The mitochondrial genomes of Tortricidae: nucleotide composition, gene variation and phylogenetic performance

Background Mitochondrial genomes (mitogenomes) have greatly improved our understanding of the backbone phylogeny of Lepidoptera, but few studies on comparative mitogenomics below the family level have been conducted. Here, we generated 13 mitogenomes of eight tortricid species, reannotated 27 previously reported mitogenomes, and systematically performed a comparative analysis of nucleotide composition, gene variation and phylogenetic performance. Results The lengths of completely sequenced mitogenomes ranged from 15,440 bp to 15,778 bp, and the gene content and organization were conserved in Tortricidae and typical for Lepidoptera. Analyses of AT-skew and GC-skew, the effective number of codons and the codon bias index all show a base bias in Tortricidae, with little heterogeneity among the major tortricid groups. Variations in the divergence rates among 13 protein-coding genes of the same tortricid subgroup and of the same PCG among tortricid subgroups were detected. The secondary structures of 22 transfer RNA genes and two ribosomal RNA genes were predicted and comparatively illustrated, showing evolutionary heterogeneity among different RNAs or different regions of the same RNA. The phylogenetic uncertainty of Enarmoniini in Tortricidae was confirmed. The synonymy of Bactrini and Olethreutini was confirmed for the first time, with the representative Bactrini consistently nesting in the Olethreutini clade. Nad6 exhibits the highest phylogenetic informativeness from the root to the tip of the resulting tree, and the combination of the third coding positions of 13 protein-coding genes shows extremely high phylogenetic informativeness. Conclusions This study presents 13 mitogenomes of eight tortricid species and represents the first detailed comparative mitogenomics study of Tortricidae. The results further our understanding of the evolutionary architectures of tortricid mitogenomes and provide a basis for future studies of population genetics and phylogenetic investigations in this group.

Genome-wide mapping implicates R-loops in lineage-specific processes and formation of DNA break hotspots in neural stem/progenitor cells

ABSTRACTRecent work has revealed classes of recurrent DNA double-strand breaks (DSBs) in neural stem/progenitor cells, including transcription-associated, promoter-proximal breaks and recurrent DSB clusters in late-replicating, long neural genes. However, the mechanistic factors promoting these different classes of DSBs in neural stem/progenitor cells are not understood. Here, we elucidated the genome-wide landscape of DNA:RNA hybrid structures called “R-loops” in primary neural stem/progenitor cells in order to assess their contribution to the different classes of DNA break “hotspots”. We report that R-loops in neural stem/progenitor cells are associated primarily with transcribed regions that replicate early and genes that show GC skew in their promoter region. Surprisingly, the majority of genes with recurrent DSB clusters in long, neural genes does not show substantial R-loop accumulation. We implicate R-loops in promoter-proximal DNA break formation in highly transcribed, early replicating regions and conclude that R-loops are not a driver of recurrent double-strand break cluster formation in most long, neural genes. Together, our study provides an understanding of how R-loops may contribute to DNA break hotspots and affect lineage-specific processes in neural stem/progenitor cells.

SkewDB: A comprehensive database of GC and a 10 other skews for over 28,000 chromosomes and plasmids

ABSTRACTGC skew denotes the relative excess of G nucleotides over C nucleotides on the leading versus the lagging replication strand of eubacteria. While the effect is small, typically around 2.5%, it is robust and pervasive. GC skew and the analogous TA skew are a localized deviation from Chargaff’s second parity rule, which states that G and C, and T and A occur with (mostly) equal frequency even within a strand.Most bacteria also show the analogous TA skew. Different phyla show different kinds of skew and differing relations between TA and GC skew.This article introduces an open access database (https://skewdb.org) of GC and 10 other skews for over 28,000 chromosomes and plasmids. Further details like codon bias, strand bias, strand lengths and taxonomic data are also included. The SkewDB database can be used to generate or verify hypotheses. Since the origins of both the second parity rule, as well as GC skew itself, are not yet satisfactorily explained, such a database may enhance our understanding of microbial DNA.

The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

The complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

Comparative Mitogenomics of Two Critically Endangered Turtles, Batagur Kachuga and Batagur Dhongoka (Testudines: Geoemydidae): Implications in Phylogenetics of Freshwater Turtles

The Red-crowned roofed turtle (Batagur kachuga) and Three-striped roofed turtle (B. dhongoka) are ‘critically endangered’ turtles in the Geoemydidae family. Herein, we generated the novel mitochondrial genome sequence of B. kachuga (16,155) and B. dhongoka (15,620) and compared it with other turtles species. Batagur mitogenome has 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and one control region (CR). The genome composition was biased toward A + T, with positive AT-skew and negative GC-skew. In the examined species, all 13 PCGs were started by ATG codons, except COI gene, which was initiated by GTG. The majority of mito-genes were encoded on the heavy strand, except eight tRNAs and the ND6 region. We observed a typical cloverleaf structure for all tRNA, excluding tRNASer (AGN), where the base pairs of the dihydrouridine (DHU) arm were abridged. Bayesian Inference (BI) based phylogenetic analysis was constructed among 39 species from six Testudines families, exhibited a close genetic relationship between Batagur and Pangshura with a high supporting value (PP ~ 0.99). It provides additional mitogenomic resources for further study of the Testudines evolutionary patterns.

Epigenetic Marks and Variation of Sequence-Based Information Along Genomic Regions Are Predictive of Recombination Hot/Cold Spots in Saccharomyces cerevisiae

Characterization and identification of recombination hotspots provide important insights into the mechanism of recombination and genome evolution. In contrast with existing sequence-based models for predicting recombination hotspots which were defined in a ORF-based manner, here, we first defined recombination hot/cold spots based on public high-resolution Spo11-oligo-seq data, then characterized them in terms of DNA sequence and epigenetic marks, and finally presented classifiers to identify hotspots. We found that, in addition to some previously discovered DNA-based features like GC-skew, recombination hotspots in yeast can also be characterized by some remarkable features associated with DNA physical properties and shape. More importantly, by using DNA-based features and several epigenetic marks, we built several classifiers to discriminate hotspots from coldspots, and found that SVM classifier performs the best with an accuracy of ∼92%, which is also the highest among the models in comparison. Feature importance analysis combined with prediction results show that epigenetic marks and variation of sequence-based features along the hotspots contribute dominantly to hotspot identification. By using incremental feature selection method, an optimal feature subset that consists of much less features was obtained without sacrificing prediction accuracy.

Characterization of the First Complete Mitochondrial Genome of Cyphonocerinae (Coleoptera: Lampyridae) with Implications for Phylogeny and Evolution of Fireflies

Complete mitochondrial genomes are valuable resources for phylogenetics in insects. The Cyphonoceridae represents an important lineage of fireflies. However, no complete mitogenome is available until now. Here, the first complete mitochondrial genome from this subfamily was reported, with Cyphonocerus sanguineus klapperichi as a representative. The mitogenome of C. sanguineus klapperichi was conserved in the structure and comparable to that of others in size and A+T content. Nucleotide composition was A+T-biased, and all genes exhibited a positive AT-skew and negative GC-skew. Two types of tandem repeat sequence units were present in the control region (136 bp × 2; 171 bp × 2 + 9 bp). For reconstruction of Lampyridae’s phylogeny, three different datasets were analyzed by both maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, the same topology was produced by both ML analysis of 13 protein-coding genes and 2rRNA and BI analysis of 37 genes. The results indicated that Lampyridae, Lampyrinae, Luciolinae (excluding Emeia) were monophyletic, but Ototretinae was paraphyletic, of which Stenocladius was recovered as the sister taxon to all others, while Drilaster was more closely related to Cyphonocerinae; Phturinae + Emeia were included in a monophyletic clade, which comprised sister groups with Lampyridae. Vesta was deeply rooted in the Luciolinae.

Phylogeny and evolution of Lasiopodomys in subfamily Arvivolinae based on mitochondrial genomics

The species of Lasiopodomys Lataste 1887 with their related genera remains undetermined owing to inconsistent morphological characteristics and molecular phylogeny. To investigate the phylogenetic relationship and speciation among species of the genus Lasiopodomys, we sequenced and annotated the whole mitochondrial genomes of three individual species, namely Lasiopodomys brandtii Radde 1861, L. mandarinus Milne-Edwards 1871, and Neodon (Lasiopodomys) fuscus Büchner 1889. The nucleotide sequences of the circular mitogenomes were identical for each individual species of L. brandtii, L. mandarinus, and N. fuscus. Each species contained 13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs, with mitochondrial genome lengths of 16,557 bp, 16,562 bp, and 16,324 bp, respectively. The mitogenomes and PCGs showed positive AT skew and negative GC skew. Mitogenomic phylogenetic analyses suggested that L. brandtii, L. mandarinus, and L. gregalis Pallas 1779 belong to the genus Lasiopodomys, whereas N. fuscus belongs to the genus Neodon grouped with N. irene. Lasiopodomys showed the closest relationship with Microtus fortis Büchner 1889 and M. kikuchii Kuroda 1920, which are considered as the paraphyletic species of genera Microtus. TMRCA and niche model analysis revealed that Lasiopodomys may have first appeared during the early Pleistocene epoch. Further, L. gregalis separated from others over 1.53 million years ago (Ma) and then diverged into L. brandtii and L. mandarinus 0.76 Ma. The relative contribution of climatic fluctuations to speciation and selection in this group requires further research.

SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

GC skew is a phenomenon observed in many bacterial genomes, wherein the two replication strands of the same chromosome contain different proportions of guanine and cytosine nucleotides. Here we demonstrate that this phenomenon, which was first discovered in the mid-1990s, can be used today as an analysis tool for the 15,000+ complete bacterial genomes in NCBI’s Refseq library. In order to analyze all 15,000+ genomes, we introduce a new method, SkewIT (Skew Index Test), that calculates a single metric representing the degree of GC skew for a genome. Using this metric, we demonstrate how GC skew patterns are conserved within certain bacterial phyla, e.g. Firmicutes, but show different patterns in other phylogenetic groups such as Actinobacteria. We also discovered that outlier values of SkewIT highlight potential bacterial mis-assemblies. Using our newly defined metric, we identify multiple mis-assembled chromosomal sequences in previously published complete bacterial genomes. We provide a SkewIT web app https://jenniferlu717.shinyapps.io/SkewIT/ that calculates SkewI for any user-provided bacterial sequence. The web app also provides an interactive interface for the data generated in this paper, allowing users to further investigate the SkewI values and thresholds of the Refseq-97 complete bacterial genomes. Individual scripts for analysis of bacterial genomes are provided in the following repository: https://github.com/jenniferlu717/SkewIT.

Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta)

Background The Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the molecular evolution of their mitochondrial genomes (mitogenomes). Results To fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes exhibit the following three features: (i) reduction in genome size and gene inventory, (ii) evolution of unique protein properties including charge, hydropathy, stability, amino acid composition, and protein size, and (iii) distinctive GC-content and skewness of nucleotides. Based on GC-skew-associated characteristics, we postulate that unidirectional DNA replication may have resulted in the rapid evolution of G-type mitogenomes. Conclusions The high divergence of G-type mitogenomes was likely driven by natural selection in the multiple extreme environments that Galdieria species inhabit combined with their highly flexible heterotrophic metabolism. We speculate that the interplay between mitogenome divergence and adaptation may help explain the dominance of Galdieria species in diverse extreme habitats.