The complete mitochondrial genome of Philus pallescens Bates, 1866 (Coleoptera: Vesperidae) and its phylogenetic implications.

We sequenced and assembled the complete mitochondrial genome of Philus pallescens from Madou, Tainan County, Taiwan. The complete mitogenome of P. pallescens is 15,750 bp long, and contains 13 protein-coding, 22 tRNA and two rDNA genes. Nucleotide compositions of the mitogenome of P. pallescens are A: 38.08%, T: 32.25%, C: 18.67%, and G: 11.00%. The AT and GC skewness of the mitogenome sequence were 0.0828 and -0.25845 respectively, showing the genome composition skewed toward adenine and cytosine. The phylogenetic position of Chrysomelidae is sister to all the other families in the superfamily Chrysomeloidea. The results indicate that Chrysomeloidea Cerambycidae is not a monophyletic group. Philus is phylogenetically close to Spiniphilus. Vesperidae is monophyletic and sister to Disteniidae. Mitogenomic data from this study will provide useful information for further studies on the population genetics, speciation, and pest management of P. pallescens.

Histology and transcriptomic analyses of barnacles with different base materials and habitats shed lights on the duplication and chemical diversification of barnacle cement proteins.

BACKGROUND: Barnacles are sessile crustaceans that attach to underwater surfaces using barnacle cement proteins. Barnacles have a calcareous or chitinous membranous base, and their substratum varies from biotic (e.g. corals/sponges) to abiotic surfaces. In this study, we tested the hypothesis that the cement protein (CP) composition and chemical properties of different species vary according to the attachment substrate and/or the basal structure. We examined the histological structure of cement glands and explored the variations in cement protein homologs of 12 barnacle species with different attachment habitats and base materials. RESULTS: Cement gland cells in the rocky shore barnacles Tetraclita japonica formosana and Amphibalanus amphitrite are eosinophilic, while others are basophilic. Transcriptome analyses recovered CP homologs from all species except the scleractinian coral barnacle Galkinia sp. A phylogenomic analysis based on sequences of CP homologs did not reflect a clear phylogenetic pattern in attachment substrates. In some species, certain CPs have a remarkable number of paralogous sequences, suggesting that major duplication events occurred in CP genes. The examined CPs across taxa show consistent bias toward particular sets of amino acid. However, the predicted isoelectric point (pI) and hydropathy are highly divergent. In some species, conserved regions are highly repetitive. CONCLUSIONS: Instead of developing specific cement proteins for different attachment substrata, barnacles attached to different substrata rely on a highly duplicated cementation genetic toolkit to generate paralogous CP sequences with diverse chemical and biochemical properties. This general CP cocktail might be the key genetic feature enabling barnacles to adapt to a wide variety of substrata.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Mytella strigata (Hanley 1843) (Bivalvia: Mytiloida: Mytilidae).

We sequenced and assembled the complete mitochondrial genome (mitogenome) sequence of the American brackish water mussel Mytella strigata. The mitogenome, reaching 16,302 bp in length, includes 13 protein-coding genes, 2 ribosomal RNA genes, and 23 transfer RNA genes. The overall nucleotide composition of mitogenome was 25.17% A, 41.86% T, 11.83% C, and 21.13% G. The most common start and stop codons were GTG and TAA, respectively. The phylogenetic analysis based on mitogenomes showed that the families Mytilidae, Ostreidae, and Veneridae are a monophyletic group. The phylogenetic position of M. strigata is sister to P. canaliculus and P. viridis. In this study, mitogenomic sequence data will provide a better understanding for future studies of population genetics, biogeography, and pest surveillance of M. strigata.

The complete mitochondrial genome of Mnais tenuis Oguma, 1913 (Odonata: Calopterygidae) and its phylogenetic implications.

We sequenced and assembled the complete mitochondrial genome of Mnais tenuis from Darshi, Taoyuan County, Taiwan. The complete mitogenome of M. tenuis is 15,131 bp long, and contains 13 protein-coding, 22 tRNA, and two rDNA genes. Nucleotide compositions of the mitogenome of the M. tenuis are A: 40.08%, T: 25.47%, C: 20.38%, and G: 14.07%. The AT and GC skewness of the mitogenome sequence was 0.2228 and -0.183, showing the A-skew and C-skew. The clade including M. tenuis and all the other Odonata species received absolute support (100%). The phylogenetic position of Anisozygoptera is sister to Anisoptera. Mnais is phylogenetically close to Psolodesmus. Mitogenomic data from this study will provide useful information for further studies for the population genetics, speciation and conservation of M. tenuis in the future.

The complete mitochondrial genome of Meretrix lusoria (Bivalvia: Veneroida: Veneridae) from Kumamoto, Japan.

We sequenced and assembled the complete mitochondrial genome sequence of the Meretrix lusoria, from Kumamoto, Japan. The length of mitogenome is 20,180 bp, including 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The nucleotide composition of the mitogenome was 25.73% for A, 42.41% for T, 9.35% for C, and 22.49% for G. The AT and GC skewness of mitogenome sequence are -0.245 and 0.412, showing the T-skew and G-skew. The reconstructed phylogenetic relationships of 25 Bivalvia species based on 12 protein-coding genes were highly supported and the clade of all Meretrix clams included had a support value of 99%. Our results shall provide a better understanding in the evolutionary histories of the Veneroida and relative species.

Characterization of the complete mitochondrial genome of Euwallacea fornicatus (Eichhoff, 1868) (Coleoptera: Curculionidae: Scolytinae) and its phylogenetic implications.

In the present report, we described the complete mitochondrial genome of Euwallacea fornicatus from Sindien, New Taipei City, Taiwan. The length of the complete mitogenome of E. fornicatus is 15,743 bp and the mitogenome contains 13 protein-coding, 22 tRNA and two rDNA genes. Nucleotide compositions of the whole mitogenome are 39.41% for A, 33.84% for T, 16.64% for C, and 10.11% for G. The AT and GC skewness of mitogenome sequence was 0.076 and -0.244, showing the A-skew and C-skew. The reconstructed phylogenetic relationships of 33 Curculionid species based on 13 mitochondrial protein-coding genes received absolute support (100%). Euwallacea fornicates is sister to the rest species in Xyleborini. The phylogenetic position of Scolytinae is sister to the clade including Cucurlioninae, Molytinae and Cryptorhynchinae. Mitogenomic data from this study will provide useful information for further studies for the population genetics, invasive history and pest control of E. fornicatus in the future.

Characterisation of the complete mitochondrial genome of Lucanus chengyuani (Coleoptera: Lucanidae).

We sequenced and assembled the complete mitochondrial genome of Lucanus chengyuani, from the Alishan, Chiayi County, Taiwan. The length of the complete mitogenome of L. chengyuani is 16,926 bp and the mitogenome contains 13 protein-coding, 22 tRNA, and 2 rDNA genes. Nucleotide compositions of the whole mitogenome of L. chengyuani are 38.37% for A, 27.96% for T, 23.03% for C, and 10.637% for G. The AT and GC skewness of mitogenome sequence are 0.157 and -0.368, showing the A-skew and C-skew. The reconstructed phylogenetic relationships of 9 Lucanidae species based on 13 mitochondrial protein-coding genes are highly supported. The clade including Neolucanus maximus and Odontolabis cuvera is sister to the rest of the stag beetle clades, which contains L. chengyuani and L. mazama. Mitogenomic data from this study will provide useful information for further studies for the population genetics, speciation, biogeography, and conservation of L. chengyuani in the future.

The complete mitochondrial genome of Hymenocera picta (Malacostraca: Decapoda: Hymenoceridae).

In this study, the complete mitochondrial genome sequence of the Hymenocera picta is reported for the first time. The length of genome is 15,786 bp, including 13 protein-coding genes, two ribosomal RNA genes, and 21 transfer RNA genes. Nucleotide composition of the whole mitogenome was 37.26% A, 28.42% T, 21.92% C, and 12.40% G. The AT and GC skewness of mitogenome sequence was 0.135 and 0.277, respectively. The reconstructed phylogenetic relationships of 22 Decapoda species based on 13 protein-coding genes were highly supported and the clade of all Palaemonoidea shrimps included had a high support value. Our results shall provide a better understanding in the evolutionary histories of the Decapoda.

The complete mitochondrial genome of Babylonia borneensis (Gastropoda: Neogastropoda: Buccinidae).

The complete mitochondrial genome sequence of the Babylonia borneensis is reported for the first time in this study. The length of genome was 15 556 bp, including 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. The nucleotide composition of the mitogenome showed AT-rich feature, with the AT content of 68.2%. Comparison of the identity of the B. borneensis mitogenome with B. areolata, B. lani and B. lutosa was 87.5%, 87.4% and 86.9%, respectively. The construction of phylogenetic tree showed high bootstrap support value. Babylonia borneensis grouped together with other Babylons and the lineages of Buccinidae was strongly supported. In this study, our results could provide a further understanding in the phylogenetic relationships of the Neogastropoda.

The complete mitochondrial genome of Poecilia formosa (Actinopterygii: Cyprinodontiformes: Poeciliidae).

The complete mitochondrial genome sequence of the Poecilia formosa is first reported in this study. The length of genome is 16 550 bp, including 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. Congeneric mitogenome sequence identity is 87.7% with P. reticulate and 93.1% with P. sphenops. The reconstructed phylogenetic relationships of 16 Cyprinodontiformes species based on 13 protein-coding genes were highly supported and the clade of all Poecilia fishes included had a support value of 100%. Our results shall provide a better understanding in the evolutionary histories of the Cyprinodontiformes.

Reverse transcription loop-mediated isothermal amplification for rapid and sensitive detection of nervous necrosis virus in groupers.

The reverse transcription loop-mediated isothermal amplification (RT-LAMP) method is a sensitive nucleic acid diagnostic method that can amplify rapidly a target template; it can be applied for the diagnosis of viral disease in grouper aquaculture. In this study, two outer and two inner primers were designed from nervous necrosis virus (NNV) coat protein gene sequence. The reaction temperature and time for the detection of NNV were optimized at 65 degrees C for 60min. The detection limit of RT-LAMP is 10(-6) NNV-RNA from infected groupers, and more sensitive than the one-step RT-PCR and nested RT-PCR. The combination of RNA rapid extraction and RT-LAMP, the process can be completed within 2h. Thus, the RT-LMAP is a rapid, sensitive, specific and efficient method for detection of NNV in groupers.