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"Evolutionary history"

Laurent Oxusoff, Pascal Préa, Yvan Perez
Investigating how recombination might modify gene order during the evolution has become a routine part of mitochondrial genome analysis. A new method of genomic maps analysis based on formal logic is described. The purpose of this method is to 1) use mitochondrial gene order of current taxa as datasets 2) calculate rearrangements between all mitochondrial gene orders and 3) reconstruct phylogenetic relationships according to these calculated rearrangements within a tree under the assumption of maximum parsimony...
2018: PloS One
Daniel M P Ardisson-Araújo, Ana Maria Rodrigues da Silva, Fernando L Melo, Ethiane Rozo Dos Santos, Daniel R Sosa-Gómez, Bergmann M Ribeiro
In this report, we described the genome of a novel baculovirus isolated from the monocot insect pest Mocis latipes , the striped grass looper. The genome has 134,272 bp in length with a G + C content of 38.3%. Based on the concatenated sequence of the 38 baculovirus core genes, we found that the virus is a betabaculovirus closely related to the noctuid-infecting betabaculoviruses including Pseudaletia unipuncta granulovirus (PsunGV), Trichoplusia ni granulovirus (TnGV), Helicoverpa armigera granulovirus (HearGV), and Xestia c-nigrum granulovirus (XecnGV)...
March 16, 2018: Viruses
Yun-Yan Zhang, En Shi, Zhao-Ping Yang, Qi-Fang Geng, Ying-Xiong Qiu, Zhong-Sheng Wang
Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P...
2018: Frontiers in Plant Science
Oneida Espinosa-Álvarez, Paola A Ortiz, Luciana Lima, André G Costa-Martins, Myrna G Serrano, Stephane Herder, Gregory A Buck, Erney P Camargo, Patrick B Hamilton, Jamie R Stevens, Marta M G Teixeira
Trypanosoma rangeli and Trypanosoma cruzi are generalist trypanosomes sharing a wide range of mammalian hosts; they are transmitted by triatomine bugs, and are the only trypanosomes infecting humans in the Neotropics. Their origins, phylogenetic relationships, and emergence as human parasites have long been subjects of interest. In the present study, taxon-rich analyses (20 trypanosome species from bats and terrestrial mammals) using ssrRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH), heat shock protein-70 (HSP70) and Spliced Leader (SL) RNA sequences, and multilocus phylogenetic analyses using 11 single copy genes from 15 selected trypanosomes, provide increased resolution of relationships between species and clades, strongly supporting two main sister lineages: lineage Schizotrypanum, comprising T...
March 12, 2018: International Journal for Parasitology
Jie-Wei Luo, Cong-Huai Lin, Yao-Bin Zhu, Xing-Yu Zheng, Yong-Xi Wu, Wei-Wei Chen, Xiao Yang
Structural changes in symbiotic human microorganisms can affect host phenotype. Liver-fire hyperactivity syndrome (LFHS) presents as bitter taste, halitosis, xerostomia, odontalgia, and other oral symptoms. LFHS is associated with hypertension (EH). In this study, tongue flora was analyzed to further understand the intrinsic relationship between tongue flora and LFHS. Samples of tongue coating, from 16 patients with EH-LFHS, 16 with EH-non-LFHS, and 16 controls, were obtained; then, 16S rRNA variable (V3-V4) regions were amplified and sequenced by MiSeq PE300 Sequencing...
2018: Evidence-based Complementary and Alternative Medicine: ECAM
Karl A G Kremling, Shu-Yun Chen, Mei-Hsiu Su, Nicholas K Lepak, M Cinta Romay, Kelly L Swarts, Fei Lu, Anne Lorant, Peter J Bradbury, Edward S Buckler
Here we report a multi-tissue gene expression resource that represents the genotypic and phenotypic diversity of modern inbred maize, and includes transcriptomes in an average of 255 lines in seven tissues. We mapped expression quantitative trait loci and characterized the contribution of rare genetic variants to extremes in gene expression. Some of the new mutations that arise in the maize genome can be deleterious; although selection acts to keep deleterious variants rare, their complete removal is impeded by genetic linkage to favourable loci and by finite population size...
March 14, 2018: Nature
Taraka Ramji Moturu, Sravan Kumar Thula, Ravi Kumar Singh, Tomasz Nodzynski, Radka Svobodová Vareková, Jirí Friml, Sibu Simon
Strigolactones (SLs) are relatively recent addition to plant hormones that reported to control different aspects of plant development. SL signalling is perceived by an α/β hydrolase DWARF 14 (D14). A close homologue of D14, KARRIKIN INSENSTIVE2 (KAI2) involved in perception of an uncharacterized molecule called Karrikin (KR). Recent studies identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMXL7 in Arabidopsis to be potential SCF-MAX2 complex mediated proteasome targets of KAI2 and D14 respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles of each but very little sequence features are known about these repressors...
March 10, 2018: Journal of Experimental Botany
Marjorie da Silva, Fernando Barbosa Noll, Adriana C Morales-Corrêa E Castro
Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P...
2018: PloS One
A Jacobs, C Doran, D S Murray, J Duffill Telsnig, K L Laskowski, N A R Jones, S K Auer, K Praebel
Many fish species face increasing challenges associated with climate change and overfishing. At the same time, aquaculture is becoming vital for food security. Gaining a deeper understanding of the basic biology of fish is therefore more important than ever. Here we synthesize and summarize key questions, opportunities and challenges in fish biology highlighted during a round-table discussion at the 50th Anniversary Symposium of The Fisheries Society of the British Isles, held at the University of Exeter, U...
March 2018: Journal of Fish Biology
Ulrike H Taron, Moritz Lell, Axel Barlow, Johanna L A Paijmans
High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species...
March 13, 2018: Genes
Andrew J Page, Alexander Wailan, Yan Shao, Kim Judge, Gordon Dougan, Elizabeth J Klemm, Nicholas R Thomson, Jacqueline A Keane
Increasingly rich metadata are now being linked to samples that have been whole-genome sequenced. However, much of this information is ignored. This is because linking this metadata to genes, or regions of the genome, usually relies on knowing the gene sequence(s) responsible for the particular trait being measured and looking for its presence or absence in that genome. Examples of this would be the spread of antimicrobial resistance genes carried on mobile genetic elements (MGEs). However, although it is possible to routinely identify the resistance gene, identifying the unknown MGE upon which it is carried can be much more difficult if the starting point is short-read whole-genome sequence data...
March 12, 2018: Microbial Genomics
Tanya M Llorens, David J Ayre, Robert J Whelan
Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no pre-fragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird-pollinated shrub Grevillea caleyi R...
March 13, 2018: Molecular Ecology
Aditi Jain, Saurabh Anand, Neer K Singh, Sandip Das
The impact of polyploidy on functional diversification of cis-regulatory elements is poorly understood. This is primarily on account of lack of well-defined structure of cis-elements and a universal regulatory code. To the best of our knowledge, this is the first report on characterization of sequence and functional diversification of paralogous and homeologous promoter elements associated with MIR164 from Brassica. The availability of whole genome sequence allowed us to identify and isolate a total of 42 homologous copies of MIR164 from diploid species-Brassica rapa (A-genome), Brassica nigra (B-genome), Brassica oleracea (C-genome), and allopolyploids-Brassica juncea (AB-genome), Brassica carinata (BC-genome) and Brassica napus (AC-genome)...
March 12, 2018: Functional & Integrative Genomics
Kelly Louise Bennett, Martha Kaddumukasa, Fortunate Shija, Rousseau Djouaka, Gerald Misinzo, Julius Lutwama, Yvonne Marie Linton, Catherine Walton
The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change...
March 2018: Ecology and Evolution
Paul G Becher, Arne Hagman, Vasiliki Verschut, Amrita Chakraborty, Elżbieta Rozpędowska, Sébastien Lebreton, Marie Bengtsson, Gerhard Flick, Peter Witzgall, Jure Piškur
Yeast volatiles attract insects, which apparently is of mutual benefit, for both yeasts and insects. However, it is unknown whether biosynthesis of metabolites that attract insects is a basic and general trait, or if it is specific for yeasts that live in close association with insects. Our goal was to study chemical insect attractants produced by yeasts that span more than 250 million years of evolutionary history and vastly differ in their metabolism and lifestyle. We bioassayed attraction of the vinegar fly Drosophila melanogaster to odors of phylogenetically and ecologically distinct yeasts grown under controlled conditions...
March 2018: Ecology and Evolution
Pascal Touzet, Sarah Villain, Laetitia Buret, Hélène Martin, Anne-Catherine Holl, Céline Poux, Joël Cuguen
Historical demographic processes and mating systems are believed to be major factors in the shaping of the intraspecies genetic diversity of plants. Among Caryophyllales, the Beta section of the genus Beta, within the Amaranthaceae/Chenopodiaceae alliance, is an interesting study model with species and subspecies ( Beta macrocarpa , Beta patula , Beta vulgaris maritima and B.v. adanensis) differing in geographical distribution and mating system. In addition, one of the species, B. macrocarpa , mainly diploid, varies in its level of ploidy with a tetraploid cytotype described in the Canary Islands and in Portugal...
March 2018: Ecology and Evolution
Monika Janišová, Katarína Skokanová, Tomáš Hlásny
Tephroseris longifolia agg. is a complex group of outcrossing perennials distributed throughout Central Europe. Recent morphological study revealed six morphotypes corresponding to five previously distinguished subspecies, together with Alpine and Pannonian morphotypes of T. longifolia subsp. longifolia . The delimited morphotypes differ in relative DNA content, geographical range, and rarity. We compared ecological niches of the six morphotypes in order to assess the impact of ecological differentiation on the speciation processes within the T...
March 2018: Ecology and Evolution
Liang Li, Liang Lü, Steven A Nadler, David I Gibson, Lu-Ping Zhang, Hui-Xia Chen, Wen-Ting Zhao, Yan-Ning Guo
Ascaridoids are among the commonest groups of zooparasitic nematodes (roundworms) and occur in the alimentary canal of all major vertebrate groups, including humans. They have an extremely high diversity and are of major socio-economic importance. However, their evolutionary history remains poorly known. Here we performed a comprehensive phylogenetic analysis of the Ascaridoidea. Our results divided the Ascaridoidea into six monophyletic major clades, i.e. the Heterocheilidae, Acanthocheilidae, Anisakidae, Ascarididae, Toxocaridae and Raphidascarididae, among which the Heterocheilidae, rather than the Acanthocheilidae, represents the sister clade to the remaining ascaridoids...
March 8, 2018: Systematic Biology
Alberto A Esteves-Ferreira, Masami Inaba, Antoine Fort, Wagner L Araújo, Ronan Sulpice
Cyanobacteria are one of the earliest branching groups of organisms on the planet, and during their evolutionary history were submitted to varying selective pressures. Nowadays, cyanobacteria can grow in a variety of conditions, using a large number of nitrogen sources. The control of the nitrogen metabolism in cyanobacteria depends on a fine-tuning regulatory network involving 2-oxoglutarate (2-OG), PII, PipX, and NtcA. This network answers to the cellular 2-OG levels, which reflects the cellular carbon/nitrogen balance, and as an output regulates gene expression, translation, protein activities and thus metabolic pathways...
March 12, 2018: Critical Reviews in Microbiology
Günther Raspotnig, Miriam Schaider, Petra Föttinger, Axel Schönhofer
By the possession of unique exocrine scent glands, Opiliones (harvestmen) arise as a perfect model for studies on the evolutionary history of secretion chemistry. Among gland compounds of harvestmen, it is the quinones that represent recurring elements across the secretions of all suborders. Reliable data on quinone-distribution, however, is only known for Laniatores (benzoquinones) and Cyphophthalmi (naphthoquinones). We here unraveled the quinone-distribution across scent gland secretions of the third large harvestman suborder, the Palpatores (= Eu- and Dyspnoi): Naphthoquinones were found in phalangiid Eupnoi across all subfamilies as well as in nemastomatid (and at least one ischyropsalid) Dyspnoi...
November 17, 2017: Frontiers in Ecology and Evolution
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