keyword
MENU ▼
Read by QxMD icon Read
search

Phylogenomics

keyword
https://www.readbyqxmd.com/read/28338821/phylogenomic-insights-into-mouse-evolution-using-a-pseudoreference-approach
#1
Brice A J Sarver, Sara Keeble, Ted Cosart, Priscilla K Tucker, Matthew D Dean, Jeffrey M Good
Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample...
February 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28334176/phylogenomic-systematics-of-ostariophysan-fishes-ultraconserved-elements-support-the-surprising-non-monophyly-of-characiformes
#2
Prosanta Chakrabarty, Brant C Faircloth, Fernando Alda, William B Ludt, Caleb D McMahan, Thomas J Near, Alex Dornburg, James S Albert, Jairo Arroyave, Melanie L J Stiassny, Laurie Sorenson, Michael E Alfaro
Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1,100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny...
February 27, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28333396/conflicting-phylogenomic-signals-reveal-a-pattern-of-reticulate-evolution-in-a-recent-high-andean-diversification-asteraceae-astereae-diplostephium
#3
Oscar M Vargas, Edgardo M Ortiz, Beryl B Simpson
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods...
March 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28333264/single-cell-transcriptomics-mega-phylogeny-and-the-genetic-basis-of-morphological-innovations-in-rhizaria
#4
Anders K Krabberød, Russell J S Orr, Jon Bråte, Tom Kristensen, Kjell R Bjørklund, Kamran Shalchian-Tabrizi
The innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport and cytokinesis, and is responsible for the diversity of eukaryotic morphologies. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton we provide the first single cell transcriptomes from uncultured, free-living unicellular eukaryotes: the polycystine radiolarian Lithomelissa setosa (Nassellaria) and Sticholonche zanclea (Taxopodida)...
March 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333217/recurrent-gene-duplication-leads-to-diverse-repertoires-of-centromeric-histones-in-drosophila-species
#5
Lisa E Kursel, Harmit S Malik
Despite their essential role in the process of chromosome segregation in most eukaryotes, centromeric histones show remarkable evolutionary lability. Not only have they been lost in multiple insect lineages, but they have also undergone gene duplication in multiple plant lineages. Based on detailed study of a handful of model organisms including Drosophila melanogaster, centromeric histone duplication is considered to be rare in animals. Using a detailed phylogenomic study, we find that Cid, the centromeric histone gene, has undergone at least four independent gene duplications during Drosophila evolution...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333201/new-statistical-criteria-detect-phylogenetic-bias-caused-by-compositional-heterogeneity
#6
David A Duchêne, Sebastian Duchêne, Simon Y W Ho
In statistical phylogenetic analyses of DNA sequences, models of evolutionary change commonly assume that base composition is stationary through time and across lineages. This assumption is violated by many data sets, but it is unclear whether the magnitude of these violations is sufficient to mislead phylogenetic inference. We investigated the impacts of compositional heterogeneity on phylogenetic estimates using a method for assessing model adequacy. Based on a detailed simulation study, we found that common frequentist criteria are highly conservative, such that the model is often rejected when the phylogenetic estimates do not show clear signs of bias...
February 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28330166/a-molecular-phylogenetic-framework-for-bacillus-subtilis-using-genome-sequences-and-its-application-to-bacillus-subtilis-subspecies-stecoris-strain-d7xpn1-an-isolate-from-a-commercial-food-waste-degrading-bioreactor
#7
Joseph Adelskov, Bharat K C Patel
A thermophilic, heterotrophic and facultatively anaerobic bacterium designated strain D7XPN1 was isolated from Baku BakuKing™, a commercial food-waste degrading bioreactor (composter). The strain grew optimally at 45 °C (growth range between 24 and 50 °C) and pH 7 (growth pH range between pH 5 and 9) in Luria Broth supplemented with 0.3 % glucose. Strain D7XPN1 tolerated up to 7 % NaCl and showed amylolytic and xylanolytic activities. 16S rRNA gene analysis placed strain D7XPN1 in the cluster represented by Bacillus subtilis and the genome analysis of the 4...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327965/carbon-dating-cancer-defining-the-chronology-of-metastatic-progression-in-colorectal-cancer
#8
H Lote, I Spiteri, L Ermini, A Vatsiou, A Roy, A McDonald, N Maka, M Balsitis, N Bose, M Simbolo, A Mafficini, A Lampis, J C Hahne, F Trevisani, Z Eltahir, G Mentrasti, C Findlay, Eaj Kalkman, M Punta, B Werner, S Lise, A Aktipis, C Maley, M Greaves, C Braconi, J White, M Fassan, A Scarpa, A Sottoriva, N Valeri
Background: HASH(0x3902000) Patients often ask oncologists how long a cancer has been present before causing symptoms or spreading to other organs. The evolutionary trajectory of cancers can be defined using phylogenetic approaches but lack of chronological references makes dating the exact onset of tumours very challenging. Patients and Methods: HASH(0x39f0190) Here we describe the case of a colorectal cancer patient presenting with synchronous lung metastasis and metachronous thyroid, chest wall and urinary tract metastases over the course of five years...
February 23, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327435/network-approaches-for-plant-phylogenomic-synteny-analysis
#9
REVIEW
Tao Zhao, M Eric Schranz
Network analysis approaches have been widely applied across disciplines. In biology, network analysis is now frequently adopted to organize protein-protein interactions, organize pathways and/or to interpret gene co-expression patterns. However, comparative genomic analyses still largely rely on pairwise comparisons and linear visualizations between genomes. In this article, we discuss the challenges and prospects for establishing a generalized plant phylogenomic synteny network approach needed to interpret the wealth of new and emerging genomic data...
March 16, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28324738/protist-evolution-stealing-genes-to-gut-it-out
#10
David Moreira, Purificación López-García
The amount and evolutionary impact of horizontal gene transfer in eukaryotes remain contentious issues. A new phylogenomic study suggests that gene transfer from prokaryotes has contributed significantly to the adaptation and metabolic evolution of Blastocystis, the most widespread human gut eukaryotic parasite.
March 20, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28320310/treetoreads-a-pipeline-for-simulating-raw-reads-from-phylogenies
#11
Emily Jane McTavish, James Pettengill, Steven Davis, Hugh Rand, Errol Strain, Marc Allard, Ruth E Timme
BACKGROUND: Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28318975/a-large-and-consistent-phylogenomic-dataset-supports-sponges-as-the-sister-group-to-all-other-animals
#12
Paul Simion, Hervé Philippe, Denis Baurain, Muriel Jager, Daniel J Richter, Arnaud Di Franco, Béatrice Roure, Nori Satoh, Éric Quéinnec, Alexander Ereskovsky, Pascal Lapébie, Erwan Corre, Frédéric Delsuc, Nicole King, Gert Wörheide, Michaël Manuel
Resolving the early diversification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera) are the sister group to all other animals ("Porifera-sister" hypothesis), consistent with a single origin of the gut, nerve cells, and muscle cells in the stem lineage of eumetazoans (bilaterians + ctenophores + cnidarians). In contrast, several other studies have recovered an alternative topology in which ctenophores are the sister group to all other animals (including sponges)...
March 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28317029/listeriomics-an-interactive-web-platform-for-systems-biology-of-listeria
#13
Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i...
March 2017: MSystems
https://www.readbyqxmd.com/read/28298350/the-acacia-ants-revisited-convergent-evolution-and-biogeographic-context-in-an-iconic-ant-plant-mutualism
#14
Philip S Ward, Michael G Branstetter
Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach-ultraconserved element sequence capture-to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants (Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28294981/the-complete-chloroplast-genome-sequences-of-six-rehmannia-species
#15
Shuyun Zeng, Tao Zhou, Kai Han, Yanci Yang, Jianhua Zhao, Zhan-Lin Liu
Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia plastomes exhibited typical quadripartite and circular structures with good synteny of gene order...
March 15, 2017: Genes
https://www.readbyqxmd.com/read/28282461/genomic-diversity-within-the-haloalkaliphilic-genus-thioalkalivibrio
#16
Anne-Catherine Ahn, Jan P Meier-Kolthoff, Lex Overmars, Michael Richter, Tanja Woyke, Dimitry Y Sorokin, Gerard Muyzer
Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but only ten species have been effectively described yet. Therefore, the assignment of the remaining strains to either existing or novel species is important and will further elucidate their genomic diversity as well as give a better general understanding of this genus...
2017: PloS One
https://www.readbyqxmd.com/read/28278505/chromosome-painting-in-callicebus-nigrifrons-provides-insights-into-the-genome-evolution-of-titi-monkeys-and-the-ancestral-callicebinae-karyotype
#17
Naiara Pereira Araújo, Alice Alves do Espírito Santo, Valéria do Socorro Pereira, Roscoe Stanyon, Marta Svartman
We studied the chromosomes of Callicebus nigrifrons with conventional and molecular cytogenetic methods. Our chromosome painting analysis in C. nigrifrons together with previous reports allowed us to hypothesize an ancestral Callicebinae karyotype with 2n = 48. The associations of human chromosomes (HSA) 2/22, 7/15, 10/11, and the inverted HSA2/16 would link Callicebus, Cheracebus, and Plecturocebus and would thus be present in the ancestral Callicebinae karyotype. Four fusions (HSA1b/1c, 3c/8b, 13/20, and 14/15/3/21) and 1 fission (HSA2/22) are synapomorphies of Callicebus...
March 10, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28276126/aquatic-adaptation-of-a-laterally-acquired-pectin-degradation-pathway-in-marine-gammaproteobacteria
#18
Jan-Hendrik Hehemann, Le Van Truong, Frank Unfried, Norma Welsch, Johannes Kabisch, Stefan E Heiden, Sabryna Junker, Dörte Becher, Andrea Thürmer, Rolf Daniel, Rudolf Amann, Thomas Schweder
Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multi-modular pectate lyases, PelA and PelB...
March 9, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28274202/identification-of-constraints-influencing-the-bacterial-genomes-evolution-in-the-pvc-super-phylum
#19
Sandrine Pinos, Pierre Pontarotti, Didier Raoult, Vicky Merhej
BACKGROUND: Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution...
March 9, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28265262/genomic-analysis-of-caldithrix-abyssi-the-thermophilic-anaerobic-bacterium-of-the-novel-bacterial-phylum-calditrichaeota
#20
Ilya V Kublanov, Olga M Sigalova, Sergey N Gavrilov, Alexander V Lebedinsky, Christian Rinke, Olga Kovaleva, Nikolai A Chernyh, Natalia Ivanova, Chris Daum, T B K Reddy, Hans-Peter Klenk, Stefan Spring, Markus Göker, Oleg N Reva, Margarita L Miroshnichenko, Nikos C Kyrpides, Tanja Woyke, Mikhail S Gelfand, Elizaveta A Bonch-Osmolovskaya
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional...
2017: Frontiers in Microbiology
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"