In this study, we established a general framework to use PacBio full-length transcriptome sequencing for the investigation of mitochondrial RNAs. As a result, we produced the first full-length human mitochondrial transcriptome using public PacBio data and characterized the human mitochondrial genome with more comprehensive and accurate information. Other results included determination of the H-strand primary transcript, identification of the ND5/ND6AS/tRNAAS transcript, discovery of palindrome small RNAs (psRNAs) and construction of the "mitochondrial cleavage" model, etc. These results reported for the first time in this study fundamentally changed annotations of human mitochondrial genome and enriched knowledge in the field of animal mitochondrial studies. The most important finding was two novel long non-coding RNAs (lncRNAs) of MDL1 and MDL1AS exist ubiquitously in animal mitochondrial genomes.

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In this study, we sequenced the first full-length insect transcriptome using the Erthesina fullo Thunberg based on the PacBio platform. We constructed the first quantitative transcription map of animal mitochondrial genomes and built a straightforward and concise methodology to investigate mitochondrial gene transcription, RNA processing, mRNA maturation and several other related topics. Most of the results were consistent with the previous studies, while to the best of our knowledge some findings were reported for the first time in this study. The new findings included the high levels of mitochondrial gene expression, the 3 0 polyadenylation and possible 5 0 m 7 G caps of rRNAs, the isoform diversity of 12S rRNA, the polycistronic transcripts and natural antisense transcripts of mitochondrial genes et al. These findings could challenge and enrich fundamental concepts of mitochondrial gene transcription and RNA processing, particularly of the rRNA primary (sequence) structure. The methodology constructed in this study can also be used to study gene expression or RNA processing of nuclear genomes.

Pentatomomorpha is one of the most diversified infraorders of the true bugs (Insecta: Hemiptera: Heteroptera). The phylogenetic relationships among superfamilies within this infraorder are still in dispute. In this study, 31 species representing 26 pentatomomorphan and four cimicomorphan putative families were chosen, and six Hox gene fragments with as many as 4 kilobases for each representative were analyzed to reconstruct the phylogeny of the Pentatomomorpha. The (Homeotic) Hox gene family is a group of nuclear genes, which is considered to determine animal segmentation. The combined nucleotide and amino acid sequences were used separately as two data matrices, and analyzed by employing maximum likelihood and Bayesian methods. Results strongly support the monophyly of Trichophora and the superfamilies Pentatomoidea, Lygaeoidea, Coreoidea, and Pyrrhocoroidea. The relationship of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Coreoidea + Pyrrhocoroidea)))) was mostly congruent with previous results based on the morphological data. Our results suggested that the Hox genes could be used as novel molecular markers for phylogenetic research on the Pentatomomorpha and other insects.

Background Coronary artery atherosclerosis is a chronic inflammatory disease. This study aimed to identify the key changes of gene expression between early and advanced carotid atherosclerotic plaque in human. Methods Gene expression dataset GSE28829 was downloaded from Gene Expression Omnibus (GEO), including 16 advanced and 13 early stage atherosclerotic plaque samples from human carotid. Differentially expressed genes (DEGs) were analyzed. Results 42,450 genes were obtained from the dataset. Top 100 up- and downregulated DEGs were listed. Functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) identification were performed. The result of functional and pathway enrichment analysis indicted that the immune system process played a critical role in the progression of carotid atherosclerotic plaque. Protein-protein interaction (PPI) networks were performed either. Top 10 hub genes were identified from PPI network and top 6 modules were inferred. These genes were mainly involved in chemokine signaling pathway, cell cycle, B cell receptor signaling pathway, focal adhesion, and regulation of actin cytoskeleton. Conclusion The present study indicated that analysis of DEGs would make a deeper understanding of the molecular mechanisms of atherosclerosis development and they might be used as molecular targets and diagnostic biomarkers for the treatment of atherosclerosis.