We sequenced and annotated the complete mitochondrial genome (mitogenome) of Bactrocera diaphora (Diptera: Tephtitidae), which is an economically important pest in the southwest area of China, India, Sri Lanka, Vietnam and Malaysia. This mitogenome is 15 890 bp in length with an A + T content of 74.103%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the inferred ancestral insects. All protein-coding genes (PCGs) start with a typical ATN codon, except cox1 that begins with TCG. Ten PCGs stop with termination codon TAA or TAG, whereas cox1, nad1 and nad5 have single T-- as the incomplete stop codon. All of the transfer RNA genes present the typical clover leaf secondary structure except trnS1 (AGN) with a looping D-arm. The A + T-rich region is located between rrnS and trnI with a length of 946 bp, and contains a 20 bp poly-T stretch and 22 bp poly-A stretch. Except the control region, the longest intergenic spacer is located between trnR and trnN that is 94 bp long with an excessive high A + T content (95.74%) and a microsatellite-like region (TA)13.
INTRODUCTION: Uropathogenic virulence factors have been identified by comparing the prevalence of these among urinary tract isolates and environmental strains. The uropathogenic-specific protein (USP) gene is present on the pathogenicity island (PAI) of uropathogenic Escherichia coli (UPEC) and, depending on its two diverse gene types and the sequential patterns of three open reading frame units (orfUs) following it, there is a method to characterize UPEC epidemiologically called PAIusp subtyping.
METHODOLOGY: A total of 162 UPEC isolates from Sabah, Malaysia, were tested for the presence of the usp gene and the sequential patterns of three orfUs following it using polymerase chain reaction (PCR). In addition, by means of triplex PCR, the prevalence of the usp gene was compared with other two VFs of UPEC, namely alpha hemolysin (α-hly) and cytotoxic necrotizing factor (cnf-1) genes encoding two toxins.
RESULTS: The results showed that the usp gene was found in 78.40% of UPEC isolates, indicating that its prevalence was comparable to that found in a previous study in Japan. The two or three orfUs were also associated with the usp gene in this study. All the PAIusp subtypes observed in Japan were present in this study, while subtype IIa was the most common in both studies. The usp gene was observed in a higher percentage of isolates when compared with α-hly and cnf-1 genes.
CONCLUSIONS: The findings in Japan and Sabah, East Malaysia, were similar, indicating that PAIusp subtyping is applicable to the characterization of UPEC strains epidemiologically elsewhere in the world.
The main aim of our study was to explore the genome sequence of the inclusion body hepatitis associated Fowl adenovirus serotype 8b (FAdV-8b) UPM04217 and to study its genomic organisation. The nucleotide sequence of the whole genome of FAdV-8b UPM04217 was determined by using the 454 Pyrosequencing platform and the Sanger sequencing method. The complete genome was found to be 44,059 bp long with 57.9% G + C content and shared 97.5% genome identity with the reference FAdV-E genome (HG isolate). Interestingly, the genome analysis using ORF Finder, Glimmer3 and FGENESV predicted a total of 39 open reading frames (ORFs) compared to the FAdV-E HG that possessed 46 ORFs. Fourteen ORFs located within the central genomic region and 16 ORFs located within the left and right ends of the genome were assigned as being the high protein-coding regions. The fusion of the small ORFs at the right end terminal specifically in ORF22 and ORF33 could be the result of gene truncation in the FAdV-E HG. The frame shift mutation in ORF25 and other mutations in ORF13 and ORF17 might have lead to the emergence of genes that could have different functions. Besides, one of the minor capsid components, pVI, in FAdV-8b UPM04217 shared the highest similarity of 93% with that of FAdV-D, while only 47% similarity was found with FAdV-E. From the gene arrangement layout of the FAdV genome, FAdV-8b UPM04217 showed intermediate evolution between the FAdV-E HG and the FAdV-D although it was apparently more similar to the FAdV-E HG.
Polyhydroxybutyrate-co-hydroxyvalerate (PHBV) is a polyhydroxyalkanoate (PHA) bioplastic group with thermoplastic properties is thus high in quality and can be degradable. PHBV can be produced by bacteria, but the process is not economically competitive with polymers produced from petrochemicals. To overcome this problem, research on transgenic plants has been carried out as one of the solutions to produce PHBV in economically sound alternative manner. Four different genes encoded with the enzymes necessary to catalyze PHBV are bktB, phaB, phaC and tdcB. All the genes came with modified CaMV 35S promoters (except for the tdcB gene, which was promoted by the native CaMV 35S promoter), nos terminator sequences and plastid sequences in order to target the genes into the plastids. Subcloning resulted in the generation of two different orientations of the tdcB, pLMIN (left) and pRMIN (right), both 17.557 and 19.967 kb in sizes. Both plasmids were transformed in immature embryos (IE) of oil palm via Agrobacterium tumefaciens. Assays of GUS were performed on one-week-old calli and 90% of the calli turned completely blue. This preliminary test showed positive results of integration. Six-months-old calli were harvested and RNA of the calli were isolated. RT-PCR was used to confirm the transient expression of PHBV transgenes in the calli. The bands were 258, 260, 315 and 200 bp in size for bktB, phaB, phaC and tdcB transgenes respectively. The data obtained showed that the bktB, phaB, phaC and tdcB genes were successfully integrated and expressed in the oil palm genome.
In this study, the complete mitogenome sequence of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae) has been sequenced by next-generation sequencing method. The length of the assembled mitogenome is 16,615 bp, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Clarion angelfish is 28.3% for A, 29.3% for C, 16.5% for G, 25.9% for T and show 85% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Clarion angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.
Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.
A significant fraction of mammalian genomes is composed of endogenous retroviral (ERV) sequences that are formed by germline infiltration of various retroviruses. In contrast to other retroviral genera, lentiviruses only rarely form ERV copies. We performed a computational search aimed at identification of novel endogenous lentiviruses in vertebrate genomes.
Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.
The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.
The mitochondrial genome sequence of the porcellanid crab, Petrolisthes haswelli is provided, making it the second for the family Porcellanidae and the third for the superfamily Galatheoidea. Petrolisthes haswelli has a mitogenome of 15,348 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the P. haswelli mitogenome is 35.66% for T, 18.65% for C, 34.35% for A and 11.34% for G, with an AT bias of 70.01%. The mitogenome gene order is identical to the mitogenome of Neopetrolisthes maculatus, the only other species of the family with a sequenced mitogenome.
The Austropotamobius pallipes complete mitogenome has been recovered using Next-Gen sequencing. Our sample of A. pallipes has a mitogenome of 15,679 base pairs (68.44% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 877 bp non-coding AT-rich region. This is the first mitogenome sequenced for a crayfish from the family Astacidae and the 4(th) for northern hemisphere genera.
The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34.46% for A, and 9.98% for G and has a 68.09% AT bias. While the mitogenome gene order for this species is consistent with aspects of the highly distinctive parastacid crayfish mitogenome gene arrangement, it has a novel gene order involving the rearrangements of a protein coding and several tRNA genes.
The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.
The mitochondrial genome of the rock pool prawn (Palaemon serenus), is sequenced, making it the third for genera of the family Palaemonidae and the first for the genus Palaemon. The mitogenome is 15,967 base pairs in length and comprises 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The P. serenus mitogenome has an AT bias of 58.97% and a base composition of 29.79% for T, 24.14% for C, 29.18% for A, and 16.89% for G. The mitogenome gene order of P. serenus is identical to Exopalaemon carinicauda.
The complete mitochondrial genome of the hermit crab Clibanarius infraspinatus was recovered by genome skimming using Next-Gen sequencing. The Clibanarius infraspinatus mitogenome has 16,504 base pairs (67.94% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1500 bp non-coding AT-rich region. The Clibanarius infraspinatus mitogenome sequence is the first for the family Diogenidae and the second for the superfamily Paguroidea and exhibits a translocation of the ND3 gene not previously reported for the Decapoda.
The mitochondrial genome sequence of the Australian crayfish, Euastacus yarraensis, is documented and compared with other Australian crayfish genera. Euastacus yarraensis has a mitogenome of 15,548 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The base composition of E. yarraensis mitogenome is 32.39% for T, 22.45% for C, 34.43% for A, and 10.73% for G, with an AT bias of 66.82%. The mitogenome gene order conforms to what is considered the primitive arrangement for parastacid crayfish.
The mitochondrial genome sequence of the Morton Bay bug, Thenus orientalis, is documented, which makes it the second mitogenome for species of the family Scyllaridae and the ninth for members of the superfamily Palinuroidae. Thenus orientalis has a mitogenome of 16,826 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of the T. orientalis mitogenome is 31.31% for T, 23.77% for C, 31.05% for A, and 13.87% for G, with an AT bias of 62.36%. In addition to a duplicated trnS1 and several other tRNA gene rearrangements, the mitogenome gene order has novel protein coding gene order with the nad6 and cob genes translocated as a block to a location downstream of the nad3 gene.
The complete mitochondrial genome of the enigmatic freshwater crayfish Engaeus lyelli was sequenced using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitogenome has 16,027 bp consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of E. lyelli is 29.01% for T, 27.13% for C, 31.43% for A, and 12.44% for G, with an AT bias of 60.44%. The species has the distinctive gene order characteristic of parastacid crayfish with the exception of some minor rearrangements involving the tRNA genes.
The complete mitochondrial genome of the commercially important snout otter clam Lutraria rhynchaena was obtained from low-coverage shotgun sequencing data on the MiSeq platform. The L. rhynchaena mitogenome has 16,927 base pairs (69% A + T content) and made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 953 bp non-coding AT-rich region. This is the first mitogenome to be sequenced from the genus Lutraria, and the seventh to be reported for the family Mactridae.
The complete mitochondrial genome of the conservationally significant Macquarie perch (Macquaria australasica) was obtained from low-coverage shotgun sequencing using the MiSeq sequencer. The M. australasica mitogenome has 16,496 base pairs (55% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Macquaria, and the third to be reported for the family Percichthyidae.