keyword
MENU ▼
Read by QxMD icon Read
search

Phylogenomics

keyword
https://www.readbyqxmd.com/read/28821546/a-supervised-statistical-learning-approach-for-accurate-legionella-pneumophila-source-attribution-during-outbreaks
#1
Andrew H Buultjens, Kyra Y L Chua, Sarah L Baines, Jason Kwong, Wei Gao, Zoe Cutcher, Stuart Adcock, Susan Ballard, Mark B Schultz, Takehiro Tomita, Nela Subasinghe, Glen P Carter, Sacha J Pidot, Lucinda Franklin, Torsten Seemann, Anders Gonçalves Da Silva, Benjamin P Howden, Timothy P Stinear
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based onL...
August 18, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28812701/contentious-relationships-in-phylogenomic-studies-can-be-driven-by-a-handful-of-genes
#2
Xing-Xing Shen, Chris Todd Hittinger, Antonis Rokas
Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly contradictory on certain, contentious relationships. Here, we use a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal of a single gene in concatenation analyses or a single site from every gene in coalescence-based analyses diminishes support and can alter the inferred topology...
April 10, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812612/phylogenomics-constrained-gene-tree-inference
#3
Siavash Mirarab
No abstract text is available yet for this article.
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812602/prenatal-development-supports-a-single-origin-of-laryngeal-echolocation-in-bats
#4
Zhe Wang, Tengteng Zhu, Huiling Xue, Na Fang, Junpeng Zhang, Libiao Zhang, Jian Pang, Emma C Teeling, Shuyi Zhang
Bat laryngeal echolocation is considered as one of the most complex and diverse modes of auditory sensory perception in animals and its evolutionary history has been the cause of many scientific controversies in the past two decades. To date, the majority of scientific evidence supports that bats (Chiroptera) are divided into two subordinal groups: Yinpterochiroptera, containing the laryngeal echolocating superfamily Rhinolophidae as sister taxa to the non-laryngeal echolocating family Pteropodidae; and Yangochiroptera, containing all other laryngeal echolocating lineages...
January 9, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28810709/parallel-evolution-of-sperm-hyper-activation-ca2-channels
#5
Jacob C Cooper, Nitin Phadnis
Sperm hyper-activation is a dramatic change in sperm behavior where mature sperm burst into a final sprint in the race to the egg. The mechanism of sperm hyper-activation in many metazoans, including humans, consists of a jolt of Ca2+ into the sperm flagellum via CatSper ion channels. Surprisingly, all nine CatSper genes have been independently lost in several animal lineages. In Drosophila, sperm hyper-activation is performed through the cooption of the polycystic kidney disease 2 (pkd2) Ca2+ channel. The parallels between CatSpers in primates and pkd2 in Drosophila provide a unique opportunity to examine the molecular evolution of the sperm hyper-activation machinery in two independent, nonhomologous calcium channels separated by > 500 million years of divergence...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28809143/bacillus-swezeyi-sp-nov-and-bacillus-haynesii-sp-nov-isolated-from-desert-soil
#6
Christopher A Dunlap, David A Schisler, Elizabeth B Perry, Nora Connor, Frederick M Cohan, Alejandro P Rooney
Two isolates of Gram-reaction-positive, facultatively anaerobic, motile, rod-shaped, endospore-forming bacteria were identified during a survey of the diversity of strains belonging to the genus Bacillus deposited in the Agriculture Research Service Culture Collection. These strains were originally isolated from soil in Evolution Canyon III (Israel) in a survey of ecological diversification. Phylogenetic analysis of the 16S rRNA gene of strains NRRL B-41294T and NRRL B-41327T determined they were closely related to members of the Bacillus licheniformis clade...
August 15, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28808007/early-photosynthetic-eukaryotes-inhabited-low-salinity-habitats
#7
Patricia Sánchez-Baracaldo, John A Raven, Davide Pisani, Andrew H Knoll
The early evolutionary history of the chloroplast lineage remains an open question. It is widely accepted that the endosymbiosis that established the chloroplast lineage in eukaryotes can be traced back to a single event, in which a cyanobacterium was incorporated into a protistan host. It is still unclear, however, which Cyanobacteria are most closely related to the chloroplast, when the plastid lineage first evolved, and in what habitats this endosymbiotic event occurred. We present phylogenomic and molecular clock analyses, including data from cyanobacterial and chloroplast genomes using a Bayesian approach, with the aim of estimating the age for the primary endosymbiotic event, the ages of crown groups for photosynthetic eukaryotes, and the independent incorporation of a cyanobacterial endosymbiont by Paulinella Our analyses include both broad taxon sampling (119 taxa) and 18 fossil calibrations across all Cyanobacteria and photosynthetic eukaryotes...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28806979/breath-giving-cooperation-critical-review-of-origin-of-mitochondria-hypotheses-major-unanswered-questions-point-to-the-importance-of-early-ecology
#8
REVIEW
István Zachar, Eörs Szathmáry
The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address...
August 14, 2017: Biology Direct
https://www.readbyqxmd.com/read/28803676/ranavirus-phylogenomics-signatures-of-recombination-and-inversions-among-bullfrog-ranaculture-isolates
#9
Sieara C Claytor, Kuttichantran Subramaniam, Nelmarie Landrau-Giovannetti, V Gregory Chinchar, Matthew J Gray, Debra L Miller, Carla Mavian, Marco Salemi, Samantha Wisely, Thomas B Waltzek
Ranaviruses are emerging pathogens of fish, amphibians, and reptiles that threaten aquatic animal industries and wildlife worldwide. Our objective was to genetically characterize ranaviruses isolated during separate bullfrog Lithobates catesbeianus die-offs that occurred eight years apart on the same North American farm. The earlier outbreak was due to a highly pathogenic strain of common midwife toad virus (CMTV) previously known only from Europe and China. The later outbreak was due to a chimeric ranavirus that displayed a novel genome arrangement and a DNA backbone typical for Frog virus 3 (FV3) strains except for interspersed fragments acquired through recombination with the CMTV isolated earlier...
August 10, 2017: Virology
https://www.readbyqxmd.com/read/28790205/comparative-genomics-of-bacillus-thuringiensis-reveals-a-path-to-specialized-exploitation-of-multiple-invertebrate-hosts
#10
Jinshui Zheng, Qiuling Gao, Linlin Liu, Hualin Liu, Yueying Wang, Donghai Peng, Lifang Ruan, Ben Raymond, Ming Sun
Understanding the genetic basis of host shifts is a key genomic question for pathogen and parasite biology. The Bacillus cereus group, which encompasses Bacillus thuringiensis and Bacillus anthracis, contains pathogens that can infect insects, nematodes, and vertebrates. Since the target range of the essential virulence factors (Cry toxins) and many isolates is well known, this group presents a powerful system for investigating how pathogens can diversify and adapt to phylogenetically distant hosts. Specialization to exploit insects occurs at the level of the major clade and is associated with substantial changes in the core genome, and host switching between insect orders has occurred repeatedly within subclades...
August 8, 2017: MBio
https://www.readbyqxmd.com/read/28789640/the-purplish-bifurcate-mussel-mytilisepta-virgata-gene-expression-atlas-reveals-a-remarkable-tissue-functional-specialization
#11
Marco Gerdol, Yuki Fujii, Imtiaj Hasan, Toru Koike, Shunsuke Shimojo, Francesca Spazzali, Kaname Yamamoto, Yasuhiro Ozeki, Alberto Pallavicini, Hideaki Fujita
BACKGROUND: Mytilisepta virgata is a marine mussel commonly found along the coasts of Japan. Although this species has been the subject of occasional studies concerning its ecological role, growth and reproduction, it has been so far almost completely neglected from a genetic and molecular point of view. In the present study we present a high quality de novo assembled transcriptome of the Japanese purplish mussel, which represents the first publicly available collection of expressed sequences for this species...
August 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28780378/homblocks-a-multiple-alignment-construction-pipeline-for-organelle-phylogenomics-based-on-locally-collinear-block-searching
#12
Guiqi Bi, Yunxiang Mao, Qikun Xing, Min Cao
Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multi-gene alignments. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multi-gene alignment in a few hours...
August 2, 2017: Genomics
https://www.readbyqxmd.com/read/28775310/phylogenetic-relationships-among-tribes-of-the-green-lacewing-subfamily-chrysopinae-recovered-based-on-mitochondrial-phylogenomics
#13
Yunlan Jiang, Ivonne J Garzón-Orduña, Shaun L Winterton, Fan Yang, Xingyue Liu
Chrysopidae (green lacewings) is the second largest family in Neuroptera, and it includes medium-size lacewings largely recognized by the presence of golden-colored eyes, bright green bodies and delicate wings with dense venation patterns. The subfamily Chrysopinae includes 97% of the species diversity in the family and it is currently divided into four tribes: Ankylopterygini, Belonopterygini, Chrysopini and Leucochrysini. Here we sequenced and annotated the nearly complete mitochondrial genomes of four species of each these tribes: Abachrysa eureka, Italochrysa insignis, Leucochrysa pretiosa, Parankyloteryx sp...
August 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28766584/transcriptional-variation-of-diverse-enteropathogenic-escherichia-coli-isolates-under-virulence-inducing-conditions
#14
Tracy H Hazen, Sean C Daugherty, Amol C Shetty, James P Nataro, David A Rasko
Enteropathogenic Escherichia coli (EPEC) bacteria are a diverse group of pathogens that cause moderate to severe diarrhea in young children in developing countries. EPEC isolates can be further subclassified as typical EPEC (tEPEC) isolates that contain the bundle-forming pilus (BFP) or as atypical EPEC (aEPEC) isolates that do not contain BFP. Comparative genomics studies have recently highlighted the considerable genomic diversity among EPEC isolates. In the current study, we used RNA sequencing (RNA-Seq) to characterize the global transcriptomes of eight tEPEC isolates representing the identified genomic diversity, as well as one aEPEC isolate...
July 2017: MSystems
https://www.readbyqxmd.com/read/28765569/locus-of-adhesion-and-autoaggregation-laa-a-pathogenicity-island-present-in-emerging-shiga-toxin-producing-escherichia-coli-strains
#15
David A Montero, Juliana Velasco, Felipe Del Canto, Jose L Puente, Nora L Padola, David A Rasko, Mauricio Farfán, Juan C Salazar, Roberto Vidal
Shiga Toxin-producing Escherichia coli (STEC) are a group of foodborne pathogens associated with diarrhea, dysentery, hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Shiga toxins are the major virulence factor of these pathogens, however adhesion and colonization to the human intestine is required for STEC pathogenesis. A subset of STEC strains carry the Locus of Enterocyte Effacement (LEE) pathogenicity island (PAI), which encodes genes that mediate the colonization of the human intestine. While LEE-positive STEC strains have traditionally been associated with human disease, the burden of disease caused by STEC strains that lacks LEE (LEE-negative) has increased recently in several countries; however, in the absence of LEE, the molecular pathogenic mechanisms by STEC strains are unknown...
August 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28764658/comparative-genomic-and-phylogenomic-analyses-of-the-bifidobacteriaceae-family
#16
Gabriele Andrea Lugli, Christian Milani, Francesca Turroni, Sabrina Duranti, Leonardo Mancabelli, Marta Mangifesta, Chiara Ferrario, Monica Modesto, Paola Mattarelli, Killer Jiří, Douwe van Sinderen, Marco Ventura
BACKGROUND: Members of the Bifidobacteriaceae family represent both dominant microbial groups that colonize the gut of various animals, especially during the suckling stage of their life, while they also occur as pathogenic bacteria of the urogenital tract. The pan-genome of the genus Bifidobacterium has been explored in detail in recent years, though genomics of the Bifidobacteriaceae family has not yet received much attention. Here, a comparative genomic analyses of 67 Bifidobacteriaceae (sub) species including all currently recognized genera of this family, i...
August 1, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28763486/comparative-analysis-of-complete-plastid-genomes-from-wild-soybean-glycine-soja-and-nine-other-glycine-species
#17
Sajjad Asaf, Abdul Latif Khan, Muhammad Aaqil Khan, Qari Muhammad Imran, Sang-Mo Kang, Khdija Al-Hosni, Eun Ju Jeong, Ko Eun Lee, In-Jung Lee
The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of G. soja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species...
2017: PloS One
https://www.readbyqxmd.com/read/28761782/targeted-ngs-for-species-level-phylogenomics-made-to-measure-or-one-size-fits-all
#18
Malvina Kadlec, Dirk U Bellstedt, Nicholas C Le Maitre, Michael D Pirie
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae)...
2017: PeerJ
https://www.readbyqxmd.com/read/28760895/molecular-epidemiology-and-phylogenomics-of-staphylococcus-aureus-bacteremia-in-latin-america-a-prospective-cohort-multicenter-study-in-nine-countries
#19
Cesar A Arias, Jinnethe Reyes, Lina Paola Carvajal, Sandra Rincon, Lorena Diaz, Diana Panesso, Gabriel Ibarra, Rafael Rios, Jose M Munita, Mauro J Salles, Carlos Alvarez-Moreno, Jaime Labarca, Coralith Garcia, Carlos M Luna, Carlos Mejia-Villatoro, Jeannete Zurita, Manuel Guzman-Blanco, Eduardo Rodriguez-Noriega, Apurva Narechania, Laura J Rojas, Paul J Planet, George M Weinstock, Eduardo Gotuzzo, Carlos Seas
Staphylococcus aureus are important pathogens causing a spectrum of diseases ranging from mild skin and soft tissue infections to life-threatening conditions. Bloodstream infections are particularly important and the treatment approach is complicated by the presence of methicillin resistance among S. aureus isolates (MRSA). Emergence of new genetic lineages of MRSA has occurred in Latin America (LA) with the rise and dissemination of the community-associated USA300 Latin American Variant (USA300-LV). Here, we prospectively characterized bloodstream MRSA recovered from selected hospitals in 9 Latin American countries...
July 31, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28757447/the-phylogeny-of-extant-starfish-asteroidea-echinodermata-including-xyloplax-based-on-comparative-transcriptomics
#20
Gregorio V Linchangco, David W Foltz, Rob Reid, John Williams, Conor Nodzak, Alexander M Kerr, Allison K Miller, Rebecca Hunter, Nerida G Wilson, William J Nielsen, Christopher L Mah, Greg W Rouse, Gregory A Wray, Daniel A Janies
Multi-locus phylogenetic studies of echinoderms based on Sanger and RNA-seq technologies and the fossil record have provided evidence for the Asterozoa-Echinozoa hypothesis. This hypothesis posits a sister relationship between asterozoan classes (Asteroidea and Ophiuroidea) and a similar relationship between echinozoan classes (Echinoidea and Holothuroidea). Despite this consensus around Asterozoa-Echinozoa, phylogenetic relationships within the class Asteroidea (sea stars or starfish) have been controversial for over a century...
July 27, 2017: Molecular Phylogenetics and Evolution
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"