The dinucleotide composition of the Zika virus genome is shaped by conflicting evolutionary pressures in mammalian hosts and mosquito vectors.

Most vertebrate RNA viruses show pervasive suppression of CpG and UpA dinucleotides, closely resembling the dinucleotide composition of host cell transcriptomes. In contrast, CpG suppression is absent in both invertebrate mRNA and RNA viruses that exclusively infect arthropods. Arthropod-borne (arbo) viruses are transmitted between vertebrate hosts by invertebrate vectors and thus encounter potentially conflicting evolutionary pressures in the different cytoplasmic environments. Using a newly developed Zika virus (ZIKV) model, we have investigated how demands for CpG suppression in vertebrate cells can be reconciled with potentially quite different compositional requirements in invertebrates and how this affects ZIKV replication and transmission. Mutant viruses with synonymously elevated CpG or UpA dinucleotide frequencies showed attenuated replication in vertebrate cell lines, which was rescued by knockout of the zinc-finger antiviral protein (ZAP). Conversely, in mosquito cells, ZIKV mutants with elevated CpG dinucleotide frequencies showed substantially enhanced replication compared to wild type. Host-driven effects on virus replication attenuation and enhancement were even more apparent in mouse and mosquito models. Infections with CpG- or UpA-high ZIKV mutants in mice did not cause typical ZIKV-induced tissue damage and completely protected mice during subsequent challenge with wild-type virus, which demonstrates their potential as live-attenuated vaccines. In contrast, the CpG-high mutants displayed enhanced replication in Aedes aegypti mosquitoes and a larger proportion of mosquitoes carried infectious virus in their saliva. These findings show that mosquito cells are also capable of discriminating RNA based on dinucleotide composition. However, the evolutionary pressure on the CpG dinucleotides of viral genomes in arthropod vectors directly opposes the pressure present in vertebrate host cells, which provides evidence that an adaptive compromise is required for arbovirus transmission. This suggests that the genome composition of arbo flaviviruses is crucial to maintain the balance between high-level replication in the vertebrate host and persistent replication in the mosquito vector.

Nocardia panacis sp. nov., a novel actinomycete with antiphytopathogen activity isolated from the rhizosphere of Panax notoginseng.

Strain YIM PH21724T was isolated from the rhizosphere of Panax notoginseng. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain exhibits close phylogenetic relatedness to Nocardia kroppenstedtii N1286T (97.70%), Nocardia farcinica NCTC 11134T (97.67%) and Nocardia puris DSM 44599T (97.40%). The menaquinones were identified as MK-9 (H4), MK-8 (H4, ω-cyclo) and MK-8 (H4), and the major fatty acids (> 10%) were identified as C16:0, C18:1 ω9c and C18:0 10-methyl. The polar lipids were found to be composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified lipid. The G + C content of the genomic DNA was determined to be 67.01 mol%. The phenotypic, chemotaxonomic, phylogenetic and genomic results clearly show strain YIM PH21724T should be classified in the genus Nocardia and represents a novel species, for which the name Nocardia panacis sp. nov. is proposed. The type strain is YIM PH21724T (= DSM 105904T = KCTC 49030T = CCTCC AA 2017043T).

Lacisediminimonas profundi gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from freshwater sediment.

A novel Gram-stain-negative bacterial strain, CHu64-6-4T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of strain CHu64-6-4T were aerobic nonmotile and formed colorless colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the family Oxalobacteraceae, exhibiting 97.2% and 97.1% 16S rRNA gene sequence similarities to Glaciimonas singularis and Paraherbaspirillum soli, respectively. Strain CHu64-6-4T showed less than 74.4% average nucleotide identity compared to the type strains of related genera within the family Oxalobacteraceae. In the UPGMA dendrogram based on the ANI values of genomic sequences, strain CHu64-6-4T formed an evolutionary lineage independent of the genera Glaciimonas and some other taxa. The chemotaxonomic results showed Q-8 as the predominant respiratory ubiquinone, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethnolamine as the major polar lipids, Summed Feature 3 (C16:1ω7c and/or iso-C15:0 2-OH), C16:0, and C18:1ω7c as the major fatty acids, and a DNA G+C content of 62.1 mol%. The combined genotypic and phenotypic data showed that strain CHu64-6-4T could be distinguished from all genera within the family Oxalobacteraceae and represents a novel genus, Lacisediminimonas profundi gen. nov., with the name Lacisediminimonas profundi sp. nov., in the family Oxalobacteraceae. The type strain is CHu64-6-4T (=KCTC 62287T=JCM 32676T).

Paenibacillus pinistramenti sp. nov., isolated from pine litter.

A Gram-stain-positive bacterium, designated strain ASL46T, was isolated from litter layer of a pine forest located in Anmyondo, Korea. Strain ASL46T was found to be an aerobic, motile, endospore-forming rod which can grow at 20-45 °C (optimum, 37 °C), at pH 6.0-11.0 (optimum, pH 7.0) and at salinities of 0-2% (w/v) NaCl (optimum, 1% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain ASL46T belongs to the genus Paenibacillus, showing highest sequence similarity to P. yonginensis DCY84T (98.3%), P. physcomitrella XBT (97.4%) and P. faecis CIP 101062T (96.6%). The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain ASL46T and P. physcomitrella XBT and P. yonginensis DCY84T yielded ANI values of 84.6 and 84.5% and DNA-DNA relatedness of 11.7 ± 0.7 and 10.9 ± 0.2%, respectively. The DNA G+C content of the genomic DNA of strain ASL46T was 52.1 mol%. The predominant isoprenoid quinone was identified as menaquinone-7 and the major cellular fatty acids were determined to be anteiso-C15:0, C16:0 and iso-C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, an unidentified phospholipid and an unidentified glycolipid. The whole-cell sugar was found to be ribose and cell wall peptidoglycan contained meso-diaminopimelic acid. On the basis of phylogenetic analyses, and phenotypic and chemotaxonomic characteristics, strain ASL46T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus pinistramenti sp. nov. is proposed. The type strain is ASL46T (= KACC 18701T = NBRC 111876T).

A systematic approach re-analyzing the effects of temperature disturbance on the microbial community of mesophilic anaerobic digestion.

Microbial communities are key drivers of ecosystem processes, but their behavior in disturbed environments is difficult to measure. How microbial community composition and function respond disturbances is a common challenge in biomedical, environmental, agricultural, and bioenergy research. A novel way to solve this problem is to use a systems-level perspective and describe microbial communities as networks. Based on a mesophilic anaerobic digestion system of swine manure as a tool, we propose a simple framework to investigate changes in microbial communities via compositions, metabolic pathways, genomic properties and interspecies relationships in response to a long-term temperature disturbance. After temperature disturbance, microbial communities tend towards a competitive interaction network with higher GC content and larger genome size. Based on microbial interaction networks, communities responded to the disturbance by showing a transition from acetotrophic (Methanotrichaceae and Methanosarcinaceae) to methylotrophic methanogens (Methanomassiliicoccaceae and Methanobacteriaceae) and a fluctuation in rare biosphere taxa. To conclude, this study may be important for exploring the dynamic relationships between disturbance and microbial communities as a whole, as well as for providing researchers with a better understanding of how changes in microbial communities relate to ecological processes.

How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome.

Bacterial xenogeneic silencers play important roles in bacterial evolution by recognizing and inhibiting expression from foreign genes acquired through horizontal gene transfer, thereby buffering against potential fitness consequences of their misregulated expression. Here, the detailed DNA binding properties of Rok, a xenogeneic silencer in Bacillus subtilis, was studied using protein binding microarray, and the solution structure of its C-terminal DNA binding domain was determined in complex with DNA. The C-terminal domain of Rok adopts a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers. Rok binds the DNA minor groove by forming hydrogen bonds to bases through N154, T156 at the N-terminal of α3 helix and R174 of wing W1, assisted by four lysine residues interacting electrostatically with DNA backbone phosphate groups. These structural features endow Rok with preference towards DNA sequences harboring AACTA, TACTA, and flexible multiple TpA steps, while rigid A-tracts are disfavored. Correspondingly, the Bacillus genomes containing Rok are rich in A-tracts and show a dramatic underrepresentation of AACTA and TACTA, which are significantly enriched in Rok binding regions. These observations suggest that the xenogeneic silencing protein and its resident genome may have evolved cooperatively.

Human exonization through differential nucleosome occupancy.

Nucleosomal modifications have been implicated in fundamental epigenetic regulation, but the roles of nucleosome occupancy in shaping changes through evolution remain to be addressed. Here we present high-resolution nucleosome occupancy profiles for multiple tissues derived from human, macaque, tree shrew, mouse, and pig. Genome-wide comparison reveals conserved nucleosome occupancy profiles across both different species and tissue types. Notably, we found significantly higher levels of nucleosome occupancy in exons than in introns, a pattern correlated with the different exon-intron GC content. We then determined whether this biased occupancy may play roles in the origination of new exons through evolution, rather than being a downstream effect of exonization, through a comparative approach to sequentially trace the order of the exonization and biased nucleosome binding. By identifying recently evolved exons in human but not in macaque using matched RNA sequencing, we found that higher exonic nucleosome occupancy also existed in macaque regions orthologous to these exons. Presumably, such biased nucleosome occupancy facilitates the origination of new exons by increasing the splice strength of the ancestral nonexonic regions through driving a local difference in GC content. These data thus support a model that sites bound by nucleosomes are more likely to evolve into exons, which we term the "nucleosome-first" model.

HIV-1 tolerates changes in A-count in a small segment of the pol gene.

BACKGROUND: The HIV-1 RNA genome has a biased nucleotide composition with a surplus of As. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has thus far not been systematically manipulated. The reason for this reservation is the likelihood that known and unknown sequence motifs will be affected by such a massive mutational approach, thus resulting in replication-impaired virus mutants. We present the first attempt to increase and decrease the A-count in a relatively small polymerase (pol) gene segment of HIV-1 RNA. RESULTS: To minimize the mutational impact, a new mutational approach was developed that is inspired by natural sequence variation as present in HIV-1 isolates. This phylogeny-instructed mutagenesis allowed us to create replication-competent HIV-1 mutants with a significantly increased or decreased local A-count. The local A-count of the wild-type (wt) virus (40.2%) was further increased to 46.9% or reduced to 31.7 and 26.3%. These HIV-1 variants replicate efficiently in vitro, despite the fact that the pol changes cause a quite profound move in HIV-SIV sequence space. CONCLUSIONS: Extrapolating these results to the complete 9 kb RNA genome, we may cautiously suggest that the A-rich signature does not have to be maintained. This survey also provided clues that silent codon changes, in particular from G-to-A, determine the subtype-specific sequence signatures.

First complete mitochondrial genome of primitive crab Homologenus malayensis (Decapoda: Brachyura: Podotremata: Homolidae).

The taxonomy and phylogeny of brachyuran crabs, and particularly of the Podotremata, have been the subjects of controversy due to their morphological diversity and complexity. The first complete mitochondrial genome (mitogenome) sequence of primitive crab Homologenus malayensis has been determined. The mitogenome is 15,793 bp in length, with A + T content 71.7%. The gene content and order are consistent with those in typical brachyuran crabs. A putative control region of 883 bp is identified due to its position (between srRNA and tRNA(Ile)) and AT richness (75.5%). Notably, the control region in H. malayensis contains nine identical specific repeat units of 42 bp and 11 identical repeat units of 2 bp with a total length of 400 bp, which is different from other crabs. These results are expected to provide useful information on both genomics and the future phylogenetic study of primitive crabs.

The complete mitochondrial genome of Aplysia kurodai (Anaspidea: Aplysiidae).

Complete mitochondrial genome is sequenced from an opisthobranch gastropod Aplysia kurodai. Mitochondrial genome size of the species is 14,113 bp. The mitochondrial genome of A. kurodai contains 13 protein coding genes, two ribosomal RNA genes, and 22 tRNA genes like mitochondrial genomes of congeneric species. The gene order of protein coding genes is identical to that of other Aplysia species. A+T content (65.9%) of the mitochondrial genome is included in the range for A+T content of congeneric species. This genome data provides evolutionary and systematic implications for the related species.

Complete mitochondrial genome of the blacktip reef shark Carcharhinus melanopterus (Carcharhiniformes: Carcharhinidae).

The complete mitochondrial genome of the blacktip reef shark Carcharhinus melanopterus is determined for the first time in this study. The gene composition and order in the mitogenome of C. melanopterus is identical to most vertebrates. The overall base composition is 31.3% A, 25.3% C, 13.3% G and 30.1% T. There are 29 bp overlaps and 21 bp short intergenic spaces in the mitogenome. Two start codons and three stop codons were found in protein-coding genes. The dihydrouridine arm of tRNA-Ser2 was replaced by a simple loop and the other tRNAs could be folded into the typical cloverleaf structure. The termination associated sequence (TAS) and the conserved sequence blocks (CSB1-3) are found in the control region.

The complete mitochondrial genome of Tanakia lanceolata (Cypriniformes: Cyprinidae).

Bitterling Tanakia lanceolata is a small sized freshwater fish species. The unique reproductive behavior makes bitterlings monophyletic. In this study, the complete mitochondrial genome of T. lanceolata is sequenced to be 16,607 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, a control region and the origin of the light strand replication. The overall base composition of T. lanceolata in descending order is A 28.3%, C 28.0%, T 26.1%, and G 17.6%, with a slight A + T bias. The mitogenome sequence data may provide useful information to the population genetics analysis of T. lanceolata and the elucidation of evolutionary mechanisms in Cyprinidae.

Complete sequence and gene organization of the mitochondrial genome of Podocnemis unifilis (Pleurodira: Podocnemididae).

The mitochondrial genome of Podocnemis unifilis (Pleurodira: Podocnemididae) is 16,493 bp in length, which contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The A+T content of the overall base composition of H-strand is 61.7% (T: 27.7%, C: 25.5%, A: 34.0%, G: 12.8%). ATP6, ATP8, CO3, ND4-6 and Cyt b genes begin with ATG as start codon, ND1, ND2 and ND4L begin with ATT, CO1 starts with GTG, CO2 starts with ATA, ND3 starts with ATC. ATP6, CO2, ND4L and ND5 genes are terminated with TAA as stop codon, ND1, ND2, ND3, ND6 and CO1 end with TAG, and the other four protein-coding genes end with an incomplete stop codon (a single stop nucleotide T or TA). A long unit repeat region is found in the control region.

The complete mitochondrial genome of the Plectorhinchus cinctus (Teleostei, Haemulidae).

We present the complete mitochondrial genome of the Plectorhinchus cinctus in this study. The mitochondrial genome is 16,523 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the light strand are 31.30% of C, 27.66% of A, 24.54% of T, and 16.50% of G. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. All the protein-coding genes begin with an ATG initiation codon except for COX1 with GTG. Five types of termination codons revealed are TAA (ND1, ND2, ATP8, ND4L, ND5), T (COXП, ND3, ND4, CYTB), TA (ATP6, COXШ), AGG (COXІ) and TAG (ND6).

The whole chloroplast genome of wild rice (Oryza australiensis).

The whole chloroplast genome of wild rice (Oryza australiensis) is characterized in this study. The genome size is 135,224 bp, exhibiting a typical circular structure including a pair of 25,776 bp inverted repeats (IRa,b) separated by a large single-copy region (LSC) of 82,212 bp and a small single-copy region (SSC) of 12,470 bp. The overall GC content of the genome is 38.95%. 110 unique genes were annotated, including 76 protein-coding genes, 4 ribosomal RNA genes, and 30t RNA genes. Among these, 18 are duplicated in the inverted repeat regions, 13 genes contain one intron, and 2 genes (rps12 and ycf3) have two introns.

The complete mitochondrial genome of Thamnaconus hypargyreus (Tetraodontiformes: Monacanthidae).

Lesser-spotted leatherjacket Thamnaconus hypargyreus (Tetraodontiformes: Monacanthidae) is an economically important fish species in the South China Sea. In this study, we designed 15 pairs of primers for amplification of the mitochondrial fragments of T. hypargyreus by PCR. The complete mitogenome sequence has 16,438 bp, containing the usual 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and 1 control region, the gene composition and order of which are similar to most of other vertebrates. Most mitochondrial genes except ND6 and eight tRNA genes are encoded on the heavy strand. The overall base composition of the heavy strand is 27.5% A, 26.0% T, 17.4% G, 29.1% C with a slight AT bias of 53.5%. There are 12 regions of gene overlaps totaling 32 bp and 11 intergenic spacer regions totaling 68 bp. This mitogenome sequence data of T. hypargyreus would provide the fundamental genetic data for further conservation genetic studies for this important fish species.

The complete mitochondrial genome of Octopus conispadiceus (Sasaki, 1917) (Cephalopoda: Octopodidae).

In this paper, we determined the complete mitochondrial genome of Octopus conispadiceus (Cephalopoda: Octopodidae). The whole mitogenome of O. conispadiceus is 16,027 basepairs (bp) in length with a base composition of 41.4% A, 34.8% T, 16.1% C, 7.7% G and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a major non-coding region (MNR). The gene arrangements of O. conispadiceus showed remarkable similarity to that of O. vulgaris, Amphioctopus fangsiao, Cistopus chinensis and C. taiwanicus.

The complete mitochondrial genome of Diqing wild boar (Sus verrucosus breed Diqing wild boar).

In the present study, the complete mitochondrial genome sequence of the diqing wild boar (Sus verrucosus breed diqing wild boar) was reported for the first time. The total length of the mitogenome was 16,506 bp. It contained the typical structure, including two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and one non-coding control region (D-loop region) as that of most other wild boars. The overall composition of the mitogenome was estimated to be 34.9% for A, 26.1% for T, 26.0% for C and 13.0% for G showing an A-T (61.0%)-rich feature. The mitochondrial genome analyzed here will provide new genetic resource to uncover wild boars' genetic diversity.

The complete mitochondrial genome of Bos gaurus gon-shan (Bovidae; Bovinae).

In the present work we undertook the complete mitochondrial genome sequencing of a wild gon-shan chinese cattle Bos gaurus gon-shan. The total length of the mitogenome was 16,356 bp with the base composition of 33.4% for A, 27.2% for T, 26.0% for C, and 13.4% for G and an A-T (60.6%)-rich feature was detected. It harbored 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of cattle.

Complete mitochondrial genome of the hardnose shark Carcharhinus macloti (Carcharhiniformes: Carcharhinidae).

The complete mitochondrial genome of Carcharhinus macloti was determined in this study. It is 16,701 bp in length and contains 37 genes with the typical gene order and transcriptional orientation in vertebrates. A total of 29 bp overlaps and 29 bp short intergenic spaces located in 22 gene junctions. The overall base composition is 31.6% A, 26.2% C, 13.0% G and 29.2% T. Two start codons (ATG and GTG) and three stop codons (AGG, TAG and TAA/T) were found in 13 protein-coding genes. The length of 22 tRNA genes ranged from 66 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The tRNA-Ser2 (GCU) lacks the dihydrouridine arm by a simple loop and can not be folded into the typical cloverleaf structure. The control region is 1066 bp in length with high A+T content (68.2%).