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Phylogenomics

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https://www.readbyqxmd.com/read/28528902/x-cells-are-globally-distributed-genetically-divergent-fish-parasites-related-to-perkinsids-and-dinoflagellates
#1
Mark A Freeman, Janina Fuss, Árni Kristmundsson, Marit F M Bjorbækmo, Jean-François Mangot, Javier Del Campo, Patrick J Keeling, Kamran Shalchian-Tabrizi, David Bass
"X-cells" have long been associated with tumor-like formations (xenomas) in marine fish, including many of commercial interest. The name was first used to refer to the large polygonal cells that were found in epidermal xenomas from flatfish from the Pacific Northwest [1]. Similar looking cells from pseudobranchial xenomas had previously been reported from cod in the Atlantic [2] and Pacific Oceans [3]. X-cell pathologies have been reported from five teleost orders: Pleuronectiformes (flatfish), Perciformes (perch-like fish), Gadiformes (cods), Siluriformes (catfish), and Salmoniformes (salmonids)...
May 13, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28525299/early-diverging-fungi-diversity-and-impact-at-the-dawn-of-terrestrial-life
#2
Mary L Berbee, Timothy Y James, Christine Strullu-Derrien
As decomposers or plant pathogens, fungi deploy invasive growth and powerful carbohydrate active enzymes to reduce multicellular plant tissues to humus and simple sugars. Fungi are perhaps also the most important mutualistic symbionts in modern ecosystems, transporting poorly soluble mineral nutrients to plants and thus enhancing the growth of vegetation. However, at their origin over a billion years ago, fungus-like plants and animals were unicellular marine microbes. Like the other multicellular kingdoms, Fungi evolved increased size, complexity, and metabolic functioning...
May 19, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28515737/the-complete-plastome-sequences-of-four-orchid-species-insights-into-the-evolution-of-the-orchidaceae-and-the-utility-of-plastomic-mutational-hotspots
#3
Zhitao Niu, Qingyun Xue, Shuying Zhu, Jing Sun, Wei Liu, Xiaoyu Ding
Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28515204/a-genetic-legacy-of-introgression-confounds-phylogeny-and-biogeography-in-oaks
#4
John D McVay, Andrew L Hipp, Paul S Manos
Oaks (Quercus L.) have long been suspected to hybridize in nature, and widespread genetic exchange between morphologically defined species is well documented in two- to six-species systems, but the phylogenetic consequences of hybridization in oaks have never been demonstrated in a phylogenetically diverse sample. Here, we present phylogenomic analyses of a ca 30 Myr clade that strongly support morphologically defined species and the resolution of novel clades of white oaks; however, historical hybridization across clade boundaries is detectable and, undiagnosed, would obscure the imprint of biogeographic history in the phylogeny...
May 17, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28506838/phylogenomic-analysis-of-the-complete-sequence-of-a-gastroenteritis-associated-cetacean-adenovirus-bottlenose-dolphin-adenovirus-1-reveals-a-high-degree-of-genetic-divergence
#5
Maja Malmberg, Consuelo Rubio-Guerri, Juliette Hayer, Daniel García-Párraga, Elvira Nieto-Pelegrín, Mar Melero, Teresa Álvaro, Mónica Valls, Jose Manuel Sánchez-Vizcaíno, Sándor Belák, Fredrik Granberg
Adenoviruses are common pathogens in vertebrates, infecting a wide range of hosts, but only having rarely been detected and correlated with disease in cetaceans. This article describes the first complete genomic sequence of a cetacean adenovirus, bottlenose dolphin adenovirus 1 (BdAdV-1), detected in captive bottlenose dolphin population (Tursiops truncatus) suffering from self-limiting gastroenteritis. The complete genome sequence of BdAdV-1 was recovered from data generated by high-throughput sequencing and validated by Sanger sequencing...
May 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28505375/between-a-pod-and-a-hard-test-the-deep-evolution-of-amoebae
#6
Seungho Kang, Alexander K Tice, Frederick W Spiegel, Jeffrey D Silberman, Tomáš Pánek, Ivan Cepicka, Martin Kostka, Anush Kosakyan, Daniel M Alcântara, Andrew J Roger, Lora L Shadwick, Alexey Smirnov, Alexander Kudryavstev, Daniel J G Lahr, Matthew W Brown
Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals and Fungi, as well as their protistan relatives, and the breviate and apusomonad flagellates. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. We present a robust phylogeny of Amoebozoa based on broad representative set of taxa in a phylogenomic framework (325 genes)...
May 15, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28504699/expansion-of-the-redox-sensitive-proteome-coincides-with-the-plastid-endosymbiosis
#7
Christian Woehle, Tal Dagan, Giddy Landan, Assaf Vardi, Shilo Rosenwasser
The redox-sensitive proteome (RSP) consists of protein thiols that undergo redox reactions, playing an important role in coordinating cellular processes. Here, we applied a large-scale phylogenomic reconstruction approach in the model diatom Phaeodactylum tricornutum to map the evolutionary origins of the eukaryotic RSP. The majority of P. tricornutum redox-sensitive cysteines (76%) is specific to eukaryotes, yet these are encoded in genes that are mostly of a prokaryotic origin (57%). Furthermore, we find a threefold enrichment in redox-sensitive cysteines in genes that were gained by endosymbiotic gene transfer during the primary plastid acquisition...
May 15, 2017: Nature Plants
https://www.readbyqxmd.com/read/28501611/multilocus-phylogeny-and-statistical-biogeography-clarify-the-evolutionary-history-of-major-lineages-of-turtles
#8
Anieli G Pereira, Juliana Sterli, Filipe R R Moreira, Carlos G Schrago
Despite their complex evolutionary history and the rich fossil record, the higher level phylogeny and historical biogeography of living turtles have not been investigated in a comprehensive and statistical framework. To tackle these issues, we assembled a large molecular dataset, maximizing both taxonomic and gene sampling. As different models provide alternative biogeographical scenarios, we have explicitly tested such hypotheses in order to reconstruct a robust biogeographical history of Testudines. We scanned publicly available databases for nucleotide sequences and composed a dataset comprising 13 loci for 294 living species of Testudines, which accounts for all living genera and 85% of their extant species diversity...
May 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28493482/emergence-of-cytochrome-bc-complexes-in-the-context-of-photosynthesis
#9
Daria V Dibrova, Daria N Shalaeva, Michael Y Galperin, Armen Y Mulkidjanian
The cytochrome bc complexes are involved in Q-cycling; they oxidize membrane quinols by high-potential electron acceptors, such as cytochromes or plastocyanin, and generate transmembrane proton gradient. In several prokaryotic lineages, and also in plant chloroplasts, the catalytic core of the cytochrome bc complexes is built of a four-helical cytochrome b that contains three hemes, a three-helical subunit IV, and an iron-sulfur Rieske protein (cytochrome b6 f-type complexes). In other prokaryotic lineages, and also in mitochondria, the cytochrome b subunit is fused with subunit IV, yielding a seven- or eight-helical cytochrome b with only two hemes (cytochrome bc1 -type complexes)...
May 11, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28487566/the-invasive-neisseria-meningitidis-menc-cc103-from-brazil-is-characterized-by-an-accessory-gene-repertoire
#10
Michel Abanto Marin, Erica Fonseca, Fernando Encinas, Fernanda Freitas, Dhian Almeida Camargo, Roney Santos Coimbra, Ivano de Filippis, Ana Carolina Vicente
Neisseria meningitidis infections are a major issue for global health. The invasive MenC ST-103 clonal complex (CC103) has been the most prevalent in meningococcal outbreaks in Brazil, occurring also in several countries worldwide. Here we have analysed the population structure and accessory genome of MenC CC103 strains from a global perspective. An in-depth phylogenomic analysis revealed a lineage of N. meningitidis causing meningitis in Brazil and the United Kingdom. This lineage was also characterized as harbouring a particular accessory genome composed of CRISPR/Cas and restriction modification systems...
May 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28487262/phylogenomic-analysis-of-a-rapid-radiation-of-misfit-fishes-syngnathiformes-using-ultraconserved-elements
#11
S J Longo, B C Faircloth, A Meyer, M W Westneat, M E Alfaro, P C Wainwright
Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders...
May 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28486123/evolution-taking-the-sting-out-of-wasp-phylogenetics
#12
Pu Tang, Alfried P Vogler
Hymenopterans - one of the 'big four' of insect orders - includes the sawflies, wasps, ants and bees. Two phylogenomic studies now resolve hymenopteran phylogeny and provide scenarios for the evolution of major lineages and key lifestyle transitions.
May 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28484436/comparative-genomic-analysis-of-the-class-epsilonproteobacteria-and-proposed-reclassification-to-epsilonbacteraeota-phyl-nov
#13
David W Waite, Inka Vanwonterghem, Christian Rinke, Donovan H Parks, Ying Zhang, Ken Takai, Stefan M Sievert, Jörg Simon, Barbara J Campbell, Thomas E Hanson, Tanja Woyke, Martin G Klotz, Philip Hugenholtz
The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28475781/2015-epidemic-of-severe-streptococcus-agalactiae-sequence-type-283-infections-in-singapore-associated-with-the-consumption-of-raw-freshwater-fish-a-detailed-analysis-of-clinical-epidemiological-and-bacterial-sequencing-data
#14
Shirin Kalimuddin, Swaine L Chen, Cindy T K Lim, Tse Hsien Koh, Thean Yen Tan, Michelle Kam, Christopher W Wong, Kurosh S Mehershahi, Man Ling Chau, Lee Ching Ng, Wen Ying Tang, Hishamuddin Badaruddin, Jeanette Teo, Anucha Apisarnthanarak, Nuntra Suwantarat, Margaret Ip, Matthew T G Holden, Li Yang Hsu, Timothy Barkham
Background: Streptococcus agalactiae (group B Streptococcus [GBS]) has not been described as a foodborne pathogen. However, in 2015, a large outbreak of severe invasive sequence type (ST) 283 GBS infections in adults epidemiologically linked to the consumption of raw freshwater fish occurred in Singapore. We attempted to determine the scale of the outbreak, define the clinical spectrum of disease, and link the outbreak to contaminated fish. Methods: Time-series analysis was performed on microbiology laboratory data...
May 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28472519/resolving-relationships-among-the-megadiverse-butterflies-and-moths-with-a-novel-pipeline-for-anchored-phylogenomics
#15
Jesse W Breinholt, Chandra Earl, Alan R Lemmon, Emily Moriarty Lemmon, Lei Xiao, Akito Y Kawahara
The advent of next-generation sequencing technology has allowed for the collection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region...
May 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28472459/resolving-rapid-radiations-within-angiosperm-families-using-anchored-phylogenomics
#16
Étienne Léveillé-Bourret, Julian R Starr, Bruce A Ford, Emily Moriarty Lemmon, Alan R Lemmon
Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are still based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur...
May 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28469029/how-do-seemingly-non-vagile-clades-accomplish-trans-marine-dispersal-trait-and-dispersal-evolution-in-the-landfowl-aves-galliformes
#17
Peter A Hosner, Joseph A Tobias, Edward L Braun, Rebecca T Kimball
Dispersal ability is a key factor in determining insular distributions and island community composition, yet non-vagile terrestrial organisms widely occur on oceanic islands. The landfowl (pheasants, partridges, grouse, turkeys, quails and relatives) are generally poor dispersers, but the Old World quail (Coturnix) are a notable exception. These birds evolved small body sizes and high-aspect-ratio wing shapes, and hence are capable of trans-continental migrations and trans-oceanic colonization. Two monotypic partridge genera, Margaroperdix of Madagascar and Anurophasis of alpine New Guinea, may represent additional examples of trans-marine dispersal in landfowl, but their body size and wing shape are typical of poorly dispersive continental species...
May 17, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28467492/the-natural-history-of-molecular-functions-inferred-from-an-extensive-phylogenomic-analysis-of-gene-ontology-data
#18
Ibrahim Koç, Gustavo Caetano-Anollés
The origin and natural history of molecular functions hold the key to the emergence of cellular organization and modern biochemistry. Here we use a genomic census of Gene Ontology (GO) terms to reconstruct phylogenies at the three highest (1, 2 and 3) and the lowest (terminal) levels of the hierarchy of molecular functions, which reflect the broadest and the most specific GO definitions, respectively. These phylogenies define evolutionary timelines of functional innovation. We analyzed 249 free-living organisms comprising the three superkingdoms of life, Archaea, Bacteria, and Eukarya...
2017: PloS One
https://www.readbyqxmd.com/read/28460034/single-copy-genes-as-molecular-markers-for-phylogenomic-studies-in-seed-plants
#19
Zhen Li, Amanda R De La Torre, Lieven Sterck, Francisco M Cánovas, Concepción Avila, Irene Merino, José Antonio Cabezas, María Teresa Cervera, Pär K Ingvarsson, Yves Van de Peer
Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants...
May 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28458658/delineation-of-taxonomic-species-within-complex-of-species-aeromonas-media-and-related-species-as-a-test-case
#20
Emilie Talagrand-Reboul, Frédéric Roger, Jean-Luc Kimper, Sophie M Colston, Joerg Graf, Fadua Latif-Eugenín, Maria José Figueras, Fabienne Petit, Hélène Marchandin, Estelle Jumas-Bilak, Brigitte Lamy
Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and the related species A. rivipollensis. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features...
2017: Frontiers in Microbiology
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