Nucleotide Composition Bias Research Articles

The complete mitochondrial genome sequence of Coenonympha amaryllis and monophyly of Satyrinae (Lepidoptera: Nymphalidae)

The complete mitochondrial genome (mitogenome) of a Satirid species Coenonympha amaryllis was assembled and annotated. The mitogenome is a DNA molecule of 15125 bp, and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 rRNAs, and 1 A–T rich region. The nucleotide composition biases toward A and T is 79.4% of the entirety, which is a typical structure of Lepidopterans. All PCGs started with ATN, except cox1, which started with CGA, 8 PCGs stop with TAN and 5 genes exhibited incomplete stop codon. Phylogenetic analysis revealed that Satyrinae is a monophyletic group and Coenonympha (C. amaryllis) as sister of the genus Triphysa (T. phryne).

A multigene phylogeny and timeline for Trichoptera (Insecta)

The Trichoptera, or caddisflies, are traditionally split into two taxonomic subdivisions: the ‘retreat‐making’ Annulipalpia and the ‘case‐making’ Integripalpia (sensu Ross). The monophyly of these groups is well documented; however, the establishment of a third subdivision, ‘Spicipalpia’, and the positions of the five ‘spicipalpian’ families is much debated. In contrast to previous molecular studies using nuclear ribosomal RNA, a recent trichopteran study (using nuclear protein‐coding genes) placed one of these ‘spicipalpian’ families, the free‐living predatory Rhyacophilidae, as the sister taxon to the rest of Trichoptera, a result that has significant implications for both the understanding of trichopteran evolution and its timing. This paper sets out to investigate the relationships of Trichoptera using several newly sequenced genes, together with previously published gene sequences. This dataset is the largest trichopteran dataset to date, covering six independent genes and > 10 000 nucleotides, and containing 185 species representing 49 families. With all data included, likelihood and Bayesian analyses support a monophyletic Annulipalpia and a monophyletic Integripalpia, which includes the ‘spicipalpians’ as a paraphyletic grade at the base of this clade. However, an analysis of the protein‐coding data alone using similar analytical methods recovers Rhyacophilidae as the most basal taxon in Trichoptera, with low support. A reanalysis correcting for nucleotide composition bias provides support for the placement of the ‘spicipalpian’ taxa as sister to the Integripalpia, consistent with the total data analysis, suggesting that the basal position of Rhyacophilidae in the uncorrected analysis could be (or is probably) an artefact of base composition. We find it likely that ancestral trichopterans made incipient cases and retreats, and these had independent origins as precocious pupal chambers. Molecular dating analysis in beast, using the birth‐death model of speciation, with a relaxed‐clock model of sequence evolution informed by 37 fossil constraints, suggests that the most recent common ancestor of Trichoptera appeared in the Permian (c. 275 Ma) in line with the first appearance of Trichoptera in the fossil record, and that vicariance explains the distribution of most trichopteran taxa. A new infraordinal name, Phryganides, is introduced for the tube‐case‐making families of Integripalpia.

Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics.

Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera.

The mitochondrial genome of Hercostomus brevipilosus (Diptera: Dolichopodidae)

The long-legged fly Hercostomus brevipilosus (Genbank accession number: MN840034) belongs to the subfamily Dolichopodinae of Dolichopodidae. The mitogenome of H. brevipilosus was sequenced, the first representative of the mitogenome of the genus Hercostomus. The mitogenome is 15,019 bp totally, consisting of 13 protein-coding genes, two rRNAs and 22 transfer RNAs. All genes have similar locations and strands with that of other published species of Dolichopodidae. The nucleotide composition biases toward A and T, which together made up 73.9％ of the entirety. Bayesian inference analysis strongly supported the monophyly of Dolichopodidae and Dolichopodinae. It suggested that Hercostomus is the sister group of Dolichopus.

The mitochondrial genome of Medetera sp. (Diptera: Dolichopodidae)

The long-legged fly Medetera sp. (Genbank accession number: MN604695) belongs to the subfamily Medeterinae of Dolichopodidae. The mitogenome of Medetera sp. was sequenced, the first representative of the mitogenome of the subfamily. The mitogenome is 14,740 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs. All genes have similar locations and strands with that of other published species of Dolichopodidae. The nucleotide composition biases toward A and T, which together made up 67.6％ of the entirety. Bayesian inference analysis strongly supported the monophyly of Dolichopodidae. It suggested that subfamily Medeterinae is the sister group of subfamily Rhaphiinae.

Characterizing the interplay between gene nucleotide composition bias and splicing

BackgroundNucleotide composition bias plays an important role in the 1D and 3D organization of the human genome. Here, we investigate the potential interplay between nucleotide composition bias and the regulation of exon recognition during splicing.ResultsBy analyzing dozens of RNA-seq datasets, we identify two groups of splicing factors that activate either about 3200 GC-rich exons or about 4000 AT-rich exons. We show that splicing factor–dependent GC-rich exons have predicted RNA secondary structures at 5′ ss and are dependent on U1 snRNP–associated proteins. In contrast, splicing factor–dependent AT-rich exons have a large number of decoy branch points, SF1- or U2AF2-binding sites and are dependent on U2 snRNP–associated proteins. Nucleotide composition bias also influences local chromatin organization, with consequences for exon recognition during splicing. Interestingly, the GC content of exons correlates with that of their hosting genes, isochores, and topologically associated domains.ConclusionsWe propose that regional nucleotide composition bias over several dozens of kilobase pairs leaves a local footprint at the exon level and induces constraints during splicing that can be alleviated by local chromatin organization at the DNA level and recruitment of specific splicing factors at the RNA level. Therefore, nucleotide composition bias establishes a direct link between genome organization and local regulatory processes, like alternative splicing.

Nucleotide composition and synonymous codon usage of open reading frames in Norovirus GII.4 variants

Norovirus GII.4 variants, a genotype in genogroup II belonging to the genus Norovirus, is a single-strand positive sense RNA containing three open reading frames (ORF1, ORF2 and ORF3) and is the most important pathogen causing nonbacterial gastroenteritis outbreaks. By using bioinformatic softwares such as Codon W, SPSS and so on, a total of 292 strains of the viruses isolated from 1974 to 2016 were analyzed for nucleotide composition and synonymous codon usage in each ORF. The result shows that it is enriched for A over the other bases in nucleotide composition, G behind the other bases in the 3rd site of all synonymous codons in the three ORFs. The patterns of nucleotide composition and codon bias of ORF2 are similar to those of ORF3 and different from those of ORF1. There are generally UpA motif and CpG motif in the codons with the lowest proportion. Correspondence analysis indicates that the codon usage may be changing over a certain time period for ORF1 in 2006 and 2012, ORF2 in 2012, and ORF3 in 2013. ENC (effective number of codons) plot and other analyses indicate that both natural selection and mutational pressure play partly roles in the ORFs, but natural selection is more important for ORF2 and ORF3. Besides, we also found all optimal codons in the ORFs. The study provides a basic understanding of the mechanism for norovirus GII.4 codon usage bias. AbbreviationsORFOpen Reading FrameENCEffective Number of CodonsCOAcorrespondence analysisRSCURelative Synonymous Codon UsageCAICodon Adaptation IndexCBICodon Bias IndexFopfrequency of optimal codonsL_symnumber of synonymous codonsL_aalength amino acidsGRAVYgrand average of hydropathicityAromaaromaticityCommunicated by Ramaswamy H. Sarma

The Complete Mitochondrial Genome of the Caecal Fluke of Poultry, Postharmostomum commutatum, as the First Representative from the Superfamily Brachylaimoidea.

Postharmostomum commutatum (Platyhelminthes: Brachylaimoidea), a parasite of the caeca of poultry, has been frequently reported from many countries and regions, including China. However, the molecular epidemiology, population genetics and phylogenetics of this parasite are poorly understood. In the present study, we determined and characterized the complete mitochondrial (mt) genome of P. commutatum, as the first representative from the superfamily Brachylaimoidea. The mt genome of P. commutatum is a circular DNA molecule of 13,799 bp in size and encodes the complete set of 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as a typical control region. The mt genome of P. commutatum presents a clear bias in nucleotide composition with a negative AT-skew on average (−0.306) and a positive GC-skew on average (0.466). Phylogenetic analyses showed that P. commutatum (superfamily Brachylaimoidea) and other ten members of the order Diplostomida were recovered as sister groups of the order Plagiorchiida, indicating that the order Diplostomida is paraphyletic. This is the first mt genome of any member of the superfamily Brachylaimoidea and should represent a rich source of genetic markers for molecular epidemiological, population genetic and phylogenetic studies of parasitic flukes of socio-economic importance in poultry.

Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs.

Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins.IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth's system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.

The complete mitochondrial genome of click beetle Agrypnus sp. (Coleoptera: Elateridae) and phylogenetic analysis

Larvae of click beetles are the most important soil-dwelling agricultural pests and are abundant throughout the world. Agrypnus sp. belongs to the subfamily Agrypninae of Elateridae. Here, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Agrypnus sp., the new representative of the mitogenome of the subfamily. This mitogenome was 16,056 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA unit genes (rRNAs). Gene order was conserved and identical to most other previously sequenced Elateridae. The nucleotide composition biases towards A and T, which together made up 70.8% of the entirety. Phylogenetic analysis based on 13 PCGs sequences showed that Agrypnus sp. got together with the same subfamily species Pyrophorus divergens, Pyrearinus termitilluminans, Ignelater luminosus, and Hapsodrilus ignifer with high support value.

The complete mitochondrial genome of Anthomyza sp. (Diptera: Anthomyzidae)

Anthomyza sp. belongs to family Anthomyzidae of superfamily Opomyzoidea. The mitogenome of Anthomyza sp. was sequenced as the first representative of the family. The mitogenome is 16,308 bp totally, consisting of 13 protein-coding genes, 2 rRNAs and 22 transfer RNAs and control region. Anthomyza sp. has the similar gene structures with other published species of Acalyptratae. The nucleotide composition biases toward A and T is 78.7% of the entirety. IQ-TREE analysis recovered the monophyly of Opomyzoidea, which is inferred from 12 species. It indicated that Opomyzoidea is assigned to be the sister of the clade of (Ephydroidea + (Tephritoidea + Lauxanioidea)).

The mitochondrial genome of Chinese endemic species Pseudolimnophila (Pseudolimnophila) brunneinota (Diptera: Limoniidae)

The mitogenome of Pseudolimnophila (Pseudolimnophila) brunneinota was sequenced, the new representative of the subfamily Limnophilinae in mitogenome. The completed mitogenome is 15,985 bp totally, comprising of 13 protein-coding genes, 2 rRNAs, 22 transfer RNAs and control region. All genes have the similar locations and strands with other published species of Tipuloidea. The nucleotide composition biases toward A and T, which together made up 78.00％of the entirety. Bayesian inference analysis strongly supported the monophyly of Chioneinae + Limnophilinae. It suggested that the phylogenetic relationship within Tipuloidea is Pediciidae + (Limoniidae ((Chioneinae + Limnophilinae)+ Limoniinae) + (Tipulidae + Cylindrotomidae)).

The complete mitochondrial genome of Silba sp. (Diptera: Lonchaeidae)

The mitochondrial genome of Silba sp. was sequenced and annotated as the first representative of family Lonchaeidae. The complete mitochondrial genome of Silba sp. is 16,008 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs, which has a similar gene structure with other published species of Diptera. The nucleotide composition biases toward A and T is 77.2% of the entirety. All PCGs start with ATN codons, except COI and ND1, and end with TAA or incomplete stop codon. Phylogenetic analyses based on 11 Diptera species supported the monophyly of superfamily Tephritoidea.

The mitochondrial genome of Nephrotoma Tenuipes (Diptera Tipulidae)

The crane fly Nephrotoma tenuipes belongs to family Tipulidae. The mitogenome of N. tenuipes was sequenced, the new representative of the mitogenome of the family Tipulidae. The nearly complete mitogenome is 14,851 bp totally, consisting of 13 protein-coding genes, 2 rRNAs and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Tipulidae. The nucleotide composition biases toward A and T, which together made up 76.04％of the entirety. Bayesian inference analysis strongly supported the monophyly of Tipuloidea. It suggested that the phylogenetic relationship within Tipuloidea is Pediciidae + (Limoniidae + (Tipulidae + Cylindrotomidae)).

The mitochondrial genome of Vulgichneumon sp. (Hymenoptera: Ichneumonidae)

The Vulgichneumon sp. belongs to the subfamily Ichneumoninae of Ichneumonidae. The mitogenome (GenBank accession number: MN178162) of Vulgichneumon sp. was sequenced, the first representative of the mitogenome of the subfamily. The nearly complete mitogenome is 15,306 bp totally, consisting of 13 protein-coding genes, 2 rRNAs and 22 transfer RNAs. The nucleotide composition biases toward A and T, which together made up 83.6% of the entirety. Bayesian inference analysis supported the monophyly of Evanioidea, Chalcidoidea, Platygastroidea, Proctotrupoidea, Ceraphronoidea, and Ichneumonoidea. This result also suggested that the clade that contains other six superfamilies was the sister group to the clade that consist of Trigonaloidea, Megalyroidea and Ichneumonoidea.

The mitochondrial genome of Empis separata (Diptera: Empididae)

The dance fly Empis separata belongs to the subfamily Empidinae of Empididae. The mitogenome (GenBank accession number: MK993569) of E. separata was sequenced, the new representative of the mitogenome of the subfamily. The complete mitogenome is 14,961 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Empididae. The nucleotide composition biases toward A and T, which together made up 76.3% of the entirety. Bayesian inference analysis strongly supported the monophyly of Empidoidea, Empididae, and Dolichopodidae. This result also suggested that Empidinae is the sister group to the clade of Trichopezinae.

The mitochondrial genome of Erannis ankeraria (Lepidoptera: Geometridae)

The measuring worm Erannis ankeraria belongs to the subfamily Ennominae of Geometridae. The mitogenome (GenBank accession number: MN046105) of E. ankeraria was sequenced, the new representative of the mitogenome of the subfamily. The nearly complete mitogenome is 15,250 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Geometridae. The nucleotide composition biases towards A and T, which together made up 79.3% of the entirety. Bayesian inference analysis strongly supported the monophyly of Bombycoidea, Geometroidea, Noctuoidea, Papilionoidea, Pyraloidea, and Tortricoidea were strongly supported. This result also suggested that the Geometroidea was the sister to Bombycoidea, and then Noctuoidea was assigned to the sister group to the clade of Geometroidea + Bombycoidea, and then Pyraloidea was the sister group to the clade that contains Geometroidea, Bombycoidea, and Noctuoidea, and then Papilionoidea was the sister group to the clade that contains these four superfamilies mentioned above.

The mitochondrial genome of Suillia sp. (Diptera: Heleomyzidae)

The mitogenome of Suillia sp. was sequenced as the first representative of the family Heleomyzidae. The mitogenome is 15,660 bp totally, consisting of 13 protein-coding genes, 2 rRNAs, and 22 transfer RNAs. The nucleotide composition biases toward A and T is 75.1％ of the entirety. All PCGs start with ATN codons except COI and ND1 and end with TAA or incomplete stop codon. Phylogenetic analyses based on 9 dipteran species supported the relationship of Opomyzoidea + (Ephydroidea + (Lauxanioidea + (Sciomyzoidea + (Sphaeroceroidea + Tephritoidea)))).

The mitochondrial genome of Conosia irrorata (Diptera: Limoniidae)

The crane fly Conosia irrorata belongs to the subfamily Limnophilinae of Limoniidae. The mitogenome (GenBank accession number: MK864103) of C. irrorata was sequenced, the new representative of the mitogenome of the subfamily. The nearly complete mitogenome is 14,634 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Limoniidae. The nucleotide composition biases toward A and T, which together made up 77.5％ of the entirety. Bayesian inference analysis strongly supported the monophyly of Tipuloidea. It suggested that the monophyletic Tipulidae was assigned to the sister to the monophyletic Cylindrotomidae. The Limoniidae is the sister group to the clade of Tipulidae + Cylindrotomidae, and Pediciidae was assigned to the sister to the group that contain Limoniidae + (Tipulidae + Cylindrotomidae).

The mitochondrial genome of Oreogeton sp. (Diptera: Empididae)

The dance fly Oreogeton sp. belongs to the subfamily Oreogetoninae of Empididae. The mitogenome of Oreogeton sp. (GenBank accession number: MK639348) was sequenced, the first representative of the mitogenome of the subfamily. The nearly complete mitogenome is 15,718 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Empididae. The nucleotide composition biases toward A and T, which together made up 77.2％of the entirety. Bayesian inference analysis strongly supported the monophyly of Empidoidea, Empididae, and Dolichopodidae. This result also suggested that Oreogetoninae was assigned to the sister group to the clade that consists of Trichopezinae and Clinocerinae, and then Empidinae is the sister to the clade that contains Oreogetoninae, Trichopezinae, and Clinocerinae.