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https://www.readbyqxmd.com/read/27909914/association-of-snp-variants-of-mhc-class-ii-drb-gene-with-thermo-physiological-traits-in-tropical-goats
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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 20, 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
#11
M P Machado, I Matos, A R Grosso, M Schartl, M 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...
October 22, 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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/27744561/evolutionary-dynamics-of-meiotic-recombination-hotspots-regulator-prdm9-in-bovids
#16
Sonika Ahlawat, Sachinandan De, Priyanka Sharma, Rekha Sharma, Reena Arora, R S Kataria, T K Datta, R K Singh
Hybrid sterility or reproductive isolation in mammals has been attributed to allelic incompatibilities in a DNA-binding protein PRDM9. Not only is PRDM9 exceptional in being the only known 'speciation gene' in vertebrates, but it is also considered to be the fastest evolving gene in the genome. The terminal zinc finger (ZF) domain of PRDM9 specifies genome-wide meiotic recombination hotspot locations in mammals. Intriguingly, PRDM9 ZF domain is highly variable between as well as within species, possibly activating different recombination hotspots...
October 15, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/27721649/genomics-study-of-mycobacterium-tuberculosis-strains-from-different-ethnic-populations-in-taiwan
#17
Horng-Yunn Dou, Yih-Yuan Chen, Ying-Tsong Chen, Jia-Ru Chang, Chien-Hsing Lin, Keh-Ming Wu, Ming-Shian Lin, Ih-Jen Su, Shih-Feng Tsai
To better understand the transmission and evolution of Mycobacterium tuberculosis (MTB) in Taiwan, six different MTB isolates (representatives of the Beijing ancient sublineage, Beijing modern sublineage, Haarlem, East-African Indian, T1, and Latin-American Mediterranean (LAM)) were characterized and their genomes were sequenced. Discriminating among large sequence polymorphisms (LSPs) that occur once versus those that occur repeatedly in a genomic region may help to elucidate the biological roles of LSPs and to identify the useful phylogenetic relationships...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27717247/comparative-transcriptomics-reveal-host-specific-nucleotide-variation-in-entomophthoralean-fungi
#18
Henrik H De Fine Licht, Annette B Jensen, Jørgen Eilenberg
Obligate parasites are under strong selection to increase exploitation of their host to survive while evading detection by host immune defences. This has often led to elaborate pathogen adaptations and extreme host specificity. Specialization on one host, however, often incurs a trade-off influencing the capacity to infect alternate hosts. Here, we investigate host adaptation in two morphologically indistinguishable and closely related obligate specialist insect-pathogenic fungi from the phylum Entomophthoromycota, Entomophthora muscae sensu stricto and E...
September 26, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27714793/genetic-drift-and-mutational-hazard-in-the-evolution-of-salamander-genomic-gigantism
#19
Erik Roger Mohlhenrich, Rachel Lockridge Mueller
Salamanders have the largest nuclear genomes among tetrapods and, excepting lungfishes, among vertebrates as a whole. Lynch and Conery (2003) have proposed the mutational-hazard hypothesis to explain variation in genome size and complexity. Under this hypothesis, noncoding DNA imposes a selective cost by increasing the target for degenerative mutations (i.e., the mutational hazard). Expansion of noncoding DNA, and thus genome size, is driven by increased levels of genetic drift and/or decreased mutation rates; the former determines the efficiency with which purifying selection can remove excess DNA, whereas the latter determines the level of mutational hazard...
October 7, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27686787/evolution-and-phylogenetic-application-of-the-mc1r-gene-in-the-cobitoidea-teleostei-cypriniformes
#20
Qiong-Ying Tang, Li-Xia Shi, Fei Liu, Dan Yu, Huan-Zhang Liu
Fish of the superfamily Cobitoidea sensu stricto (namely loaches) exhibit extremely high diversity of color patterns, but so far little is known about their evolutionary mechanism. Melanocortin 1 receptor gene (MC1R) plays an important role during the synthesis of melanin and formation of animal body color patterns. In this study, we amplified and sequenced the partial MC1R gene for 44 loach individuals representing 31 species of four families. Phylogenetic analyses yielded a topology congruent with previous studies using multiple nuclear loci, showing that each of the four families was monophyletic with sister relationships of Botiidae+ (Cobitidae+(Balitoridae+Nemacheilidae))...
September 18, 2016: Dong Wu Xue Yan Jiu, Zoological Research
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