Xuhao Song

The complete mitochondrial genome of Epicauta chinensis (Coleoptera: Meloidae) and phylogenetic analysis among Coleopteran insects.

The blister beetle is an important resource insect due to its defensive substance cantharidin, which was widely used in pharmacology and plant protection. We determined the complete mitochondrial genome of Epicauta chinensis Laporte (Coleoptera: Tenebrionoidae: Meloidae). The circular genome is 15,717 bp long, encoding 13 protein-coding genes (PCGs), two ribosomal RNAs and 22 tRNAs and containing a A+T-rich region with gene arrangement identical to other Coleopteran species. Twelve PCGs start with typical ATN codon, while ATP8 gene initiate with GTT for first report in Insecta. All PCGs terminate with conventional stop codon TAA or TAG. All tRNAs in E. chinensis are predicted to fold into typical cloverleaf secondary structure, except tRNA-Ser(AGN), in which the dihydrouracil arm (DHU arm) could not form stable stem-loop structure. The secondary structure of lrRNA and srRNA comprises 48 helices and 32 helices respectively. The 1101 bp A+T-rich region contains a 15 bp poly-T stretch and microsatellite-like repeats rather than large tandem repetitive sequences. Phylogenetic analysis, based on 13 PCGs of 45 Coleopteran species, show that E. chinensis grouped with Tenebrionidae species. It also support the topology of (((Chrysomelidae+Curculionoidea)+(Cucujoidea+Cleroidea))+Tenebrionoidea) within Cucujiformia.

Quorum-sensing molecules N -acyl homoserine lactones inhibit Trueperella pyogenes infection in mouse model

Trueperella pyogenes is a gram-positive opportunistic pathogen normally causes mastitis, liver abscesses and pneumonia of economically important livestock. It has been suggested that gram-negative bacteria can suppress the growth and virulence of T. pyogenes in vitro by using the quorum-sensing (QS) signal molecules and cause the transition of predominant species. However, whether these QS signals can be used as potential anti-virulence drugs against T. pyogenes infection is unclear. In this study, the in vivo inhibitory effect N-acyl homoserine lactones (AHLs) from Escherichia coli and Pseudomonas aeruginosa on T. pyogenes was tested by using mouse model. Mice were first peritoneally infected with T. pyogenes followed by intravenous injection of N-Octanoyl-DL-homoserine lactone (C8HSL) or N-(3-oxododecanoyl) homoserine-l-lactone (C12HSL). The results showed that C8HSL and C12HSL significantly reduced bacterial load and increased the survival rate of mice against T. pyogenes challenge. Additionally, the treatment of AHLs promoted the secretion of IL-1β, IL-6, IL-8 and TNF-α in mouse peritoneal fluid, and significantly decreased the expression levels of virulence genes of residual T. pyogenes. Importantly, murine macrophages rapidly phagocytosed bacteria when they were treated with AHLs compared to untreated cells. Collectively, our findings provide a major advance in understanding the inhibitory effect of AHLs in vivo and a promise for developing new clinical or veterinary treatments of T. pyogenes-related infection.

Comparative transcriptome analysis of Trueperella pyogenes reveals a novel antimicrobial strategy

Trueperella pyogenes is a prevalent opportunistic bacterium that normally causes diverse suppurative lesions, endometritis and pneumonia in various economically important animals. Although the genomic information of this species has been announced, little is known about its functional profiles. In this study, by performing a comparative transcriptome analysis between the highly and moderately virulent T. pyogenes isolates, we found the expression of a LuxR-type DNA-binding response regulator, PloR, was significantly up-regulated in the highly virulent T. pyogenes. Protein crystal structure prediction and primary functional assessment suggested that, the quorum-sensing signal molecules of Gram-negative bacteria such as Pseudomonas aeruginosa and Escherichia coli could significantly inhibit the growth, biofilm production and hemolysis of T. pyogenes by binding to the upstream sensor histidine kinase, PloS. Therefore, the PloS/PlosR two-component regulatory system might dominate the virulence of T. pyogenes. Our findings provide a major advance in understanding the pathogenesis of T. pyogenes, and may shed new light on the development of novel therapeutic strategies to control T. pyogenes infection.

Phylogenetic analysis of the Black Stork Ciconia nigra (Ciconiiformes: Ciconiidae) based on complete mitochondrial genome

Abstract The Black Stork, Ciconia nigra belongs to family Ciconiidae, which is evaluated as Least Concern by IUCN. In this study, the complete mitochondrial genome of C. nigra was first sequenced and characterized, which was 17,795 bp in length. The mt-genome has tandem repeats of 80 bp and 78 bp repeat units, and AAACAAC and AAACAAACAAC tandem repeats in D-loop region. It is notable that a single extra base “C” at position 174 was inserted in gene ND3. Bayesian inference, maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand protein-coding genes. Phylogenetic analyses showed that Ardeidae diverged earlier than Ciconiidae, Cathartida and Threskiornithidae, and Ciconiidae had closest relationship to Cathartida. C. nigra diverged first among three Ciconia birds.

Transcriptome-Derived Tetranucleotide Microsatellites and Their Associated Genes from the Giant Panda (Ailuropoda melanoleuca)

Recently, an increasing number of microsatellites or simple sequence repeats (SSRs) have been found and characterized from transcriptomes. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In this work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, 4 CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these 4 CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes containing these 4 CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers will pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda.

The complete mitochondrial genome of the Leopoldamys edwardsi (Rodentia: Muridae).

Abstract The complete mitochondrial genome of L. edwardsi was first sequenced and characterized. The genome was 16,284 bases in length and the composition and arrangement of its genes are analogous to most other rodents. The nucleotide sequence date of 12 heavy-strand protein-coding genes of L. edwardsi and other 26 Muridae species were used for phylogenetic analyses. Trees constructed using Maximum Likelihood, Neighbor Joining and Minimum Evolution demonstrated that L. edwardsi was closer to the genus Niviventer than Rattus. Combing previous research, it suggests that Edward’s long-tailed rat is more suitable to be classified into genus Leopoldamys and named as Leopoldamys edwardsi. This study suggested that R. edwardsi is inappropriate for the other name of L. edwardsi.

Complete mitochondrial genome sequence of Arboreal Brown-toothed Shrew, Episoriculus macrurus

Abstract The Arboreal Brown-toothed Shrew (Episoriculus macrurus) belongs to the family Soricidae, and distributes in China, Nepal, India, Myanma, and Vietnam. In this study, the complete mitochondrial genome sequence of E. macrurus was determined. The mitogenome is 16,943 bp in length. Phylogenetic trees were constructed by the methods of Bayesian inference and maximum likelihood. The results showed that in the family of Soricidae, Crocidurinae differentiated earlier than Soricinae. Episoriculus was more close to Nectogale or Neomys rather than Sorex, and Blarinella was close to Sorex. This study contributes to illuminating the taxonomic status of E. macrurus.