keyword
MENU ▼
Read by QxMD icon Read
search

Phylogenomics

keyword
https://www.readbyqxmd.com/read/28445543/comparative-genomic-analysis-between-corynebacterium-pseudotuberculosis-strains-isolated-from-buffalo
#1
Marcus Vinicius Canário Viana, Henrique Figueiredo, Rommel Ramos, Luis Carlos Guimarães, Felipe Luiz Pereira, Fernanda Alves Dorella, Salah Abdel Karim Selim, Mohammad Salaheldean, Artur Silva, Alice R Wattam, Vasco Azevedo
Corynebacterium pseudotuberculosis is a Gram-positive, pleomorphic, facultative intracellular pathogen that causes Oedematous Skin Disease (OSD) in buffalo. To better understand the pathogenic mechanisms of OSD, we performed a comparative genomic analysis of 11 strains of C. pseudotuberculosis isolated from different buffalo found to be infected in Egypt during an outbreak that occurred in 2008. Sixteen previously described pathogenicity islands (PiCp) were present in all of the new buffalo strains, but one of them, PiCp12, had an insertion that contained both a corynephage and a diphtheria toxin gene, both of which may play a role in the adaptation of C...
2017: PloS One
https://www.readbyqxmd.com/read/28435885/phylogenomic-reconstruction-of-the-oomycete-phylogeny-derived-from-37-genomes
#2
Charley G P McCarthy, David A Fitzpatrick
The oomycetes are a class of microscopic, filamentous eukaryotes within the Stramenopiles-Alveolata-Rhizaria (SAR) supergroup which includes ecologically significant animal and plant pathogens, most infamously the causative agent of potato blight Phytophthora infestans. Single-gene and concatenated phylogenetic studies both of individual oomycete genera and of members of the larger class have resulted in conflicting conclusions concerning species phylogenies within the oomycetes, particularly for the large Phytophthora genus...
March 2017: MSphere
https://www.readbyqxmd.com/read/28435864/microbial-arms-race-ballistic-nematocysts-in-dinoflagellates-represent-a-new-extreme-in-organelle-complexity
#3
Gregory S Gavelis, Kevin C Wakeman, Urban Tillmann, Christina Ripken, Satoshi Mitarai, Maria Herranz, Suat Özbek, Thomas Holstein, Patrick J Keeling, Brian S Leander
We examine the origin of harpoon-like secretory organelles (nematocysts) in dinoflagellate protists. These ballistic organelles have been hypothesized to be homologous to similarly complex structures in animals (cnidarians); but we show, using structural, functional, and phylogenomic data, that nematocysts evolved independently in both lineages. We also recorded the first high-resolution videos of nematocyst discharge in dinoflagellates. Unexpectedly, our data suggest that different types of dinoflagellate nematocysts use two fundamentally different types of ballistic mechanisms: one type relies on a single pressurized capsule for propulsion, whereas the other type launches 11 to 15 projectiles from an arrangement similar to a Gatling gun...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28432541/genome-characteristics-of-the-proteorhodopsin-containing-marine-flavobacterium-polaribacter-dokdonensis-dsw-5
#4
Kiyoung Yoon, Ju Yeon Song, Min-Jung Kwak, Soon-Kyeong Kwon, Jihyun F Kim
Bacteria in the genus Polaribacter, belonging to the family Flavobacteriaceae, are typically isolated from marine environments. Polaribacter dokdonensis DSW-5, the type strain of the species, is a Gram-negative bacterium isolated from the East Sea of Korea. Whole genome shotgun sequencing was performed with the HiSeq 2000 platform and paired-end reads were generated at 188-fold coverage. The sequencing reads were assembled into two contigs with a total length of 3.08 Mb. The genome sequences of DSW-5 contain 2,776 proteincoding sequences and 41 RNA genes...
April 22, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28432484/complete-mitochondrial-genome-sequences-of-korean-native-horse-from-jeju-island-uncovering-the-spatio-temporal-dynamics
#5
Sook Hee Yoon, Jaemin Kim, Donghyun Shin, Seoae Cho, Woori Kwak, Hak-Kyo Lee, Kyoung-Do Park, Heebal Kim
The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods...
April 21, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28429538/finding-a-partner-in-the-ocean-molecular-and-evolutionary-bases-of-the-response-to-sexual-cues-in-a-planktonic-diatom
#6
Swaraj Basu, Shrikant Patil, Daniel Mapleson, Monia Teresa Russo, Laura Vitale, Cristina Fevola, Florian Maumus, Raffaella Casotti, Thomas Mock, Mario Caccamo, Marina Montresor, Remo Sanges, Maria Immacolata Ferrante
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes...
April 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28422140/the-evolutionary-history-of-bears-is-characterized-by-gene-flow-across-species
#7
Vikas Kumar, Fritjof Lammers, Tobias Bidon, Markus Pfenninger, Lydia Kolter, Maria A Nilsson, Axel Janke
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28421090/comparative-genomics-and-phylogenomics-of-east-asian-tulips-amana-liliaceae
#8
Pan Li, Rui-Sen Lu, Wu-Qin Xu, Tetsuo Ohi-Toma, Min-Qi Cai, Ying-Xiong Qiu, Kenneth M Cameron, Cheng-Xin Fu
The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629-25,859 bp) separated by the large single-copy (81,482-82,218 bp) and small single-copy (17,366-17,465 bp) regions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28419279/primates-lice-and-bacteria-speciation-and-genome-evolution-in-the-symbionts-of-hominid-lice
#9
Bret M Boyd, Julie M Allen, Nam-Phuong Nguyen, Pranjal Vachaspati, Zach Quicksall, Tandy Warnow, Lawrence Mugisha, Kevin P Johnson, David L Reed
Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28417603/squamate-conserved-loci-sqcl-a-unified-set-of-conserved-loci-for-phylogenomics-and-population-genetics-of-squamate-reptiles
#10
Sonal Singhal, Maggie Grundler, Guarino Colli, Daniel L Rabosky
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches - anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) - and both approaches have proven useful for addressing questions in phylogenomics, phylogeography, and population genomics...
April 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28406289/phylogenomic-analysis-of-the-microviridin-biosynthetic-pathway-coupled-with-targeted-chemo-enzymatic-synthesis-yields-potent-protease-inhibitors
#11
Muhammad N Ahmed, Emmanuel Reyna-González, Bianca Schmid, Vincent Wiebach, Roderich D Süssmuth, Elke Dittmann, David P Fewer
Natural products and their semisynthetic derivatives are an important source of drugs for the pharmaceutical industry. Bacteria are prolific producers of natural products and encode a vast diversity of natural product biosynthetic gene clusters. However, much of this diversity is inaccessible to natural product discovery. Here, we use a combination of phylogenomic analysis of the microviridin biosynthetic pathway and chemo-enzymatic synthesis of bioinformatically predicted microviridins to yield new protease inhibitors...
April 26, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28404776/dry-habitats-were-crucibles-of-domestication-in-the-evolution-of-agriculture-in-ants
#12
Michael G Branstetter, Ana Ješovnik, Jeffrey Sosa-Calvo, Michael W Lloyd, Brant C Faircloth, Seán G Brady, Ted R Schultz
The evolution of ant agriculture, as practised by the fungus-farming 'attine' ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The 'out-of-the-rainforest' hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required...
April 12, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28401633/functional-soil-metagenomics-elucidation-of-polycyclic-aromatic-hydrocarbon-degradation-potential-following-12-years-of-in-situ-bioremediation
#13
Márcia Duarte, Agnes Nielsen, Amélia Camarinha-Silva, Ramiro Vilchez-Vargas, Thomas Bruls, Melissa L Wos-Oxley, Ruy Jauregui, Dietmar H Pieper
A culture-independent function-based screening approach was used to assess the microbial aerobic catabolome for polycyclic aromatic hydrocarbons degradation of a soil subjected to 12 years of in situ bioremediation. A total of 422,750 fosmid clones were screened for key aromatic ring-cleavage activities using 2,3-dihydroxybiphenyl as substrate. Most of the genes encoding ring-cleavage enzymes on the 768 retrieved positive fosmids could not be identified using primer-based approaches and, thus, 205 fosmid inserts were sequenced...
April 12, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28396823/genomic-comparisons-of-a-bacterial-lineage-that-inhabits-both-marine-and-terrestrial-deep-subsurface-systems
#14
Sean P Jungbluth, Tijana Glavina Del Rio, Susannah G Tringe, Ramunas Stepanauskas, Michael S Rappé
It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth's crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of "Candidatus Desulforudis audaxviator" MP104C...
2017: PeerJ
https://www.readbyqxmd.com/read/28394415/phylogenetic-position-of-the-coral-symbiont-ostreobium-ulvophyceae-inferred-from-chloroplast-genome-data
#15
Heroen Verbruggen, Vanessa R Marcelino, Michael D Guiry, M Chiela M Cremen, Christopher J Jackson
The green algal genus Ostreobium is an important symbiont of corals, playing roles in reef decalcification and providing photosynthates to the coral during bleaching events. A chloroplast genome of a cultured strain of Ostreobium was available, but low taxon sampling and Ostreobium's early-branching nature left doubt about its phylogenetic position. Here we generate and describe chloroplast genomes from four Ostreobium strains as well as Avrainvillea mazei and Neomeris sp., strategically sampled early-branching lineages in the Bryopsidales and Dasycladales, respectively...
April 10, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28390323/the-impact-of-gc-bias-on-phylogenetic-accuracy-using-targeted-enrichment-phylogenomic-data
#16
Silas Bossert, Elizabeth A Murray, Bonnie B Blaimer, Bryan N Danforth
The field of sequence based phylogenetic analyses is currently being transformed by novel hybrid-based targeted enrichment methods, such as the use of ultraconserved elements (UCEs). Rather than analyzing relationships among organisms using a small number of genes, these methods now allow us to evaluate relationships with many hundreds to thousands of individual gene loci. However, the inclusion of thousands of loci does not necessarily overcome the long-standing challenge of incongruence among phylogenetic trees derived from different genes or gene regions...
April 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28389276/whole-genome-sequencing-of-shigella-sonnei-through-pulsenet-latin-america-and-caribbean-advancing-global-surveillance-of-foodborne-illnesses
#17
Kate Susan Baker, Josefina Campos, Mariana Pichel, Anabella Della Gaspera, Francisco Duarte-Martínez, Elena Campos-Chacón, Hilda María Bolaños-Acuña, Caterina Guzman-Verri, Alison E Mather, Susana Diaz Velasco, Maria Luz Zamudio Rojas, Jessica Forbester, Thomas Richard Connor, Karen Helena Keddy, Anthony Marius Smith, Enedia A Lopez de Delgado, Giovanny Angiolillo, Nirvia Cuaical, Jorge Fernandez, Carolina Aguayo, Melissa Morales Aguilar, Claudia Valenzuela, Ana Judith Morales Medrano, Alfredo Sirok Esteve, Natalie Weiler Gustafson, Paula Lucia Diaz Guevara, Lucy Angeline Montaño, Enrique Perez, Nicholas R Thomson
OBJECTIVE: Shigella sonnei is a globally-important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic...
April 4, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28387837/genomic-sequencing-of-neisseria-gonorrhoeae-to-respond-to-the-urgent-threat-of-antimicrobial-resistant-gonorrhea
#18
A Jeanine Abrams, David L Trees
The development of resistance of Neisseria gonorrhoeae to available first-line antibiotics, including penicillins, tetracyclines, fluoroquinolones and cephalosporins, has led to the circulation of multidrug-resistant gonorrhea at a global scale. Advancements in high-throughput whole-genome sequencing (WGS) provide useful tools that can be used to enhance gonococcal detection, treatment and management capabilities, which will ultimately aid in the control of antimicrobial resistant gonorrhea worldwide. In this minireview, we discuss the application of WGS of N...
April 6, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28387771/who-lives-in-a-fungus-the-diversity-origins-and-functions-of-fungal-endobacteria-living-in-mucoromycota
#19
Paola Bonfante, Alessandro Desirò
Bacterial interactions with plants and animals have been examined for many years; differently, only with the new millennium the study of bacterial-fungal interactions blossomed, becoming a new field of microbiology with relevance to microbial ecology, human health and biotechnology. Bacteria and fungi interact at different levels and bacterial endosymbionts, which dwell inside fungal cells, provide the most intimate example. Bacterial endosymbionts mostly occur in fungi of the phylum Mucoromycota and include Betaproteobacteria (Burkhoderia-related) and Mollicutes (Mycoplasma-related)...
April 7, 2017: ISME Journal
https://www.readbyqxmd.com/read/28386012/giant-viruses-with-an-expanded-complement-of-translation-system-components
#20
Frederik Schulz, Natalya Yutin, Natalia N Ivanova, Davi R Ortega, Tae Kwon Lee, Julia Vierheilig, Holger Daims, Matthias Horn, Michael Wagner, Grant J Jensen, Nikos C Kyrpides, Eugene V Koonin, Tanja Woyke
The discovery of giant viruses blurred the sharp division between viruses and cellular life. Giant virus genomes encode proteins considered as signatures of cellular organisms, particularly translation system components, prompting hypotheses that these viruses derived from a fourth domain of cellular life. Here we report the discovery of a group of giant viruses (Klosneuviruses) in metagenomic data. Compared with other giant viruses, the Klosneuviruses encode an expanded translation machinery, including aminoacyl transfer RNA synthetases with specificities for all 20 amino acids...
April 7, 2017: Science
keyword
keyword
13490
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"