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https://www.readbyqxmd.com/read/28053111/evolutionary-interplay-between-structure-energy-and-epistasis-in-the-coat-protein-of-the-%C3%AF-x174-phage-family
#1
Rodrigo A F Redondo, Harold P de Vladar, Tomasz Włodarski, Jonathan P Bollback
Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28051058/purifying-selection-and-genetic-drift-shaped-pleistocene-evolution-of-the-mitochondrial-genome-in-an-endangered-australian-freshwater-fish
#2
A Pavlova, H M Gan, Y P Lee, C M Austin, D M Gilligan, M Lintermans, P Sunnucks
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB)...
January 4, 2017: Heredity
https://www.readbyqxmd.com/read/28049516/genetic-clustering-and-polymorphism-of-the-merozoite-surface-protein-3-of-plasmodium-knowlesi-clinical-isolates-from-peninsular-malaysia
#3
Jeremy Ryan De Silva, Yee Ling Lau, Mun Yik Fong
BACKGROUND: The simian malaria parasite Plasmodium knowlesi has been reported to cause significant numbers of human infection in South East Asia. Its merozoite surface protein-3 (MSP3) is a protein that belongs to a multi-gene family of proteins first found in Plasmodium falciparum. Several studies have evaluated the potential of P. falciparum MSP3 as a potential vaccine candidate. However, to date no detailed studies have been carried out on P. knowlesi MSP3 gene (pkmsp3). The present study investigates the genetic diversity, and haplotypes groups of pkmsp3 in P...
January 3, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28024871/balancing-selection-on-allorecognition-genes-in-the-colonial-ascidian-botryllus-schlosseri
#4
Marie L Nydam, Emily E Stephenson, Claire E Waldman, Anthony W De Tomaso
Allorecognition is the capability of an organism to recognize its own or related tissues. The colonial ascidian Botryllus schlosseri, which comprises five genetically distinct and divergent species (Clades A-E), contains two adjacent genes that control allorecognition: fuhc(sec) and fuhc(tm). These genes have been characterized extensively in Clade A and are highly polymorphic. Using alleles from 10 populations across the range of Clade A, we investigated the type and strength of selection maintaining this variation...
December 24, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27951521/virulence-in-newcastle-disease-virus-a-genotyping-and-molecular-evolution-spectrum-perspective
#5
Wentao Fan, Yang Wang, Shenghua Wang, Ziqiang Cheng, Huijun Guo, Xiaona Zhao, Jianzhu Liu
In our research, the molecular evolutions of NDV F and HN genes were analyzed. The phylogenetic analyses of NDV sequences indicated that NDV could be divided into two genotypes: Class I (lentogenic strains) and Class II (velogenic or mesogenic strains). Each genotype possesses high gene homology. Furthermore, the selected pressure analysis showed that the dN/dS of velogenic, mesogenic NDV strains F gene was significantly high and the ω(dN/dS) is 1.1725>1. These results imply that mutations in velogenic, mesogenic NDV F gene are favored by positive natural selection and it has acted to diversify NDV virulence at the nucleotide and amino acid level...
December 7, 2016: Research in Veterinary Science
https://www.readbyqxmd.com/read/27909914/association-of-snp-variants-of-mhc-class-ii-drb-gene-with-thermo-physiological-traits-in-tropical-goats
#6
Abdulmojeed Yakubu, Adebowale E Salako, Marcos De Donato, Sunday O Peters, Michael I Takeet, Mathew Wheto, Moses Okpeku, Ikhide G Imumorin
Host defense in vertebrates depend on many secreted regulatory proteins such as major histocompatibility complex (MHC) class II which provide important regulatory and effector functions of T cells. Gene polymorphism in the second exon of Capra-DRB gene in three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS), and Sahel (SH)] was analyzed by restriction fragment length polymorphisms (RFLP). Four restriction enzymes, BsaHI, AluI, HaeIII, and SacII, were utilized. The association between the polymorphic sites and some heat tolerance traits were also investigated in a total of 70 WAD, 90 RS, and 50 SH goats...
December 1, 2016: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/27881098/genomic-determination-of-minimum-multi-locus-sequence-typing-schemas-to-represent-the-genomic-phylogeny-of-mycoplasma-hominis
#7
Aleksey Jironkin, Rebecca J Brown, Anthony Underwood, Victoria J Chalker, Owen B Spiller
BACKGROUND: Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. hominis, which would aid in understanding pathogen epidemiology and transmission. Due to availability and costs of whole genome sequencing and the challenges in obtaining adequate M. hominis DNA, the use of whole genome sequence analysis to provide clinical guidance is unpractical for this bacterial species as well as other fastidious organisms...
November 23, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27872816/evidence-of-triple-mutant-pfdhps-isgnga-haplotype-in-plasmodium-falciparum-isolates-from-north-east-india-an-analysis-of-sulfadoxine-resistant-haplotype-selection
#8
Manuj K Das, Sumi Chetry, Mohan C Kalita, Prafulla Dutta
BACKGROUND: North-east region of India has consistent role in the spread of multi drug resistant Plasmodium (P.) falciparum to other parts of Southeast Asia. After rapid clinical treatment failure of Artemisinin based combination therapy-Sulphadoxine/Pyrimethamine (ACT-SP) chemoprophylaxis, Artemether-Lumefantrine (ACT-AL) combination therapy was introduced in the year 2012 in this region for the treatment of uncomplicated P. falciparum malaria. In a DNA sequencing based polymorphism analysis, seven codons of P...
December 2016: Genomics Data
https://www.readbyqxmd.com/read/27867038/comparative-mitogenomic-analysis-of-three-species-of-periwinkles-littorina-fabalis-l-obtusata-and-l-saxatilis
#9
João P Marques, Graciela Sotelo, Tomas Larsson, Kerstin Johannesson, Marina Panova, Rui Faria
The flat periwinkles, Littorina fabalis and L.obtusata, offer an interesting system for local adaptation and ecological speciation studies. In order to provide genomic resources for these species, we sequenced their mitogenomes together with that of the rough periwinkle L.saxatilis by means of next-generation sequencing technologies. The three mitogenomes present the typical repertoire of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Although the latter could not be fully recovered in flat periwinkles using short-reads due to a highly repetitive fragment, in L...
November 17, 2016: Marine Genomics
https://www.readbyqxmd.com/read/27857066/positive-and-strongly-relaxed-purifying-selection-drive-the-evolution-of-repeats-in-proteins
#10
Erez Persi, Yuri I Wolf, Eugene V Koonin
Protein repeats are considered hotspots of protein evolution, associated with acquisition of new functions and novel phenotypic traits, including disease. Paradoxically, however, repeats are often strongly conserved through long spans of evolution. To resolve this conundrum, it is necessary to directly compare paralogous (horizontal) evolution of repeats within proteins with their orthologous (vertical) evolution through speciation. Here we develop a rigorous methodology to identify highly periodic repeats with significant sequence similarity, for which evolutionary rates and selection (dN/dS) can be estimated, and systematically characterize their evolution...
November 18, 2016: Nature Communications
https://www.readbyqxmd.com/read/27846808/pinpointing-genes-underlying-annual-perennial-transitions-with-comparative-genomics
#11
Andrew J Heidel, Christiane Kiefer, George Coupland, Laura E Rose
BACKGROUND: Transitions between perennial and an annual life history occur often in plant lineages, but the genes that control whether a plant is an annual or perennial are largely unknown. To identify genes that confer differences between annuals and perennials we compared the gene content of four pairs of sister lineages (Arabidopsis thaliana/Arabidopsis lyrata, Arabis montbretiana/Arabis alpina, Arabis verna/Aubrieta parviflora and Draba nemorosa/Draba hispanica) in the Brassicaceae in which each pair contains one annual and one perennial, plus one extra annual species (Capsella rubella)...
November 15, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27822527/differential-functional-constraints-cause-strain-level-endemism-in-polynucleobacter-populations
#12
Naseer Sangwan, Iratxe Zarraonaindia, Jarrad T Hampton-Marcell, Herbert Ssegane, Tifani W Eshoo, Geeta Rijal, M Cristina Negri, Jack A Gilbert
The adaptation of bacterial lineages to local environmental conditions creates the potential for broader genotypic diversity within a species, which can enable a species to dominate across ecological gradients because of niche flexibility. The genus Polynucleobacter maintains both free-living and symbiotic ecotypes and maintains an apparently ubiquitous distribution in freshwater ecosystems. Subspecies-level resolution supplemented with metagenome-derived genotype analysis revealed that differential functional constraints, not geographic distance, produce and maintain strain-level genetic conservation in Polynucleobacter populations across three geographically proximal riverine environments...
May 2016: MSystems
https://www.readbyqxmd.com/read/27812410/evolution-of-genes-involved-in-feeding-preference-and-metabolic-processes-in-calliphoridae-diptera-calyptratae
#13
Gisele Antoniazzi Cardoso, Marco Antonio Tonus Marinho, Raquel Dietsche Monfardini, Ana Maria Lima de Azeredo Espin, Tatiana Teixeira Torres
BACKGROUND: The genotype-phenotype interactions among traits governing feeding preference are of fundamental importance to behavioral genetics and evolutionary biology. The genetic basis of behavioral traits has been explored in different taxa using different approaches. However, the complex nature of the genetic mechanisms undergirding behavior is poorly understood. Here, we present an evolutionary study of candidate genes related to parasitism in Calliphoridae (Diptera: Calyptratae)...
2016: PeerJ
https://www.readbyqxmd.com/read/27806254/taste-receptors-and-gustatory-associated-g-proteins-in-channel-catfish-ictalurus-punctatus
#14
Sen Gao, Shikai Liu, Jun Yao, Tao Zhou, Ning Li, Qi Li, Rex Dunham, Zhanjiang Liu
Taste sensation plays a pivotal role in nutrient identification and acquisition. This is particularly true for channel catfish (Ictalurus punctatus) that live in turbid waters with limited visibility. This biological process is mainly mediated by taste receptors expressed in taste buds that are distributed in several organs and tissues, including the barbels and skin. In the present study, we identified a complete repertoire of taste receptor and gustatory associated G protein genes in the channel catfish genome...
October 23, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27773705/genomic-organization-and-evolution-of-olfactory-receptors-and-trace-amine-associated-receptors-in-channel-catfish-ictalurus-punctatus
#15
Sen Gao, Shikai Liu, Jun Yao, Ning Li, Zihao Yuan, Tao Zhou, Qi Li, Zhanjiang Liu
BACKGROUND: Channel catfish (Ictalurus punctatus) live in turbid waters with limited visibility to chase prey within a certain distance. This can be compensated through detecting specific water-soluble substances by the olfactory receptors (ORs) and trace amine associated receptors (TAARs) expressed on the olfactory epithelium. METHODS: We identified the OR and TAAR repertoires in channel catfish, and characterized the genomic organizations of these two gene families by data mining available genomic resources...
October 21, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27770608/non-canonical-expression-patterns-and-evolutionary-rates-of-sex-biased-genes-in-a-seasonal-fish
#16
Miguel P Machado, Isa Matos, Ana R Grosso, Manfred Schartl, Maria M Coelho
Sex determination is a highly variable process that utilizes many different mechanisms to initiate the cascade of differentiation processes. The molecular pathways controlling sexual development are less conserved than previously assumed, and appear to require active maintenance in some species; indeed, the developmental decision of gonad phenotype in gonochoristic species is not fixed at an early developmental stage. Much of the knowledge about sex determination mechanisms was derived from research on gonochoristic, non-seasonal breeders...
December 2016: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/27767073/the-2014-ebola-virus-outbreak-in-west-africa-highlights-no-evidence-of-rapid-evolution-or-adaptation-to-humans
#17
Xingguang Li, Junjie Zai, Haizhou Liu, Yi Feng, Fan Li, Jing Wei, Sen Zou, Zhiming Yuan, Yiming Shao
Following its immergence in December 2013, the recent Zaire Ebola virus (EBOV) outbreak in West Africa has spread and persisted for more than two years, making it the largest EBOV epidemic in both scale and geographical region to date. In this study, a total of 726 glycoprotein (GP) gene sequences of the EBOV full-length genome obtained from West Africa from the 2014 outbreak, combined with 30 from earlier outbreaks between 1976 and 2008 were used to investigate the genetic divergence, evolutionary history, population dynamics, and selection pressure of EBOV among distinct epidemic waves...
October 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27765638/assessment-of-nuclear-and-mitochondrial-genes-in-precise-identification-and-analysis-of-genetic-polymorphisms-for-the-evaluation-of-leishmania-parasites
#18
Reza Fotouhi-Ardakani, Shahriar Dabiri, Soheila Ajdari, Mohammad Hossein Alimohammadian, Elnaz AlaeeNovin, Neda Taleshi, Parviz Parvizi
The polymorphism and genetic diversity of Leishmania genus has status under discussion depending on many items such as nuclear and/or mitochondrial genes, molecular tools, Leishmania species, geographical origin, condition of micro-environment of Leishmania parasites and isolation of Leishmania from clinical samples, reservoir host and vectors. The genetic variation of Leishmania species (L. major, L. tropica, L. tarentolae, L. mexicana, L. infantum) were analyzed and compared using mitochondrial (COII and Cyt b) and nuclear (nagt, ITS-rDNA and HSP70) genes...
December 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27760179/genome-wide-analysis-classification-evolution-and-expression-analysis-of-the-cytochrome-p450-93-family-in-land-plants
#19
Hai Du, Feng Ran, Hong-Li Dong, Jing Wen, Jia-Na Li, Zhe Liang
Cytochrome P450 93 family (CYP93) belonging to the cytochrome P450 superfamily plays important roles in diverse plant processes. However, no previous studies have investigated the evolution and expression of the members of this family. In this study, we performed comprehensive genome-wide analysis to identify CYP93 genes in 60 green plants. In all, 214 CYP93 proteins were identified; they were specifically found in flowering plants and could be classified into ten subfamilies-CYP93A-K, with the last two being identified first...
2016: PloS One
https://www.readbyqxmd.com/read/27746792/genome-wide-identification-and-evolution-analysis-of-trehalose-6-phosphate-synthase-gene-family-in-nelumbo-nucifera
#20
Qijiang Jin, Xin Hu, Xin Li, Bei Wang, Yanjie Wang, Hongwei Jiang, Neil Mattson, Yingchun Xu
Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly available Nelumbo nucifera (lotus) genome sequence database was analyzed which led to identification of nine lotus TPS genes (NnTPS). It was found that at least two introns are included in the coding sequences of NnTPS genes. When the motif compositions were analyzed we found that NnTPS generally shared the similar motifs, implying that they have similar functions...
2016: Frontiers in Plant Science
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