No abstract

The phylogeny of true bugs (Hemiptera: Heteroptera), one of the most diverse insect groups in terms of morphology and ecology, has been the focus of attention for decades with respect to several deep nodes between the suborders of Hemiptera and the infraorders of Heteroptera. Here, we assembled a phylogenomic data set of 53 taxa and 3102 orthologous genes to investigate the phylogeny of Hemiptera-Heteroptera, and both concatenation and coalescent methods were used. A binode-control approach for data filtering was introduced to reduce the incongruence between different genes, which can improve the performance of phylogenetic reconstruction. Both hypotheses (Coleorrhyncha + Heteroptera) and (Coleorrhyncha + Auchenorrhyncha) received support from various analyses, in which the former is more consistent with the morphological evidence. Based on a divergence time estimation performed on genes with a strong phylogenetic signal, the origin of true bugs was dated to 290-268 Ma in the Permian, the time in Earth's history with the highest concentration of atmospheric oxygen. During this time interval, at least 1007 apomorphic amino acids were retained in the common ancestor of the extant true bugs. These molecular apomorphies are located in 553 orthologous genes, which suggests the common ancestor of the extant true bugs may have experienced large-scale evolution at the genome level.

Heteroptera are among the most diverse hemimetabolous insects. Seven infraorders have been recognized within this suborder of Hemiptera. Apart from the well-established sister-group relationship between Cimicomorpha and Pentatomomorpha (= Terheteroptera), the two terminal lineages, the relationships among the other five infraorders are still controversial, of which three (Gerromorpha, Nepomorpha and Leptopodomorpha) are intimately connected to aquatic environments. However, the various and often conflicting available phylogeny hypotheses do not offer a clear background for a connection between diversification and palaeoenvironments. In this study, a molecular data set representing 79 taxa and 10 149 homologous sites is used to infer the phylogenetic relationships within Heteroptera. Bayesian inference, maximum-likelihood and maximum parsimony analyses were employed. The results of phylogenetic inferences largely confirm the widely accepted phylogenetic context. Estimation of the divergence time based on the phylogenetic results revealed that Gerromorpha, Nepomorpha and Leptopodomorpha originated successively during the period from the Late Permian to Early Triassic . This timescale is consistent with the origin and radiation time of various aquatic holometabolans. Our results indicate that the aquatic and semi-aquatic true bugs evolved under environmental conditions of high air temperature and humidity in an evolutionary scenario similar to that of the aquatic holometabolans.

Pentatomoidea (stink bugs and their relatives) is the third largest superfamily in Heteroptera, or the true bugs. The phylogenetic relationships among the families within Pentatomoidea remain controversial. The family Lestoniidae is morphologically highly specialized, currently including only two species endemic to Australia. Previous researchers have suggested a close relationship of Lestoniidae to either Plataspidae or Acanthosomatidae, based on morphological characters. In this study, phylogenetic tree reconstruction revealed that Lestoniidae and Acanthosomatidae form a monophyletic clade. In addition, in comparisons of the secondary structures of 18S and 28S rRNAs representing 15 families of Pentatomoidea, four length-variable regions in 18S and 28S rRNAs that can serve as autapomorphies for the clade Lestoniidae + Acanthosomatidae were recognized. Among them, E in 18S rRNA and D3-1 and D5-1 in 28S rRNA are unique in length in Lestoniidae and Acanthosomatidae. Based on the new molecular evidence and morphological evidence published by previous authors, Lestoniidae is suggested to be a highly specialized group derived from a common ancestor with Acanthosomatidae.

BackgroundViral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas. Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied. HeLa is a well characterized HPV+ cervical cancer cell line.ResultWe developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip. Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing. Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions. Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level. By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins.ConclusionOur results reveal the heterogeneity of a virus-infected cell line. It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-015-0091-4) contains supplementary material, which is available to authorized users.

The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.

No abstract

Insecta s. str. (=Ectognatha), comprise the largest and most diversified group of living organisms, accounting for roughly half of the biodiversity on Earth. Understanding insect relationships and the specific time intervals for their episodes of radiation and extinction are critical to any comprehensive perspective on evolutionary events. Although some deeper nodes have been resolved congruently, the complete evolution of insects has remained obscure due to the lack of direct fossil evidence. Besides, various evolutionary phases of insects and the corresponding driving forces of diversification remain to be recognized. In this study, a comprehensive sample of all insect orders was used to reconstruct their phylogenetic relationships and estimate deep divergences. The phylogenetic relationships of insect orders were congruently recovered by Bayesian inference and maximum likelihood analyses. A complete timescale of divergences based on an uncorrelated log-normal relaxed clock model was established among all lineages of winged insects. The inferred timescale for various nodes are congruent with major historical events including the increase of atmospheric oxygen in the Late Silurian and earliest Devonian, the radiation of vascular plants in the Devonian, and with the available fossil record of the stem groups to various insect lineages in the Devonian and Carboniferous.