Signals of selection in conditionally expressed genes in the diversification of three horned beetle species.

Species radiations may be facilitated by phenotypic differences already present within populations, such as those arising through sex-specific development or developmental processes biased towards particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among- and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the genus: horn location, polarity of sexual dimorphism and degree of nutritional sensitivity. Our approach combined de novo transcript assembly, assessment of amino acid substitutions (dN/dS) across orthologous gene pairs and integration of gene function and conditional gene expression data. We identified 17 genes across the three species pairs related to axis patterning, development and metabolism with dN/dS > 1 and detected elevated dN/dS in genes related to metabolism and biosynthesis in the most closely related species pair, which is characterized by a loss of nutritional polyphenism and a reversal of sexual dimorphism. Further, we found that genes that are conditionally expressed (i.e. as a function of sex, nutrition or body region) within one of our focal species also showed significantly stronger signals of positive or relaxed purifying selection between species divergent along the same morphological axis (i.e. polarity of sexual dimorphism, degree of nutritional sensitivity or location of horns). Our findings thus reveal a positive relationship between intraspecific differentiation due to condition-specific development and genetic divergences among species.

Standard finishing categories for high-throughput sequencing of viral genomes.

Viral genome sequencing has become the cornerstone of almost all aspects of virology. In particular, high-throughput, next-generation viral genome sequencing has become an integral part of molecular epidemiological investigations into outbreaks of viral disease, such as the recent outbreaks of Middle Eastern respiratory syndrome, Ebola virus disease and Zika virus infection. Multiple institutes have acquired the expertise and necessary infrastructure to perform such investigations, as evidenced by the accumulation of thousands of novel viral sequences over progressively shorter time periods. The authors recently proposed a nomenclature comprised of five high-throughput sequencing standard categories to describe the quality of determined viral genome sequences. These five categories (standard draft, high quality, coding complete, complete and finished) cover all levels of viral genome finishing and can be applied to sequences determined by any technology platform or assembly technique.

Le séquençage des génomes viraux est devenu la pierre angulaire de pratiquement toutes les facettes de la virologie. En particulier, le séquençage à haut débit de nouvelle génération est désormais une partie intégrante des enquêtes d'épidémiologie moléculaire relatives aux foyers de maladies virales, par exemple les récentes épidémies du syndrome respiratoire du Moyen-Orient, la maladie due au virus Ebola ou l'infection par le virus Zika. Nombre d'institutions ont acquis les compétences techniques et les infrastructures nécessaires pour réaliser ce type d'enquêtes, comme en témoigne l'accumulation de milliers de séquences virales nouvelles obtenues en un laps de temps de plus en plus court. Les auteurs ont récemment élaboré une nomenclature constituée de cinq catégories de référence décrivant la qualité des séquences d'un génome viral obtenues par séquençage à haut débit. Ces cinq catégories (ébauche de référence, séquence de haute qualité, séquence codante complète, séquence complète et séquence finie) couvrent toutes les étapes de la finition du génome viral et s'appliquent quelle que soit la plateforme technologique ou la technique d'assemblage utilisée pour déterminer la séquence.

La secuenciación del genoma vírico se ha erigido a día de hoy en la piedra angular de casi todos los aspectos de la virología. La secuenciación de alto rendimiento de próxima generación, en particular, es ahora un componente integral de las investigaciones de epidemiología molecular sobre brotes de enfermedades víricas como los registrados últimamente de síndrome respiratorio de Oriente Medio, enfermedad por el virus del Ebola o infección por el virus Zika. Numerosas instituciones se han dotado de las competencias técnicas y la infraestructura necesaria para llevar a cabo tales investigaciones, como deja patente la acumulación de miles de nuevas secuencias víricas en periodos de tiempo cada vez más cortos. En fechas recientes los autores han propuesto una nomenclatura compuesta de cinco categorías de referencia que sirven para describir la calidad de las secuencias de genoma vírico determinadas por secuenciación de alto rendimiento. Estas cinco categorías (borrador normal, gran calidad, codificación completa, completa y acabada) cubren toda la gradación de acabados en la secuenciación de genoma vírico y pueden ser aplicadas a las secuencias obtenidas por cualquier dispositivo técnico o cualquier técnica de ensamblaje.

Correction: Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences.

[This corrects the article DOI: 10.1371/journal.pone.0171363.].

Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences.

Burkholderia pseudomallei (Bp), the agent of melioidosis, causes disease ranging from acute and rapidly fatal to protracted and chronic. Bp is highly infectious by aerosol, can cause severe disease with nonspecific symptoms, and is naturally resistant to multiple antibiotics. However, no vaccine exists. Unlike many Bp strains, which exhibit random variability in traits such as colony morphology, Bp strain MSHR5848 exhibited two distinct and relatively stable colony morphologies on sheep blood agar plates: a smooth, glossy, pale yellow colony and a flat, rough, white colony. Passage of the two variants, designated "Smooth" and "Rough", under standard laboratory conditions produced cultures composed of > 99.9% of the single corresponding type; however, both could switch to the other type at different frequencies when incubated in certain nutritionally stringent or stressful growth conditions. These MSHR5848 derivatives were extensively characterized to identify variant-associated differences. Microscopic and colony morphology differences on six differential media were observed and only the Rough variant metabolized sugars in selective agar. Antimicrobial susceptibilities and lipopolysaccharide (LPS) features were characterized and phenotype microarray profiles revealed distinct metabolic and susceptibility disparities between the variants. Results using the phenotype microarray system narrowed the 1,920 substrates to a subset which differentiated the two variants. Smooth grew more rapidly in vitro than Rough, yet the latter exhibited a nearly 10-fold lower lethal dose for mice than Smooth. Finally, the Smooth variant was phagocytosed and replicated to a greater extent and was more cytotoxic than Rough in macrophages. In contrast, multiple locus sequence type (MLST) analysis, ribotyping, and whole genome sequence analysis demonstrated the variants' genetic conservation; only a single consistent genetic difference between the two was identified for further study. These distinct differences shown by two variants of a Bp strain will be leveraged to better understand the mechanism of Bp phenotypic variability and to possibly identify in vitro markers of infection.

Draft Genomes for Eight Burkholderia mallei Isolates from Turkey.

Burkholderia mallei, the etiologic agent of glanders, is a Gram-negative, nonmotile, facultative intracellular pathogen. Although glanders has been eradicated from many parts of the world, the threat of B. mallei being used as a weapon is very real. Here we present draft genome assemblies of 8 Burkholderia mallei strains that were isolated in Turkey.

Complete Genome Sequences of Zika Virus Strains Isolated from the Blood of Patients in Thailand in 2014 and the Philippines in 2012.

Here, we present the complete genome sequences of two Zika virus (ZIKV) strains, Zika virus/Homo sapiens-tc/THA/2014/SV0127-14 and Zika virus/H. sapiens-tc/PHL/2012/CPC-0740, isolated from the blood of patients collected in Thailand, 2014, and the Philippines, 2012, respectively. Sequencing and phylogenetic analysis showed that both strains belong to the Asian lineage.

Whole-genome sequences of 24 Brucella strains.

Brucella species are intracellular zoonotic pathogens which cause, among other pathologies, increased rates of abortion in ruminants. Human infections are generally associated with exposure to contaminated and unpasteurized dairy products; however Brucellae have been developed as bioweapons. Here we present 17 complete and 7 scaffolded genome assemblies of Brucella strains.

Draft Genome Assembly of Bordetella bronchiseptica ATCC 10580, a Historical Canine Clinical Isolate.

We present the scaffolded genome of Bordetella bronchiseptica ATCC 10580, assembled into 98 contigs. This 5.1-Mb assembly (68.2% G+C content) contains 4,870 coding regions. The strain was originally isolated from canine lung tissue and is used in quality control testing.

Draft Genome Assembly of Delftia acidovorans Type Strain 2167.

The Delftia acidovorans 2167 (ATCC 15668, Delftia type strain) genome was sequenced into a 6-contig scaffolded assembly of 6.78-Mb. This environmental microbe, previously named to both the Comamonas and Pseudomonas genera, is an opportunistic pathogen and often the subject of phylogenetic placement debates.

Complete Genome Assembly of a Quality Control Reference Isolate, Moraxella catarrhalis Strain ATCC 25240.

Generally an opportunistic pathogen in the United States, Moraxella catarrhalis has acquired resistance to multiple antibacterial/antimicrobial agents. Here, we present the complete 1.9-Mb genome of M. catarrhalis strain ATCC 25240, as deposited in NCBI under the accession number CP008804.

Twenty Whole-Genome Bacillus sp. Assemblies.

Bacilli are genetically and physiologically diverse, ranging from innocuous to highly pathogenic. Here, we present annotated genome assemblies for 20 strains belonging to Bacillus anthracis, B. atrophaeus, B. cereus, B. licheniformis, B. macerans, B. megaterium, B. mycoides, and B. subtilis.

Draft Genome Assembly of Klebsiella pneumoniae Type Strain ATCC 13883.

Klebsiella pneumoniae is a common cause of antibiotic-resistant bacterial infections in immunocompromised individuals. Here, we present the 5.54-Mb scaffolded assembly of the type strain K. pneumoniae type strain ATCC 13883, as deposited in GenBank under accession no. JOOW00000000.

Whole-genome sequences of nine francisella isolates.

Primarily a zoonotic disease, Francisella tularensis is a fastidious intracellular pathogen and is listed as a CDC category A pathogen with notably high pathogenicity. Here we present the scaffolded genome assemblies of nine Francisella strains: eight F. tularensis and one F. philomiragia.

Draft Genome Assembly of Neisseria lactamica Type Strain A7515.

We present the scaffolded genome assembly of Neisseria lactamica type strain A7515 (ATCC 23970) as submitted to NCBI under accession no. JOVI00000000. This type strain of the lactose-fermenting Neisseria species is often used in quality control testing and intra-genus phylogenetic analyses. The assembly includes four contigs placed into a single scaffold.

Complete Genome Assembly of Reference Strain Ochrobactrum anthropi ATCC 49687.

Ochrobactrum anthropi is an occasional cause of nosocomial infections; however, interest in the organism lies in its phylogenetic proximity to the genus Brucella. Here, we present the 4.9-Mb finished genome of Ochrobactrum anthropi ATCC 49687, most commonly used as an exclusionary reference organism.

Complete Genome Assembly of Enterococcus faecalis 29212, a Laboratory Reference Strain.

Enterococcus faecalis is a nonmotile Gram-positive coccus, found both as a commensal organism in healthy humans and animals and as a causative agent of multiple diseases, in particular endocarditis. We sequenced the genome of E. faecalis ATCC 29212, a commonly used reference strain in laboratory studies, to complete "finished" annotated assembly (3 Mb).

Whole-genome assemblies of 56 burkholderia species.

Burkholderia is a genus of betaproteobacteria that includes three notable human pathogens: B. cepacia, B. pseudomallei, and B. mallei. While B. pseudomallei and B. mallei are considered potential biowarfare agents, B. cepacia infections are largely limited to cystic fibrosis patients. Here, we present 56 Burkholderia genomes from 8 distinct species.

Whole-Genome Sequence of Listeria monocytogenes Type Strain 53 XXIII.

Listeria monocytogenes causes the food-borne illness listeriosis that primarily infects "vulnerable" groups (e.g., elderly adults, pregnant women, very young children, and the immunocompromised). We sequenced the genome of L. monocytogenes XXIII (ATCC 15313) and assembled it into a single scaffold (three contigs) and deposited the annotated assembly into GenBank as accession no. JOOX00000000.

Whole-Genome Yersinia sp. Assemblies from 10 Diverse Strains.

Yersinia spp. are animal pathogens, some of which cause human disease. We sequenced 10 Yersinia isolates (from six species: Yersinia enterocolitica, Y. fredericksenii, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, and Y. ruckeri) to high-quality draft or complete status. The genomes range in size from 3.77 to 4.94 Mbp.

Draft Genome Assemblies of Proteus mirabilis ATCC 7002 and Proteus vulgaris ATCC 49132.

The pleomorphic swarming bacilli of the genus Proteus are common human gut commensal organisms but also the causative agents of recurrent urinary tract infections and bacteremia. We sequenced and assembled the 3.99-Mbp genome of Proteus mirabilis ATCC 7002 (accession no. JOVJ00000000) and the 3.97-Mbp genome of Proteus vulgaris ATCC 49132 (accession no. JPIX00000000), both of which are commonly used reference strains.