) is an ascomycetous yeast genus whose species are associated mostly with angiosperms and their insect pollinators over all continents. The wide distribution of the genus, its association with angiosperm flowers, and the fact that it includes some of the best-studied yeasts in terms of biogeography and ecology make Metschnikowia an excellent group to investigate a possible co-radiation with angiosperm lineages. We performed phylogenetic analyses implementing Bayesian inference and likelihood methods, using a concatenated matrix (≈2.6Kbp) of nuclear DNA (ACT1, 1st and 2nd codon positions of EF2, Mcm7, and RPB2) sequences. We included 77 species representing approximately 90% of the species in the family. Bayesian and parsimony methods were used to perform ancestral character reconstructions within Metschnikowia in three key morphological characters. Patterns of evolution of yeast habitats and divergence times were explored in the Metschnikowia clade lineages with the purpose of inferring the time of origin of angiosperm-associated habitats within Metschnikowiaceae. This paper presents the first phylogenetic hypothesis to include nearly all known species in the family. The polyphyletic nature of Clavispora was confirmed and Metschnikowia species (and their anamorphs) were shown to form two groups: one that includes mostly floricolous, insect-associated species distributed in mostly tropical areas (the large-spored Metschnikowia clade and relatives) and another that comprises more heterogeneous species in terms of habitat and geographical distribution. Reconstruction of character evolution suggests that sexual characters (ascospore length, number of ascospores, and ascus formation) evolved multiple times within Metschnikowia. Complex and dynamic habitat transitions seem to have punctuated the course of evolution of the Metschnikowiaceae with repeated and independent origins of angiosperm-associated habitats. The origin of the family is placed in the Late Cretaceous (71.7Ma) with most extant species arising from the Early Eocene. Therefore, the Metschnikowiaceae likely radiated long after the Mid-Cretaceous radiations of angiosperms and their diversification seems to be driven by repeated radiation on a pre-existing diverse resource.

Editorial [Hot Topic: Replicating Strand Asymmetry in Bacterial and Eukaryotic Genomes (Guest Editor: Feng-Biao Guo)

It is my pleasure as a Guest Editor of Current Genomics to present you with a ‘hot topic issue’ on DNA replication. DNA replication adopts a set of asymmetric mechanisms. One of them is the division of leading and lagging strands. In 1991, the nucleotide composition bias between the two replicating strands was originally found in genomes of echinoderm and vertebrate mitochondria. In the following twenty years, more and more bacterial genomes are found to have much different nucleotide composition between the two replicating strands. More importantly, eukaryotes and even mammalians are found to have such strand bias (asymmetry) in recent years. Besides composition bias, there are also other types of biases between two replicating strands, such as gene orientation bias, gene function bias and substitution rate bias. This topic of replicating strand bias has attracted numerous researchers to perform abundant and in-depth researches. In my view, it will continue to be one of the hot topics of genomics. A better understanding of replicating strand asymmetry will greatly advance our knowledge about the mechanism of DNA replication. This theme issue aims mainly to summarize various types of biases between the two replicating strands in bacterial and eukaryotic genomes. Another aim is to try to elucidate the underlying mechanisms of various strand biases. Therefore, this theme issue includes papers reviewing types, extents, application and underlying mechanism of strand asymmetry both in bacterial and eukaryotic genomes. K. Arakawa and M. Tomita reviewed the measures of strand bias that have been proposed to date, including the ΔGC skew, the predictability score of linear discriminant analysis for gene orientation and so on. These methods measure the general composition bias, gene distribution bias and the composition bias of certain oligonucleotides, respectively. Although these measures were predominantly designed for and applied in analyzing replication-related mutational processes of prokaryotes, the authors also give research examples in eukaryotes. X. Xia summarized the diverse patterns of strand asymmetry among different taxonomic groups and made four suggestions. The survey was involved with bacterial, archaeal and mitochondrial genomes. The four suggestions concern the numbers of replication origins and replicating mechanism in certain taxa. Lin et al. reviewed composition bias between light and heavy strands of animal mitochondrial genomes. They discussed the influence of replication-associated mutation pressure on nucleotide and amino acid compositions as well as gene organization in these genomes. H. Seligmann reviewed coding constraints on replication-associated strand composition bias in mitochondrial genomes. He concludes that the bias is the most at 3rd and least at 2nd codon positions across mitochondrial genomes. There are not bias at synonymous positions forming off frame stops and in regions coding for putative overlapping genes. Also, he compared transcription and replication associated biases of nucleotide composition and mutation rate. The review from V.V. Khrustalev and E.V. Barkovsky focuses on their hypothesis on the formation of replicating strand asymmetries in prokaryotes. In this review, they summarized various proofs supporting the theory. The hypothesis is that the combined effects of cytosine deamination and guanine oxidation produce more nonsense mutations in genes from lagging strands than in genes from leading strands, and hence lead to the composition bias and gene density bias. All of the above papers reviewed mainly on computational researches. Because all types of strand asymmetries derive from the asymmetric mechanism of replication and/or transcription, we have also arrange one review concerning experiment works of DNA replication and transcription. In the paper by Lin and Pasero, mechanisms of the two processes are touched and the focus is put on interference between them. Overall, these reviews provide a fascinating survey of the types, extents, mechanisms and applications of replicating strand asymmetry. I hope that this issue will be useful for the researchers and students in the filed. Finally, I would like to thank all the reviewers for their valuable suggestions and comments, which have led to the improvement of review articles.

Analysis of Codon Usage in Herpesvirus Glycoprotein B (gB) Gene

Due to the degeneracy of genetic code, most amino acids are coded by more than one codon (synonymous codons). The synonymous codons are not used at equal frequencies both within and between organisms. Of the total 33 herpesvirus gB genes, approximately 9.1% of the total gB genes had low codon bias (ENC&lt;35), 72.7% of the gB genes had high ENC values (ENC&gt;50), indicating that these gB genes had random codon usage in herpesviruses. There might be no direct correlation between the codon usage bias and the host, which indicates that the tRNA abundance of the host was not the main factor influencing the codon usage bias. A plot of ENC vs. GC3 indicates that mutational bias may be a more important factor than tRNA abundance in determining codon usage bias of herpesvirus gB genes. Pearson correlation coefficients between the ENC value and corresponding GC%, cumulative GC% in 2nd (GC2%) and 3rd codon position (GC3%) of each herpesvirus gB gene were -0.621 (p&lt;0.01), -0.656 (p&lt;0.01) and -0.712 (p&lt;0.01), respectively, which implies that significant correlations existed between them. But no significant correlations existed between ENC and cumulative GC% in 1st codon position of each herpesviral gB gene. Furthermore, significant correlations also existed between GC% and GC3% of 33 herpesvirus gB genes (r=0.856, p&lt;0.01). So it seems that, GC content, and particularly GC content at the 3rd base position, contributing greatly to the effective number of codons, indicating that the mutational bias dominates over translational selection. Further analysis on the relationship between gene length and ENC of 33 herpesvirus gB genes demonstrated that the two factors were not correlated. Significant correlations were found between the gene expression levels assessed by CAI value and ENC (r = -0.424, p&lt;0.05) and GC3 values (r = 0.644, p&lt;0.01).

Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata

As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.

On the evolution rate in mammalian mitochondrial genomes

AbstractThe methods of phylogenetic inference have become more and more realistic and effective since the evolution rate was taken into account. In order to study the evolution rate more comprehensively, all 13 protein coding genes in 123 mammalian mitochondrial genomes are analyzed. The evolution rates of different codon position are analyzed as well. The evolution rate is estimated by Shannon entropy. We find that the distribution of 3rd codon position doesn’t follow gamma distribution and the results suggest that it follows a mixed distribution of gamma distribution and normal distribution. The relationship between different codon positions is also studied. We find that there are significant positive correlation between three codon positions. Especially between 1st codon position and 2nd codon position, there is strong linear relationship.