Nucleotide Composition Bias Research Articles

The mitochondrial genome of Formicosepsis sp. (Diptera: Cypselosomatidae)

The mitochondrial genome of Formicosepsis sp. was sequenced and annotated as the first representative of family Cypselosomatidae and superfamily Nerioidea. The part mitochondrial genome of Formicosepsis sp. is 15,144 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 76.4% of the entirety. IQ-tree analysis revealed that the outgroups Anopheles oryzalimnetes and Simulium variegatum diverged from the rest. The Nerioidea represented by Formicosepsis sp. was sister group to Opomyzoidea. The Sciomyzoidea consisting of Sciomyzidae and Sepsidae is a monophyletic clade at the base of Acalyptratae.

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

The dance fly Hilara sp. belongs to the subfamily Empidinae of Empididae. The mitogenome (GenBank accession number: MN064659) of Hilara sp. was sequenced, the new representative of the mitogenome of the subfamily. The nearly complete mitogenome is 14,927 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 Empididae. The nucleotide composition biases towards A and T, which together made up 75.7％of the entirety. Bayesian inference analysis strongly supported the monophyly of Empidoidea, Empididae, and Dolichopodidae. It is clear that the phylogenetic relationship within Empidoidea: Dolichopodinae was the sister group to Neurigoninae, and Empidinae was the sister group to Trichopezinae, and the clade that contains Dolichopodinae and Neurigoninae was assigned to the sister group to the clade that contains Empidinae and Trichopezinae.

The mitochondrial genome of Argyra pingwuensis (Diptera: Dolichopodidae)

The long-legged fly Argyra pingwuenesis Qilemoge, Wang et Yang (Genbank accession number: MK905737) belongs to the subfamily Diaphorinae of Dolichopodidae. The mitogenome of A. pingwuenesis was sequenced, the first representative of the mitogenome of the subfamily. The mitogenome is 15,859 bp long, 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 Dolichopodidae. The nucleotide composition biases toward A and T, which together made up 74.6% of the entirety. Bayesian inference analysis strongly supported the monophyly of Dolichopodidae. It suggested that subfamily Diaphorinae is the sister group of subfamily Rhaphiinae.

Interplay between coding and exonic splicing regulatory sequences

The inclusion of exons during the splicing process depends on the binding of splicing factors to short low-complexity regulatory sequences. The relationship between exonic splicing regulatory sequences and coding sequences is still poorly understood. We demonstrate that exons that are coregulated by any given splicing factor share a similar nucleotide composition bias and preferentially code for amino acids with similar physicochemical properties because of the nonrandomness of the genetic code. Indeed, amino acids sharing similar physicochemical properties correspond to codons that have the same nucleotide composition bias. In particular, we uncover that the TRA2A and TRA2B splicing factors that bind to adenine-rich motifs promote the inclusion of adenine-rich exons coding preferentially for hydrophilic amino acids that correspond to adenine-rich codons. SRSF2 that binds guanine/cytosine-rich motifs promotes the inclusion of GC-rich exons coding preferentially for small amino acids, whereas SRSF3 that binds cytosine-rich motifs promotes the inclusion of exons coding preferentially for uncharged amino acids, like serine and threonine that can be phosphorylated. Finally, coregulated exons encoding amino acids with similar physicochemical properties correspond to specific protein features. In conclusion, the regulation of an exon by a splicing factor that relies on the affinity of this factor for specific nucleotide(s) is tightly interconnected with the exon-encoded physicochemical properties. We therefore uncover an unanticipated bidirectional interplay between the splicing regulatory process and its biological functional outcome.

Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908\u2009m in the Mariana Trench

Small amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.

Complete mitochondrial genome of Heterostomus Sp. (Diptera, Xylophagidae)

Among all species of flies, Xylophagidae is one of the most primitive Brachycera families. We sequenced and annotated the mitochondrial genome of Heterostomus sp., the first representative of subfamily Xylophaginae with complete mitochondrial data. This mitogenome is 15,897 bp totally, which consists of 22 transfer RNAs, 13 protein-coding genes, two ribosomal RNAs and non-coding control regions. All genes have the conservational arrangement like other published species of Brachycera. The nucleotide composition biases toward A and T, the overall A + T% was up to 78.7% of the entire mitogenome. Both Bayesian inference and ML analysis strongly supported the monophyly of Xylophagidae. Our results also suggested that Xylophagomorpha is the sister group to Stratiomyomorpha.

The mitochondrial genome of Syntormon pallipes (Diptera: Dolichopodidae)

The long-legged fly Syntormon pallipes belongs to the subfamily Sympycninae of Dolichopodidae. The mitogenome of S. pallipes was sequenced as the first representative of the subfamily. The mitogenome is 15,583 bp long, consisting of 13 protein-coding genes, 2 rRNAs, and 22 transfer RNAs. Syntormon pallipes has the similar gene structures with other published species of Dolichopodidae. The nucleotide composition biases toward A, and T is 78.1% of the entirety. Bayesian inference analysis strongly supported the monophyly of Dolichopodidae, which was inferred from 14 species. It indicated that Sympycninae and Hydrophorinae were assigned to be the sister of the clade of ((Rhaphiinae + Neurigoninae) + (Dolichopodinae + Sciapodinae)).

The mitochondrial genome of Tipula (Formotipula) melanomera gracilispina (Diptera: Tipulidae)

The crane fly Tipula (Formotipula) melanomera gracilispina belongs to the Tipulidae. The mitogenome of T. (F.) melanomera gracilispina was sequenced, the new representative of the mitogenome of the family. The nearly complete mitogenome is 14,575 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 Tipuloidea. 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 Tipuloidea. It suggested that monophyletic Tipulidae was assigned to the sister to the monophyletic Cylindrotomidae and the Limoniidae is the sister group to the clade of Tipulidae + Cylindrotomidae.

The mitochondrial genome of Limonia phragmitidis (Diptera Limoniidae)

The crane fly Limonia phragmitidis belongs to family Limoniidae. The mitogenome of L. phragmitidis was sequenced, the new representative of the mitogenome of the family Limoniidae. The nearly complete mitogenome is 16,020 bp totally, consisting of 13 protein-coding genes, 2 rRNAs, and 22 transfer RNAs. All genes have similar locations and strands with that of other published species of Limoniidae. The nucleotide composition biases toward A and T, which together made up 75.5％of the entirety. Bayesian inference analysis strongly supported the monophyly of Tipuloidea. It suggested that the phylogenetic relationship within Tipuloidea, Pediciidae + (Limoniidae + (Tipulidae + Cylindrotomidae)).

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

The dance fly, Ocydromia sp. belongs to the subfamily Ocydromiinae of Empididae. The mitogenome (GenBank accession number: MK514083) of Ocydromia sp. was sequenced, the first representative of the mitogenome of the subfamily. The nearly complete mitogenome is 16,078 bp totally, consisting of 13 protein-coding genes, 2 rRNAs, and 22 transfer RNAs. All genes have similar locations and strands with that of other published species of Empididae. The nucleotide composition biases toward A and T, which together made up 79.1％ 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 Ocydromiinae.

Strand-specific Single-stranded DNA Sequencing (4S-seq) of E. coli genomes.

Most bacterial genomes have biased nucleotide composition, and the asymmetry is considered to be caused by a single-stranded DNA (ssDNA) deamination arising from the bacterial replication machinery. In order to evaluate the relationship experimentally, the position and frequency of ssDNA formed during replication must be verified clearly. Although many ssDNA detection technologies exist, almost all methods have been developed for eukaryotic genomes. To apply these to bacterial genomes, which harbor a smaller amount of DNA than those of eukaryotes, more efficient, new methods are required. Therefore, we developed a novel strand-specific ssDNA sequencing method, called 4S-seq, for the bacterial genome. The 4S-seq method enriches ssDNA in the extracted genomic DNA by a dsDNA-specific nuclease and implements a strand-specific library using a biotin label with a customized tag. As a result, the 4S-seq is able to calculate the ssDNA content in each strand (Watson/Crick) at each position of the genome efficiently.

Complete mitochondrial genome of Macrosteles quadrimaculatus (Matsumura) (Hemiptera: Cicadellidae: Deltocephalinae) with a shared tRNA rearrangement and its phylogenetic implications

Comparative studies of leafhopper mitochondrial genomes suggest that genome rearrangements are very rare in these insects but that nucleotide sequences are informative of phylogenetic relationships at various levels of divergence. A recent study reported that tRNA cluster trnW-trnC-trnY is rearranged to trnC-trnW-trnY in the Aster Leafhopper, Macrosteles quadrilineatus, an economically important North American species. The complete mitochondrial genome of the East Asian species, Macrosteles quadrimaculatus, sequenced and annotated here for the first time, reveals that this species shares the same tRNA rearrangement, suggesting it is a genus-level trait. The entire mitogenome of M. quadrimaculatus is a circular molecule 15,734 bp in size comprising 37 genes and one control region, which is similar to other studied hemipteran mitogenomes. The whole mitogenome sequence shows heavily A + T biased nucleotide composition (77.7%) and moderately positive AT-skews (0.120). Except for the nad5 gene which starts with TTG and ends with incomplete codon T, all protein-coding genes begin with ATN codons and terminate with TAA. All tRNA genes have typical cloverleaf secondary structures, except for trnS1, in which dihydrouridine (DHU) stem is simplified to form a loop structure. Phylogenetic analysis based on nucleotide sequence datasets recovered Macrosteles as monophyletic and sister to the rest of Deltocephalinae.

Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata.

Squamate reptiles are a major component of vertebrate biodiversity whose crown-clade traces its origin to a narrow window of time in the Mesozoic during which the main subclades diverged in rapid succession. Deciphering phylogenetic relationships among these lineages has proven challenging given the conflicting signals provided by genomic and phenomic data. Most notably, the placement of Iguania has routinely differed between data sources, with morphological evidence supporting a sister relationship to the remaining squamates (Scleroglossa hypothesis) and molecular data favoring a highly nested position alongside snakes and anguimorphs (Toxicofera hypothesis). We provide novel insights by generating an expanded morphological dataset and exploring the presence of phylogenetic signal, noise, and biases in molecular data. Our analyses confirm the presence of strong conflicting signals for the position of Iguania between morphological and molecular datasets. However, we also find that molecular data behave highly erratically when inferring the deepest branches of the squamate tree, a consequence of limited phylogenetic signal to resolve this ancient radiation with confidence. This, in turn, seems to result from a rate of evolution that is too high for historical signals to survive to the present. Finally, we detect significant systematic biases, with iguanians and snakes sharing faster rates of molecular evolution and a similarly biased nucleotide composition. A combination of scant phylogenetic signal, high levels of noise, and the presence of systematic biases could result in the misplacement of Iguania. We regard this explanation to be at least as plausible as the complex scenario of convergence and reversals required for morphological data to be misleading. We further evaluate and discuss the utility of morphological data to resolve ancient radiations, as well as its impact in combined-evidence phylogenomic analyses, with results relevant for the assessment of evidence and conflict across the Tree of Life.

The mitochondrial genome of Drino Sp. (Diptera, Tachinidae)

The tachinid fly Drino sp. belongs to the subfamily Exoristinae of Tachinidae. We sequenced and annotated the mitogenome of Drino sp. which makes this species first representative of the tribe Eryciini (Tachinidae: Exoristinae) with nearly complete mitochondrial data. This mitogenome is 15437 bp in total, which consists of 22 transfer RNAs, 13 protein-coding genes, 2 ribosomal RNAs and non-coding control region. All genes have the conservational arrangement with other published species of Tachinidae. The nucleotide composition biases toward A and T, the overall A + T% was up to 80.4% of the entire mitogenome. Bayesian inference analysis strongly supported the monophyly of Tachinidae and Exoristinae. Our results also suggested that Exoristinae is the sister group to Phasiinae, and Dexiinae is the sister group to the clade of Phasiinae + Exoristinae.

The mitochondrial genome of Hybos serratus (Diptera: Empididae)

The dance fly Hybos serratus Yang et Yang belongs to the subfamily Hybotinae of Empididae. The mitogenome of H. serratus was sequenced, the first representative of the mitogenome of the subfamily. The nearly complete mitogenome is 15,997 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 towards A and T, which together made up 79% of the entirety. Bayesian inference analysis strongly supported the monophyly of Empidoidea and Dolichopodidae. This result also suggested that Hybotinae is assigned to the sister group to the clade of Dolichopodidae and Empididae.

The mitochondrial genome of Rhaphium baihuashanum (Diptera: Dolichopodidae)

The long-legged fly Rhaphium baihuashanum Yang belongs to the subfamily Rhaphiinae of Dolichopodidae. The mitogenome of R. baihuashanum was sequenced, the first representative of the mitogenome of the subfamily. The mitogenome is 15,173 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 Dolichopodidae. The nucleotide composition biases toward A and T, which together made up 74.1％ of the entirety. Bayesian inference analysis strongly supported the monophyly of Dolichopodidae. It suggested that Rhaphiinae is the sister group to the clade of ((Hydrophorinae + Neurigoninae) + (Sciapodinae + Dolichopodinae)).

Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.

Off-target oligoprobe’s interaction with partially complementary nucleotide sequences represents a problem for many bio-techniques. The goal of the study was to identify oligoprobe sequence characteristics that control the ratio between on-target and off-target hybridization. To understand the complex interplay between specific and genome-wide off-target (cross-hybridization) signals, we analyzed a database derived from genomic comparison hybridization experiments performed with an Affymetrix tiling array. The database included two types of probes with signals derived from (i) a combination of specific signal and cross-hybridization and (ii) genomic cross-hybridization only. All probes from the database were grouped into bins according to their sequence characteristics, where both hybridization signals were averaged separately. For selection of specific probes, we analyzed the following sequence characteristics: vulnerability to self-folding, nucleotide composition bias, numbers of G nucleotides and GGG-blocks, and occurrence of probe’s k-mers in the human genome. Increases in bin ranges for these characteristics are simultaneously accompanied by a decrease in hybridization specificity—the ratio between specific and cross-hybridization signals. However, both averaged hybridization signals exhibit growing trends along with an increase of probes’ binding energy, where the hybridization specific signal increases significantly faster in comparison to the cross-hybridization. The same trend is evident for the S function, which serves as a combined evaluation of probe binding energy and occurrence of probe’s k-mers in the genome. Application of S allows extracting a larger number of specific probes, as compared to using only binding energy. Thus, we showed that high values of specific and cross-hybridization signals are not mutually exclusive for probes with high values of binding energy and S. In this study, the application of a new set of sequence characteristics allows detection of probes that are highly specific to their targets for array design and other bio-techniques that require selection of specific probes.

Comparative analysis of the Liriomyza chinensis mitochondrial genome with other Agromyzids reveals conserved genome features

Liriomyza chinensis is a serious pest of onions in many countries, especially in East Asia. We sequenced the complete mitochondrial genome of this species and compared it with five other Agromyzidae species. The L. chinensis mitogenome is a double-stranded 16,175 bp circular molecule with an A + T content of 78.3%. It contains 37 genes and a control region as do the sequenced Liriomyza species. The mitogenomes of L. chinensis and other Agromyzidae species showed a clear bias in nucleotide composition with a positive AT-skew. Most PCGs used standard ATN as start codons, and TAN as termination codons. The tRNAs exhibited the typical clover-leaf structure, except for tRNASer(AGN) and the two rRNA genes are conserved with those of other Agromyzids. The L. chinensis mitogenome control region included several conserved regions, including a poly-T, two (TA)n and one poly-A stretch, which are considered important replication and transcription. The 13 PCGs were used to study the phylogeny of L. chinensis and five related Agromyzids. Analysis by maximum likelihood, Bayesian inference and genetic distance suggest congruent phylogenetic relationships in Liriomyza spp. and provide a useful supplement to taxonomic classification by morphology.

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

RNA binding proteins (RBPs) orchestrate the production, processing, and function of mRNAs. Here, we present the affinity landscapes of 78 human RBPs using an unbiased assay that determines the sequence, structure, and context preferences of these proteins invitro by deep sequencing of bound RNAs. These data enable construction of "RNA maps" of RBP activity without requiring crosslinking-based assays. We found an unexpectedly low diversity of RNA motifs, implying frequent convergence of binding specificity toward a relatively small set of RNA motifs, many with low compositional complexity. Offsetting this trend, however, we observed extensive preferences for contextual features distinct from short linear RNA motifs, including spaced "bipartite" motifs, biased flanking nucleotide composition, and bias away from or toward RNA structure. Our results emphasize the importance ofcontextual features in RNA recognition, which likely enable targeting of distinct subsets of transcripts by different RBPs that recognize the same linear motif.

Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera)

BackgroundMitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets. Various strategies have been proposed to ameliorate the effects of potential mt-genome biases, including dense taxon sampling, removal of third codon positions or purine-pyrimidine coding and the use of site-heterogeneous models. In this study, we sequenced the mt-genomes of five additional Tingidae species and discussed the compositional and mutational rate heterogeneity in mt-genomes and its effect on the phylogenetic inferences of Cimicomorpha by implementing the bias-reduction strategies mentioned above.ResultsHeterogeneity in nucleotide composition and mutational biases were found in mt protein-coding genes, and the third codon exhibited high levels of saturation. Dense taxon sampling of Tingidae and Reduviidae and the other common strategies mentioned above were insufficient to recover the monophyly of the well-established group Cimicomorpha. When the sites with weak phylogenetic signals in the dataset were removed, the remaining dataset of mt-genomes can support the monophyly of Cimicomorpha; this support demonstrates that mt-genomes possess strong phylogenetic signals for the inference of higher-level phylogeny of this group. Comparison of the ratio of the removal of amino acids for each PCG showed that ATP8 has the highest ratio while CO1 has the lowest. This pattern is largely congruent with the evolutionary rate of 13 PCGs that ATP8 represents the highest evolutionary rate, whereas CO1 appears to be the lowest. Notably, the value of Ka/Ks ratios of all PCGs is less than 1, indicating that these genes are likely evolving under purifying selection.ConclusionsOur results demonstrate that mt-genomes have sites with strong phylogenetic signals for the inference of higher-level phylogeny of Cimicomorpha. Consequently, bioinformatic approaches to removing sites with weak phylogenetic signals in mt-genome without relying on an a priori tree topology would greatly improve this field.