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Phylogenomics

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https://www.readbyqxmd.com/read/28210253/genomic-analysis-of-a-new-serovar-of-leptospira-weilii-serogroup-manhao
#1
Yinghua Xu, Huajun Zheng, Ying Zhang, Yuezhu Wang, Jinlong Zhang, Zhe Li, Shenghui Cui, Xiaofang Xin, Qiang Ye, Yung-Fu Chang, Junzhi Wang
Leptospirosis, caused by pathogenic Leptospira spp., is recognized as an important emerging zoonotic disease throughout the world. In this study, multiple approaches were used to characterize the recently discovered serovar Heyan strain L231. This strain can infect guinea pigs and belonged to the pathogenic species L. weilii. Genome sequencing analysis revealed the draft genome of 4.2 M bp with a G+C content of 40.67% for strain L231, and a total of 4,794 ORFs were identified. The strain L231 genome was found to have a larger LPS biosynthesis locus than that of strains L...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28201585/patterns-and-processes-of-mycobacterium-bovis-evolution-revealed-by-phylogenomic-analyses
#2
José S L Patané, Joaquim Martins, Ana Beatriz Castelão, Christiane Nishibe, Luciana Montera, Fabiana Bigi, Martin J Zumárraga, Angel A Cataldi, Antônio Fonseca Junior, Eliana Roxo, Ana Luiza, A R Osório, Kláudia S Jorge Ufms, Tyler C Thacker, Nalvo F Almeida, Flabio R Araújo, João C Setubal
No abstract text is available yet for this article.
February 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28198668/comparative-analysis-of-corynebacterium-glutamicum-genomes-a-new-perspective-for-the-industrial-production-of-amino-acids
#3
Junjie Yang, Sheng Yang
BACKGROUND: Corynebacterium glutamicum is a non-pathogenic bacterium widely used in industrial amino acid production and metabolic engineering research. Although the genome sequences of some C. glutamicum strains are available, comprehensive comparative genome analyses of these species have not been done. Six wild type C. glutamicum strains were sequenced using next-generation sequencing technology in our study. Together with 20 previously reported strains, we present a comprehensive comparative analysis of C...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28193159/erratum-to-phylogenomics-of-strongylocentrotid-sea-urchins
#4
Kord M Kober, Giacomo Bernardi
No abstract text is available yet for this article.
February 13, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28192210/phylogenomics-of-trypanosoma-cruzi-few-evidence-of-tci-tcii-mosaicism-in-tciii-challenges-the-hypothesis-of-an-ancient-tci-tcii-hybridization
#5
Nicolás Tomasini, Patricio Diosque
Phylogenetic relationships among major lineages of Trypanosoma cruzi are still debatable. Particularly, it is controversial the origin of two main lineages: TcIII and TcIV. Some authors proposed that these lineages have been the result of an ancient hybridization between TcI and TcII, and this was one of the most accepted evolutionary models in the scientific community for several years. In the present paper we analyse several genomes of T. cruzi in order to examine if there is evidence supporting that TcIII is an ancient TcI/TcII hybrid...
February 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28187150/phylogenomic-analyses-reveal-the-diversity-of-laccase-coding-genes-in-fonsecaea-genomes
#6
Leandro Ferreira Moreno, Peiying Feng, Vinicius Almir Weiss, Vania Aparecida Vicente, J Benjamin Stielow, Sybren de Hoog
The genus Fonsecaea comprises black yeast-like fungi of clinical relevance, including etiologic agents of chromoblastomycosis and cerebral phaeohyphomycosis. Presence of melanin and assimilation of monoaromatic hydrocarbons and alkylbenzenes have been proposed as virulence factors. Multicopper oxidase (MCO) is a family of enzymes including laccases, ferroxidases and ascorbate oxidases which are able to catalyze the oxidation of various aromatic organic compounds with the reduction of molecular oxygen to water...
2017: PloS One
https://www.readbyqxmd.com/read/28186635/diversification-of-rosaceae-since-the-late-cretaceous-based-on-plastid-phylogenomics
#7
Shu-Dong Zhang, Jian-Jun Jin, Si-Yun Chen, Mark W Chase, Douglas E Soltis, Hong-Tao Li, Jun-Bo Yang, De-Zhu Li, Ting-Shuang Yi
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics...
February 10, 2017: New Phytologist
https://www.readbyqxmd.com/read/28186341/embracing-discordance-phylogenomic-analyses-provide-evidence-for-allopolyploidy-leading-to-cryptic-diversity-in-a-mediterranean-campanula-campanulaceae-clade
#8
Andrew A Crowl, Cody Myers, Nico Cellinese
The Mediterranean Basin harbors a remarkable amount of biodiversity, a high proportion of which is endemic to this region. Here we present an in-depth study of an angiosperm species complex, in which cryptic taxonomic diversity has been hypothesized. Specifically, we focus on four currently recognized species in the Roucela complex, a well-supported clade in the Campanulaceae/Campanuloideae: Campanula creutzburgii, C. drabifolia, C. erinus, and C. simulans. This study takes a phylogenomic approach, utilizing near-complete plastomes and 130 nuclear loci, to uncover cryptic diversity and test hypotheses regarding hybridization and polyploidy within this clade...
February 10, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28185556/a-performance-study-of-the-impact-of-recombination-on-species-tree-analysis
#9
Zhiwei Wang, Kevin J Liu
BACKGROUND: The most widely used state-of-the-art methods for reconstructing species phylogenies from genomic sequence data assume that sampled loci are identically and independently distributed. In principle, free recombination between loci and a lack of intra-locus recombination are necessary to satisfy this assumption. Few studies have quantified the practical impact of recombination on species tree inference methods, and even fewer have used genomic sequence data for this purpose...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28185042/phylogenomic-relationship-of-feijoa-acca-sellowiana-o-berg-burret-with-other-myrtaceae-based-on-complete-chloroplast-genome-sequences
#10
Lilian Oliveira de Machado, Leila do Nascimento Vieira, Valdir Marcos Stefenon, Fábio de Oliveira Pedrosa, Emanuel Maltempi de Souza, Miguel Pedro Guerra, Rubens Onofre Nodari
Given their distribution, importance, and richness, Myrtaceae species comprise a model system for studying the evolution of tropical plant diversity. In addition, chloroplast (cp) genome sequencing is an efficient tool for phylogenetic relationship studies. Feijoa [Acca sellowiana (O. Berg) Burret; CN: pineapple-guava] is a Myrtaceae species that occurs naturally in southern Brazil and northern Uruguay. Feijoa is known for its exquisite perfume and flavorful fruits, pharmacological properties, ornamental value and increasing economic relevance...
February 9, 2017: Genetica
https://www.readbyqxmd.com/read/28183834/grass-plastomes-reveal-unexpected-paraphyly-with-endemic-species-of-micrairoideae-from-india-and-new-haplotype-markers-in-arundinoideae
#11
Melvin R Duvall, Shrirang R Yadav, Sean V Burke, William P Wysocki
PREMISE OF THE STUDY: We investigated the little-studied Arundinoideae/Micrairoideae clade of grasses with an innovative plastome phylogenomic approach. This method gives robust results for taxa of uncertain phylogenetic placement. Arundinoideae comprise ∼45 species, although historically was much larger. Arundinoideae is notable for the widely invasive Phragmites australis. Micrairoideae comprise nine genera and ∼200 species. Some are threatened with extinction, including Hubbardia, some Isachne spp...
February 9, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28181409/metabolic-diversity-of-the-emerging-pathogenic-lineages-of-klebsiella-pneumoniae
#12
Camille Blin, Virginie Passet, Marie Touchon, Eduardo P C Rocha, Sylvain Brisse
Multidrug resistant and hypervirulent clones of Klebsiella pneumoniae are emerging pathogens. To understand the association between genotypic and phenotypic diversity in this process, we combined genomic, phylogenomic, and phenotypic analysis of a diverse set of K. pneumoniae and closely related species. These species were able to use an unusually large panel of metabolic substrates for growth, many of which were shared between all strains. We analysed the substrates used by only a fraction of the strains, identified some of their genetic basis, and found that many could not be explained by the phylogeny of the strains...
February 9, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28179101/molecular-phylogenomic-study-and-the-role-of-exogenous-spermidine-in-the-metabolic-adjustment-of-endogenous-polyamine-in-two-rice-cultivars-under-salt-stress
#13
Jayita Saha, Kalyan Giri
Compelling evidences anticipated the well acclamation of involvement of exogenous and endogenous polyamines (PAs) in conferring salt tolerance in plants. Intracellular PA's anabolism and catabolism should have contributed to maintain endogenous PAs homeostasis to induce stress signal networks. In this report, the evolutionary study has been conducted to reveal the phylogenetic relationship of genes encoding enzymes of the anabolic and catabolic pathway of PAs among the five plant lineages including green algae, moss, lycophyte, dicot and monocot along with their respective exon-intron structural patterns...
February 5, 2017: Gene
https://www.readbyqxmd.com/read/28177197/army-ant-invasions-reveal-phylogeographic-processes-across-the-isthmus-of-panama
#14
Seán G Brady
Female army ants cannot fly, making them very poor dispersers across water barriers. This dependence on terrestrial corridors motivated the investigation by Winston et al. (), published in this issue of Molecular Ecology, into the role of Panamanian isthmus formation in the diversification of Eciton army ants. Complete closure of this isthmus occurred around three million years ago (3 Ma), but it has also been hypothesized that earlier, temporary land connections facilitated additional colonization events between South and Central America over the past 13 million years or more...
February 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28176777/phylointeractomics-reconstructs-functional-evolution-of-protein-binding
#15
Dennis Kappei, Marion Scheibe, Maciej Paszkowski-Rogacz, Alina Bluhm, Toni Ingolf Gossmann, Sabrina Dietz, Mario Dejung, Holger Herlyn, Frank Buchholz, Matthias Mann, Falk Butter
Molecular phylogenomics investigates evolutionary relationships based on genomic data. However, despite genomic sequence conservation, changes in protein interactions can occur relatively rapidly and may cause strong functional diversification. To investigate such functional evolution, we here combine phylogenomics with interaction proteomics. We develop this concept by investigating the molecular evolution of the shelterin complex, which protects telomeres, across 16 vertebrate species from zebrafish to humans covering 450 million years of evolution...
February 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28176377/novel-taxa-of-thermally-dimorphic-systemic-pathogens-in-the-ajellomycetaceae-onygenales
#16
Karolina Dukik, Jose F Muñoz, Yanping Jiang, Peiying Feng, Lynne Sigler, J Benjamin Stielow, Joanna Freeke, Azadeh Jamalian, Bert Gerrits van den Ende, Juan G McEwen, Oliver K Clay, Ilan S Schwartz, Nelesh P Govender, Tsidiso G Maphanga, Christina A Cuomo, Leandro F Moreno, Chris Kenyon, Andrew M Borman, Sybren de Hoog
Recent discoveries of novel systemic fungal pathogens with thermally dimorphic yeast-like phases have challenged the current taxonomy of the Ajellomycetaceae, a family currently comprising the genera Blastomyces, Emmonsia, Emmonsiellopsis, Helicocarpus, Histoplasma, Lacazia and Paracoccidioides. Our morphological, phylogenetic and phylogenomic analyses demonstrated species relationships and their specific phenotypes, clarified generic boundaries and provided the first annotated genome assemblies to support the description of two new species...
February 7, 2017: Mycoses
https://www.readbyqxmd.com/read/28173480/incomplete-lineage-sorting-in-mammalian-phylogenomics
#17
Celine Scornavacca, Nicolas Galtier
No abstract text is available yet for this article.
January 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28173059/phylogenomic-reconstruction-of-sportive-lemurs-genus-lepilemur-recovered-from-mitogenomes-with-inferences-for-madagascar-biogeography
#18
Runhua Lei, Cynthia L Frasier, Melissa T R Hawkins, Shannon E Engberg, Carolyn A Bailey, Steig E Johnson, Adam T McLain, Colin P Groves, George H Perry, Stephen D Nash, Russell A Mittermeier, Edward E Louis
No abstract text is available yet for this article.
March 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28172670/comparative-phylogenomic-assessment-of-mitochondrial-introgression-among-several-species-of-chipmunks-tamias
#19
Brice A J Sarver, John R Demboski, Jeffrey M Good, Nicholas Forshee, Samuel S Hunter, Jack Sullivan
No abstract text is available yet for this article.
January 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28171752/endosymbiosis-did-plastids-evolve-from-a-freshwater-cyanobacterium
#20
Jan de Vries, John M Archibald
Photosynthetic eukaryotes are the product of an endosymbiotic event between a eukaryotic host and a cyanobacterium that became today's plastid. A new phylogenomic study suggests that the closest relative of plastids among extant cyanobacteria is the recently discovered freshwater-dwelling Gloeomargarita lithophora.
February 6, 2017: Current Biology: CB
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