Full genome sequencing and genetic characterization of Eubenangee viruses identify Pata virus as a distinct species within the genus Orbivirus

Eubenangee virus has previously been identified as the cause of Tammar sudden death syndrome (TSDS). Eubenangee virus (EUBV), Tilligery virus (TILV), Pata virus (PATAV) and Ngoupe virus (NGOV) are currently all classified within the Eubenangee virus species of the genus Orbivirus, family Reoviridae. Full genome sequencing confirmed that EUBV and TILV (both of which are from Australia) show high levels of aa sequence identity (>92%) in the conserved polymerase VP1(Pol), sub-core VP3(T2) and outer core VP7(T13) proteins, and are therefore appropriately classified within the same virus species. However, they show much lower amino acid (aa) identity levels in their larger outer-capsid protein VP2 (<53%), consistent with membership of two different serotypes - EUBV-1 and EUBV-2 (respectively). In contrast PATAV showed significantly lower levels of aa sequence identity with either EUBV or TILV (with <71% in VP1(Pol) and VP3(T2), and <57% aa identity in VP7(T13)) consistent with membership of a distinct virus species. A proposal has therefore been sent to the Reoviridae Study Group of ICTV to recognise 'Pata virus' as a new Orbivirus species, with the PATAV isolate as serotype 1 (PATAV-1). Amongst the other orbiviruses, PATAV shows closest relationships to Epizootic Haemorrhagic Disease virus (EHDV), with 80.7%, 72.4% and 66.9% aa identity in VP3(T2), VP1(Pol), and VP7(T13) respectively. Although Ngoupe virus was not available for these studies, like PATAV it was isolated in Central Africa, and therefore seems likely to also belong to the new species, possibly as a distinct 'type'. The data presented will facilitate diagnostic assay design and the identification of additional isolates of these viruses.     

Morphological and ITS rDNA-based phylogenetic identification of two new species in Tinctoporellus

Two new poroid wood-inhabiting basidiomycetes, Tinctoporellus bubalinus and T. hinnuleus, are described and illustrated based on morphological characteristics and phylogenetic analysis of rDNA ITS sequences. Tinctoporellus bubalinus is characterized by annual, resupinate basidiocarps, white to buff coloured pore surface and thin- to slightly thick-walled, richly branched and contorted dendrohyphidia. Tinctoporellus hinnuleus is characterized by annual, resupinate basidiocarps, cinnamon, clay-buff to fawn pore surface, thin-walled, richly branched and contorted brown dendrohyphidia. Discriminating characters between the new species and the closely related species are discussed. A key to accepted species in Tinctoporellus is provided.     

Complete genome sequencing and analysis of an anti-tumor Newcastle disease virus strain

HBNU/LSRC/F3, a Newcastle disease virus (NDV) strain stored in our lab, exhibited an anti-tumor ability in our previous studies. Nonetheless, very little is known about its genome sequence, which is vital for further study. Here, the complete HBNU/LSRC/F3 genome was fully sequenced and compared with other NDV sequences. Its genome contained 15,192 nucleotides (nt) consisting of two termini and six genes in the following order: 3′-Le-NP-P-M-F-HN-L-Tr-5′. Phylogenetic analysis indicated that this NDV strain belonged to the Class II genotype IX group. A multibasic amino acid (aa) sequence was found at the cleavage site (¹¹²RRQRR↓F¹¹⁷) within the fusion (F) protein, and a 6 nt insertion was present in the 5′ non-coding region of the NP gene. The whole genome sequence was highly similar to other genotype IX NDV genomes reported in China. Overall, this study provides insight into the sequence characteristics of genotype IX NDVs, which will be useful for subsequent investigations.     

The complete mitochondrial genome of Chrysolophus pictus (Galliformes: Phasianidae) and a phylogenetic analysis with related species

The 16,678 bp mitochondrial genome of the Chrysolophus pictus has been sequenced in this paper. To determine the phylogentic position of C. pictus with related species within Phasianidae, the phylogenetic tree was reconstructed with the concatenated nucleotide dataset of the 12 heavy-strand-encoded protein genes. The phylogenetic analysis was carried out using maximum parsimony (MP) and Bayesian inference (BI) methods. MP and BI phylogenetic trees here showed similar topology and consistently suggested that C. pictus shared a close relationship with Phasianus versicolor. The results also showed that the Meleagris gallopavo possessed a basal phylogenetic position within Phasianidae, which may imply that it should be classified into the Phasianidae.     

Use of rpoB gene sequence analysis for phylogenetic identification of Cronobacter species

Here, we report the RNA polymerase beta-subunit gene (rpoB) as a new molecular marker for the identification of the Cronobacter species. The results indicated that members of the Cronobacter genus are more easily discriminated by rpoB sequencing than 16S rRNA sequencing, and reliable identification could be achieved by rpoB gene sequence comparison.     

The genus Meira: phylogenetic placement and description of a new species

The genus Meira currently contains three recently described species of mite-associated basidiomycete yeasts from Israel and Japan and is placed in the Exobasidiomycetes (Ustilaginomycotina) Incertae sedis. A previously undescribed species of Meira was isolated from the phylloplane of a magnolia leaf in Louisiana, USA. Herein, we describe Meira miltonrushii sp. nov. and include phylogenetic analyses from three rDNA loci to resolve the placement of Meira. This study provides evidence that Meira belongs to the family Brachybasidiaceae in the Exobasidiales and supports the placement of another mite-associated yeast genus, Acaromyces, within Cryptobasidiaceae (Exobasidiales). We also examine sequences produced by numerous environmental studies that suggest Meira species can be found as endophytes of many plant species. To our knowledge, this is the first record of a member of the genus Meira in North America.     

Value of recN sequences for species identification and as a phylogenetic marker within the family "Leuconostocaceae"

The genera Leuconostoc, Oenococcus, and Weissella (family "Leuconostocaceae") constitute a group of lactic acid bacteria of great interest in food microbiology. From the taxonomic point of view, they are considered phylogenetically coherent according to their 16S rRNA gene sequences and other macromolecules. These three genera were the focus of the present study; specifically, the resolution and discriminatory power of recN (encoding a DNA repair and genetic recombination protein) as a molecular marker at the species level were investigated. For this purpose, partial sequences (about 1200 nt) were obtained from 23 type strains and from several additional strains following direct amplification of recN and subsequent sequencing. Phylogeny was evaluated according to different treeing methods (neighbor joining, maximum likelihood, and maximum parsimony) and the inclusion of variability filters. The results showed that recN, used either alone or in combination with 16S rRNA data, can serve as a phylogenetic marker as well as a tool for species identification.     

Anatomical and ITS rDNA-based phylogenetic identification of two new West African resupinate thelephoroid species

An anatomical approach coupled with molecular phylogeny of 84 sequences of thelephoroid taxa have been used to describe two new West African resupinate Thelephorales, namely, Tomentella agereri and Tomentella maroana. T. agereri presents a maximal sequence similarity of 94% with its genetically closest species, Tomentalla pilosa, according to a Blastn search in public GenBanks. By molecular phylogenetics, it is nested within the T. pilosa complex, a well-supported (bootstrap support of 100%) monophyletic clade composed of cystidiate and differentiated rhizomorphic species, although it presents contrasting anatomical features including the lack of cystidia, the presence of undifferentiated rhizomorphs, and basidiospores with very short aculei, up to 0.5 μm. Tomentalla maroana is close, by molecular phylogenetic study, to T. ellisii, T. pisoniae, and T. hjortstamiana. The phylogenetic proximity between T. maroana and T. ellisii is supported by morphological characters between the two species, namely, a crustose adherent basidiocarp, a differentiated sterile margin, and a granular hymenium. The two species deviate from each other by 11.38–12.37% with regard to the ITS rDNA sequences, whereas the intraspecific genetic distances vary from 1.68% to 2.9% among the three specimens assigned to T. maroana. Discriminating characters as well as genetic distance between the new species and the closely related species are discussed in detail.     

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.     

Genetic variations in the chloroplast genome and phylogenetic clustering of Lycoris species

The genus Lycoris of Amaryllidaceae comprises approximately 20 species that are distributed only in the moist warm temperate woodlands of eastern Asia. The objectives of this study were: (1) to clarify the phylogeny of the Lycoris species by using the definitive DNA sequencing method and (2) to examine the possible maternal donor of the hybrid origin Lycoris species and the Japanese triploid strains of Lycoris radiata var. radiata. The nucleotide sequence of the maturase K (matK) gene and the noncoding intergenic spacer (IGS) between the atpB and rbcL genes in the chloroplast genome were determined in a total of 27 strains of 11 species of the genus Lycoris. Variation among taxa was mainly due to nucleotide substitution, although deletions and an insertion were found in the IGS. For two chloroplast regions, the phylogenetic trees showed essentially similar topology, indicating the existence of four clades, I, II, III, and IV. For all the species except L. radiata, intraspecific variation was smaller than interspecific variation. For L. radiata, triploid strains were divided into clades I and II, and diploid strains were divided into clades I and IV. This implies that the diploid species of L. radiata var. pumila is a probable ancestral species. The clustering indicated that the chloroplast genome has not evolved in parallel with the karyotype in genus Lycoris. Regarding the hybrid origin species, the maternal parents of L. squamigara, L. albiflora and L. rosea were revealed to be L. longituba, L. radiata and L. radiata var pumila, respectively. We also suggest that a diploid strain of L. radiata var. pumila in clade I might be a candidate of the maternal donor of the Japanese triploid strains. A possible model of the maternal donor of Lycoris species is proposed.     

Automated DNA sequencing and analysis of the human genome

In the past few years, striking advances have been made in automating DNA sequence analysis. Currently, efforts are underway to automate and improve DNA purification, mapping, and data processing procedures. The predictable advances in these technologies should soon place us in a position to sequence the entire human genome. The information derived from this project will have profound implications for basic biology and clinical medicine alike.     

InterPro as a new tool for complete genome analysis: An example of comparative analysis

InterPro, an integrated documentation resource for protein families, protein domains, and functional sites, was developed to amalgamate the individual efforts of the PROSITE, PRINTS, Pfam, and ProDom databases. InterPro can be used for the computational functional classification of newly determined amino acid sequences that lack biochemical characterization and for comparative genome analysis. InterPro contains over 3500 entries for more than 1 000 000 hits in SWISS-PROT and TrEMBL. The database is accessible for text-and sequence-based searches at http://www.ebi.ac.uk/interpro/. InterPro was used for the complete analysis of the proteome of the pathogenic microorganism Mycobacterium tuberculosis and the comparison with the predicted protein-coding sequences of the complete genomes of Bacillus subtilis and Escherichia coli. It was found that 64.8% of proteins in the proteome of M. tuberculosis matched InterPro entries and can be classified by their functions. The comparison with B. subtilis and E. coli provided information on the most common protein families and domains and on the most highly represented protein families in each organism. Thus, InterPro is a useful tool for general comparison of complete proteomes and their compositions.     

Decoding the genome beyond sequencing: the new phase of genomic research

While our understanding of gene-based biology has greatly improved, it is clear that the function of the genome and most diseases cannot be fully explained by genes and other regulatory elements. Genes and the genome represent distinct levels of genetic organization with their own coding systems; Genes code parts like protein and RNA, but the genome codes the structure of genetic networks, which are defined by the whole set of genes, chromosomes and their topological interactions within a cell. Accordingly, the genetic code of DNA offers limited understanding of genome functions. In this perspective, we introduce the genome theory which calls for the departure of gene-centric genomic research. To make this transition for the next phase of genomic research, it is essential to acknowledge the importance of new genome-based biological concepts and to establish new technology platforms to decode the genome beyond sequencing.     

Molecular cloning, sequencing, and phylogenetic relationships of a new potyvirus: sugarcane streak mosaic virus, and a reevaluation of the classification of the potyviridae

The nucleic acid of a serologically distinct potyvirus, originally isolated out of sugar cane from Pakistan, was reverse transcribed and the 3' terminal 2000 bp was PCR amplified, cloned, and sequenced. Phylogenetic comparisons of viruses representing each genus of the Potyviridae show that the Pakistani isolate is most closely related to the rymoviruses wheat streak mosaic virus (WSMV) and brome streak mosaic virus. We therefore propose that this new virus species be named sugar cane streak mosaic virus to reflect its similarity to WSMV. The phylogenetic data also show that the genus Rymovirus contains at least two unique evolutionary lineages. Thus the current taxonomy, based on transmission vector, is paraphyletic. We present an analysis of the taxonomic relationships among members of the family and propose a classification that both resolves the paraphyly and more accurately represents the evolutionary history of the Potyviridae.     

Complete nucleotide sequence of the Coturnix chinensis (blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species

Coturnix chinensis (blue-breasted quail) has been classically grouped in Galliformes Phasianidae Coturnix, based on morphologic features and biochemical evidence. Since the blue-breasted quail has the smallest body size among the species of Galliformes, in addition to a short generation time and an excellent reproductive performance, it is a possible model fowl for breeding and physiological studies of the Coturnix japonica (Japanese quail) and Gallus gallus domesticus (chicken), which are classified in the same family as blue-breasted quail. However, since its phylogenetic position in the family Phasianidae has not been determined conclusively, the sequence of the entire blue-breasted quail mitochondria (mt) genome was obtained to provide genetic information for phylogenetic analysis in the present study. The blue-breasted quail mtDNA was found to be a circular DNA of 16,687 base pairs (bp) with the same genomic structure as the mtDNAs of Japanese quail and chicken, though it is smaller than Japanese quail and chicken mtDNAs by 10 bp and 88 bp, respectively. The sequence identity of all mitochondrial genes, including those for 12S and 16S ribosomal RNAs, between blue-breasted quail and Japanese quail ranged from 84.5% to 93.5%; between blue-breasted quail and chicken, sequence identity ranged from 78.0% to 89.6%. In order to obtain information on the phylogenetic position of blue-breasted quail in Galliformes Phasianidae, the 2,184 bp sequence comprising NADH dehydrogenase subunit 2 and cytochrome b genes available for eight species in Galliformes [Japanese quail, chicken, Gallus varius (green junglefowl), Bambusicola thoracica (Chinese bamboo partridge), Pavo cristatus (Indian peafowl), Perdix perdix (gray partridge), Phasianus colchicus (ring-neck pheasant), and Tympanchus phasianellus (sharp-tailed grouse)] together with that of Aythya americana (redhead) were examined using a maximum likelihood (ML) method. The ML analyses on the first/second codon positions, the third codon positions, and amino acid sequence consistently demonstrated that blue-breasted quail and Japanese quail are in the same phylogenetic cluster.     

Two new species and a phylogenetic analysis of the genus Tectidrilus (0Iigochaeta, Tubifcidae)

Tectidrilus probus sp.n. and Tectidrilus profusus sp.n. are described from offshore localities in southern California. Both species appear closely related to T. diversus Ersëus, 1982, which occurs in the same area, but they differ from the latter by possessing small oesophageal diverticula; T. probus differs also by its very small spermathecal vestibules. Tectidrilus profusus is a highly apomorphic form with elaborate, partly muscular, male ducts and spermathecae. Monophyly of Tectidrilus is supported by the short clitellum and the unisetal 'bundles' in postclitellar segments. Patterns of apomorphic character states within the genus are analyzed under the principle of Camin-Sokal parsimony (irreversibility of character states), giving three equally parsimonious cladograms. In the strict consensus tree of these cladograms, eight of the twelve members of Tectidrilus form an apomorphic group defined by the papillated body wall, but the individual species within this group cannot be unequivocally resolved from each other.