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https://www.readbyqxmd.com/read/29226632/novel-bovine-associated-pvapn-plasmid-type-in-rhodococcus-equi-identified-from-lymph-nodes-of-slaughtered-cattle-and-lungs-of-people-living-with-hiv-aids
#1
M G Ribeiro, G H B Lara, P da Silva, M M J Franco, A L de Mattos-Guaraldi, A P C de Vargas, R I Sakate, F R Pavan, B S Colhado, F V R Portilho, R G Motta, T Kakuda, S Takai
Rhodococcus equi is a well-recognized Gram-positive intracellular facultative bacterium that is opportunistic in nature, which causes pyogranulomatous infections in humans and multiple host animals. The pathogenicity of the microorganism has been attributed to the presence of plasmid-encoded virulence-associated proteins (Vap). To date, three host-associated virulence plasmid types of R. equi have been identified as follows: the circular pVAPA and pVAPB, related, respectively, to equine and porcine isolates, and a recently described linear pVAPN plasmid associated with bovine strains, although these three types are found in human isolates...
December 10, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29225593/diverse-cone-snail-species-harbor-closely-related-streptomyces-species-with-conserved-chemical-and-genetic-profiles-including-polycyclic-tetramic-acid-macrolactams
#2
Michelle Quezada, Cuauhtemoc Licona-Cassani, Pablo Cruz-Morales, Angela A Salim, Esteban Marcellin, Robert J Capon, Francisco Barona-Gómez
Streptomyces are Gram-positive bacteria that occupy diverse ecological niches including host-associations with animals and plants. Members of this genus are known for their overwhelming repertoire of natural products, which has been exploited for almost a century as a source of medicines and agrochemicals. Notwithstanding intense scientific and commercial interest in Streptomyces natural products, surprisingly little is known of the intra- and/or inter-species ecological roles played by these metabolites. In this report we describe the chemical structures, biological properties, and biosynthetic relationships between natural products produced by Streptomyces isolated from internal tissues of predatory Conus snails, collected from the Great Barrier Reef, Australia...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29223357/phylogenomic-detection-and-functional-prediction-of-genes-potentially-important-for-plant-meiosis
#3
Luoyan Zhang, Hongzhi Kong, Hong Ma, Ji Yang
Meiosis is a specialized type of cell division necessary for sexual reproduction in eukaryotes. A better understanding of the cytological procedures of meiosis has been achieved by comprehensive cytogenetic studies in plants, while the genetic mechanisms regulating meiotic progression remain incompletely understood. The increasing accumulation of complete genome sequences and large-scale gene expression datasets has provided a powerful resource for phylogenomic inference and unsupervised identification of genes involved in plant meiosis...
December 6, 2017: Gene
https://www.readbyqxmd.com/read/29222102/tracking-the-taxonomy-of-the-genus-bifidobacterium-based-on-a-phylogenomic-approach
#4
Gabriele Andrea Lugli, Christian Milani, Sabrina Duranti, Leonardo Mancabelli, Marta Mangifesta, Francesca Turroni, Alice Viappiani, Douwe van Sinderen, Marco Ventura
For decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species with reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identify apparent misclassifications in current bifidobacterial taxonomy...
December 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29222063/evolutionary-dynamism-in-bryophytes-phylogenomic-inferences-confirm-rapid-radiation-in-the-moss-family-funariaceae
#5
Rafael Medina, Matthew Johnson, Yang Liu, Nicholas Wilding, Terry A Hedderson, Norman Wickett, Bernard Goffinet
Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture...
December 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29220515/busco-applications-from-quality-assessments-to-gene-prediction-and-phylogenomics
#6
Robert M Waterhouse, Mathieu Seppey, Felipe A Simão, Mosè Manni, Panagiotis Ioannidis, Guennadi Klioutchnikov, Evgenia V Kriventseva, Evgeny M Zdobnov
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic datasets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29218053/marker-development-for-phylogenomics-the-case-of-orobanchaceae-a-plant-family-with-contrasting-nutritional-modes
#7
Xi Li, Baohai Hao, Da Pan, Gerald M Schneeweiss
Phylogenomic approaches, employing next-generation sequencing (NGS) techniques, have revolutionized systematic and evolutionary biology. Target enrichment is an efficient and cost-effective method in phylogenomics and is becoming increasingly popular. Depending on availability and quality of reference data as well as on biological features of the study system, (semi-)automated identification of suitable markers will require specific bioinformatic pipelines. Here, we established a highly flexible bioinformatic pipeline, BaitsFinder, to identify putative orthologous single copy genes (SCGs) and to construct bait sequences in a single workflow...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29216844/comparative-analyses-of-plastid-genomes-from-fourteen-cornales-species-inferences-for-phylogenetic-relationships-and-genome-evolution
#8
Chao-Nan Fu, Hong-Tao Li, Richard Milne, Ting Zhang, Peng-Fei Ma, Jing Yang, De-Zhu Li, Lian-Ming Gao
BACKGROUND: The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. RESULTS: All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region...
December 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29206296/comparative-plastome-genomics-and-phylogenomics-of-brachypodium-flowering-time-signatures-introgression-and-recombination-in-recently-diverged-ecotypes
#9
Rubén Sancho, Carlos P Cantalapiedra, Diana López-Alvarez, Sean P Gordon, John P Vogel, Pilar Catalán, Bruno Contreras-Moreira
Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B...
December 5, 2017: New Phytologist
https://www.readbyqxmd.com/read/29205924/genomic-epidemiology-of-the-emerging-pathogen-batrachochytrium-dendrobatidis-from-native-and-invasive-amphibian-species-in-chile
#10
A Valenzuela-Sánchez, S J O'Hanlon, M Alvarado-Rybak, D E Uribe-Rivera, A A Cunningham, M C Fisher, C Soto-Azat
Emerging fungal diseases represent a threat to food security, animal and human health worldwide. Amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has been associated with catastrophic and well-documented amphibian population declines and extinctions. For the first time, Bd was cultured from native and non-native wild amphibians in Chile. Phylogenomic analyses revealed that Chilean isolates AVS2, AVS4 and AVS7 group within the global panzootic lineage of Bd (BdGPL) in a single highly supported clade that includes a genotype previously isolated from the United Kingdom...
December 5, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29205127/phylogenomic-analysis-of-the-species-of-the-mycobacterium-tuberculosis-complex-demonstrates-that-mycobacterium-africanum-mycobacterium-bovis-mycobacterium-caprae-mycobacterium-microti-and-mycobacterium-pinnipedii-are-later-heterotypic-synonyms-of-mycobacterium
#11
Marco A Riojas, Katya J McGough, Cristin J Rider-Riojas, Nalin Rastogi, Manzour Hernando Hazbón
The species within the Mycobacterium tuberculosis Complex (MTBC) have undergone numerous taxonomic and nomenclatural changes, leaving the true structure of the MTBC in doubt. We used next-generation sequencing (NGS), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) to investigate the relationship between these species. The type strains of Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii were sequenced via NGS. Pairwise dDDH and ANI comparisons between these, previously sequenced MTBC type strain genomes (including 'Mycobacterium canettii', 'Mycobacterium mungi' and 'Mycobacterium orygis') and M...
December 5, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29201131/the-male-sexual-apparatus-in-the-order-scorpiones-arachnida-a-comparative-study-of-functional-morphology-as-a-tool-to-define-hypotheses-of-homology
#12
Lionel Monod, Lucie Cauwet, Edmundo González-Santillán, Siegfried Huber
Background: Insemination in scorpions is carried out by means of a partly sclerotized structure, the spermatophore, which is composed of two separate halves, the hemispermatophores. In most genera these reproductive structures can be used to differentiate species. However, many taxa such as the genus Euscorpius and the family Diplocentridae lack the morphological diversity observed in the copulatory organs of many other arthropods, rendering them useless for species level taxonomy. Such structural stasis, however, suggests that hemispermatophores have evolved relatively slowly and may thus provide a stronger phylogenetic signal for recognizing supra-generic ranks than previously thought...
2017: Frontiers in Zoology
https://www.readbyqxmd.com/read/29199080/improved-modeling-of-compositional-heterogeneity-supports-sponges-as-sister-to-all-other-animals
#13
Roberto Feuda, Martin Dohrmann, Walker Pett, Hervé Philippe, Omar Rota-Stabelli, Nicolas Lartillot, Gert Wörheide, Davide Pisani
The relationships at the root of the animal tree have proven difficult to resolve, with the current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum Ctenophora) are the sister group of all other animals [1-5]. The choice of evolutionary models seems to be at the core of the problem because Porifera tends to emerge as the sister group of all other animals ("Porifera-sister") when site-specific amino acid differences are modeled (e.g., [6, 7]), whereas Ctenophora emerges as the sister group of all other animals ("Ctenophora-sister") when they are ignored (e...
November 22, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29198740/early-transmissible-ampicillin-resistance-in-zoonotic-salmonella-enterica-serotype-typhimurium-in-the-late-1950s-a-retrospective-whole-genome-sequencing-study
#14
Alicia Tran-Dien, Simon Le Hello, Christiane Bouchier, François-Xavier Weill
BACKGROUND: Ampicillin, the first semi-synthetic penicillin active against Enterobacteriaceae, was released onto the market in 1961. The first outbreaks of disease caused by ampicillin-resistant strains of Salmonella enterica serotype Typhimurium were identified in the UK in 1962 and 1964. We aimed to date the emergence of this resistance in historical isolates of S enterica serotype Typhimurium. METHODS: In this retrospective, whole-genome sequencing study, we analysed 288 S enterica serotype Typhimurium isolates collected between 1911 and 1969 from 31 countries on four continents and from various sources including human beings, animals, feed, and food...
November 29, 2017: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29194520/trajectories-and-drivers-of-genome-evolution-in-surface-associated-marine-phaeobacter
#15
Heike M Freese, Johannes Sikorski, Boyke Bunk, Carmen Scheuner, Jan P Meier-Kolthoff, Cathrin Spröer, Lone Gram, Jörg Overmann
The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome...
November 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29186447/large-scale-phylogenomic-analysis-resolves-a-backbone-phylogeny-in-ferns
#16
Hui Shen, Dongmei Jin, Jiang-Ping Shu, Xi-Le Zhou, Ming Lei, Ran Wei, Hui Shang, Hong-Jin Wei, Rui Zhang, Li Liu, Yu-Feng Gu, Xian-Chun Zhang, Yue-Hong Yan
Background: Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results: With the aim to obtain a robust fern phylogeny, we carried out a large scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders...
November 24, 2017: GigaScience
https://www.readbyqxmd.com/read/29184540/ecogenomics-and-taxonomy-of-cyanobacteria-phylum
#17
Juline M Walter, Felipe H Coutinho, Bas E Dutilh, Jean Swings, Fabiano L Thompson, Cristiane C Thompson
Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29182740/speciation-generates-mosaic-genomes-in-kangaroos
#18
Maria A Nilsson, Yichen Zheng, Vikas Kumar, Matthew J Phillips, Axel Janke
The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of eleven kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict...
November 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29180655/transition-metal-binding-selectivity-in-proteins-and-its-correlation-with-the-phylogenomic-classification-of-the-cation-diffusion-facilitator-protein-family
#19
Shiran Barber-Zucker, Boaz Shaanan, Raz Zarivach
Divalent d-block metal cations (DDMCs), such as Fe, Zn and Mn, participate in many biological processes. Understanding how specific DDMCs are transported to and within the cell and what controls their binding selectivity to different proteins is crucial for defining the mechanisms of metalloproteins. To better understand such processes, we scanned the RCSB Protein Data Bank, performed a de novo structural-based comprehensive analysis of seven DDMCs and found their amino acid binding and coordination geometry propensities...
November 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29179736/phylogenetic-analysis-of-the-core-histone-doublet-and-dna-topo-ii-genes-of-marseilleviridae-evidence-of-proto-eukaryotic-provenance
#20
Albert J Erives
BACKGROUND: While the genomes of eukaryotes and Archaea both encode the histone-fold domain, only eukaryotes encode the core histone paralogs H2A, H2B, H3, and H4. With DNA, these core histones assemble into the nucleosomal octamer underlying eukaryotic chromatin. Importantly, core histones for H2A and H3 are maintained as neofunctionalized paralogs adapted for general bulk chromatin (canonical H2 and H3) or specialized chromatin (H2A.Z enriched at gene promoters and cenH3s enriched at centromeres)...
November 28, 2017: Epigenetics & Chromatin
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