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https://www.readbyqxmd.com/read/29281964/the-molecular-evolutionary-dynamics-of-oxidative-phosphorylation-oxphos-genes-in-hymenoptera
#1
Yiyuan Li, Rui Zhang, Shanlin Liu, Alexander Donath, Ralph S Peters, Jessica Ware, Bernhard Misof, Oliver Niehuis, Michael E Pfrender, Xin Zhou
BACKGROUND: The primary energy-producing pathway in eukaryotic cells, the oxidative phosphorylation (OXPHOS) system, comprises proteins encoded by both mitochondrial and nuclear genes. To maintain the function of the OXPHOS system, the pattern of substitutions in mitochondrial and nuclear genes may not be completely independent. It has been suggested that slightly deleterious substitutions in mitochondrial genes are compensated by substitutions in the interacting nuclear genes due to positive selection...
December 28, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29278771/genome-wide-identification-and-analysis-of-the-evolution-and-expression-patterns-of-the-cellulose-synthase-gene-superfamily-in-gossypium-species
#2
Xianyan Zou, Zhang Zhen, Qun Ge, Senmiao Fan, Aiying Liu, Wankui Gong, Junwen Li, Juwu Gong, Yuzhen Shi, Yanling Wang, Ruixian Liu, Li Duan, Kang Lei, Qi Zhang, Xiao Jiang, Shuya Zhang, Tingting Jia, Lipeng Zhang, Haihong Shang, Youlu Yuan
The cellulose synthase gene superfamily, which includes the cellulose synthase (Ces) and cellulose synthase-like (Csl) families, is involved in the synthesis of cellulose and hemicellulose. This superfamily is critical for cotton fiber development in Gossypium species. Applying a series of bioinformatic methods, we identified 228 Ces/Csl genes from four Gossypium species (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii). These genes were then grouped into 11 subfamilies based on phylogenetic relationships...
December 23, 2017: Gene
https://www.readbyqxmd.com/read/29277542/evolution-of-the-mc5r-gene-in-placental-mammals-with-evidence-for-its-inactivation-in-multiple-lineages-that-lack-sebaceous-glands
#3
Mark S Springer, John Gatesy
MC5R is one of five melanocortin receptor genes found in placental mammals. MC5R plays an important role in energy homeostasis and is also expressed in the terminal differentiation of sebaceous glands. Among placental mammals there are multiple lineages that either lack or have degenerative sebaceous glands including Cetacea (whales, dolphins, and porpoises), Hippopotamidae (hippopotamuses), Sirenia (manatees and dugongs), Proboscidea (elephants), Rhinocerotidae (rhinos), and Heterocephalus glaber (naked mole rat)...
December 19, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29274514/distribution-of-single-nucleotide-polymorphisms-and-protein-domain-architecture-of-toll-like-receptor-2-in-pahari-cattle-indian-non-descript-indigenous-breed
#4
Verma Subhash, Sodhi Monika, Salwan Richa, Shekhar Chander, Singh Geetanjali, Sharma Mandeep
Distribution of polymorphism in TLR2 gene was studied in Pahari (Indian non-descript indigenous breed) cattle of Himachal Pradesh. The complete sequence of TLR2 gene consisted of 136bp 5'-UTR, 2355bp CDS and 1316bp 3'UTR. The phylogenetic analysis revealed clustering of Indian Zebu with Bos taurus as the nearest neighbour. The nucleotide sequences of TLR2 revealed the occurrence of 19 SNPs including 47% non-synonymous and 53% synonymous SNPs within TLR domain among all bovines. The dS/dN ratio (ω)<1 at polymorphic sites revealed purifying selection and thus, indicating the presence of highly conserved domains...
December 15, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/29273445/selective-pressure-on-the-protein-coding-genes-of-the-pufferfish-is-correlated-with-phenotypic-traits
#5
Hyeonju Ahn, Chul Lee, Bo-Hye Nam, Eun Bae Kim, Kelsey Caetano-Anolles, Heebal Kim
The pufferfish accumulates neurotoxic tetrodotoxin in its body and inflates by filling its stomach with water. These traits are unique to this species, and may be a result of adaptation post-divergence of Tetraodontidae. However, evolution of the protein-coding genes in the pufferfish has not yet been well elucidated. Detection of positive selection on these genes can help us understand the mechanisms associated with functional evolution. We downloaded well-annotated gene information of two pufferfish species, Takifugu rubripes and Tetraodon nigroviridis, from the public ENSEMBL database...
December 19, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29238521/limited-polymorphism-of-the-functional-mhc-class-ii-b-gene-in-the-black-spotted-frog-pelophylax-nigromaculatus-identified-by-locus-specific-genotyping
#6
Hong-Yi Liu, Fei Xue, Jie Gong, Qiu-Hong Wan, Sheng-Guo Fang
Amphibians can be more vulnerable to environmental changes and diseases than other species because of their complex life cycle and physiological requirements. Therefore, understanding the adaptation of amphibians to environmental changes is crucial for their conservation. Major histocompatibility complex (MHC) presents an excellent tool for the investigation of adaptive variations and the assessment of adaptive potential because it can be under strong diversifying selection. Here, we isolated the MHC class II B (MHCIIB) gene from cDNA sequences of the black-spotted frog (Pelophylax nigromaculatus), a widespread amphibian species in China, and designed locus-specific primers to characterize adaptive variability of this amphibian...
December 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29228598/analysis-of-molecular-evolution-of-nucleocapsid-protein-in-newcastle-disease-virus
#7
Wentao Fan, Yuliang Xu, Pu Zhang, Peng Chen, Yiran Zhu, Ziqiang Cheng, Xiaona Zhao, Yongxia Liu, Jianzhu Liu
The present study investigated the molecular evolution of nucleocapsid protein (NP) in different Newcastle disease virus (NDV) genotypes. The evolutionary timescale and rate were estimated using the Bayesian Markov chain Monte Carlo (MCMC) method. The p-distance, Bayesian skyline plot (BSP), and positively selected sites were also analyzed. The MCMC tree indicated that NDV diverged about 250 years ago with a rapid evolution rate (1.059 × 10-2 substitutions/site/year) and that different NDV genotypes formed three lineages...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220511/unbiased-estimate-of-synonymous-and-non-synonymous-substitution-rates-with-non-stationary-base-composition
#8
Laurent Guéeguen, Laurent Duret
The measurement of synonymous and non-synonymous substitution rates (dS and dN) is useful for assessing selection operating on protein sequences or for investigating mutational processes affecting genomes. In particular, the ratio dNdS is expected to be a good proxy for ω, the ratio of fixation robabilities of non-synonymous mutations relative to that of neutral mutations. Standard methods for estimating dN, dS or ω rely on the assumption that the base composition of sequences is at the equilibrium of the evolutionary process...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29220486/transcriptome-signatures-of-selection-drift-introgression-and-gene-duplication-in-the-evolution-of-an-extremophile-endemic-plant
#9
Angela K Hawkins, Elyssa R Garza, Valerie A Dietz, Oscar J Hernandez, W Daryl Hawkins, A Millie Burrell, Alan E Pepper
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g. N, P, K, Ca), as well as toxic levels of heavy metals (e.g. Ni, Cr, Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29207953/genomic-signature-of-highland-adaptation-in-fish-a-case-study-in-tibetan-schizothoracinae-species
#10
Chao Tong, Fei Tian, Kai Zhao
BACKGROUND: Genome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals. Tibetan Schizothoracinae species are ideal model systems to study speciation and adaptation of fish. The Schizothoracine fish, Gymnocypris przewalskii ganzihonensis had underwent the ecological niche shift from salt water to freshwater, and also experienced a recent split from Gymnocypris przewalskii przewalskii. In addition, G. p. ganzihonensis inhabited harsh aquatic environment including low temperature and hypoxia as well as other Schizothoracinae species, its genetic mechanism of highland adaptation have yet to be determined...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29207506/longitudinal-surveillance-of-porcine-rotavirus-b-strains-from-the-united-states-and-canada-and-in-silico-identification-of-antigenically-important-sites
#11
Frances K Shepherd, Michael P Murtaugh, Fangzhou Chen, Marie R Culhane, Douglas G Marthaler
Rotavirus B (RVB) is an important swine pathogen, but control and prevention strategies are limited without an available vaccine. To develop a subunit RVB vaccine with maximal effect, we characterized the amino acid sequence variability and predicted antigenicity of RVB viral protein 7 (VP7), a major neutralizing antibody target, from clinically infected pigs in the United States and Canada. We identified genotype-specific antigenic sites that may be antibody neutralization targets. While some antigenic sites had high amino acid functional group diversity, nine antigenic sites were completely conserved...
December 3, 2017: Pathogens
https://www.readbyqxmd.com/read/29203331/a-crucial-role-of-paralogous-%C3%AE-defensin-genes-in-the-chinese-alligator-innate-immune-system-revealed-by-the-first-determination-of-a-crocodilia-defensin-cluster
#12
Ke-Yi Tang, Xin Wang, Qiu-Hong Wan, Sheng-Guo Fang
The β-defensin, one of the antimicrobial peptides (AMPs), is a significant component of the innate immune with a broad range of antimicrobial activities. Differing from the widely-studied mammals and birds, limited information about β-defensins has been reported in reptiles, especially in crocodilians. As a same ancient species as dinosaurs and the most endangered species of 23 crocodilians, the survival of Chinese alligator (Alligator sinensis) means a powerful immune system and possible involvement of AMPs in its immune resistance...
December 1, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29191157/genome-wide-analysis-of-the-solanum-tuberosum-potato-trehalose-6-phosphate-synthase-tps-gene-family-evolution-and-differential-expression-during-development-and-stress
#13
Yingchun Xu, Yanjie Wang, Neil Mattson, Liu Yang, Qijiang Jin
BACKGROUND: Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molecular evolution, and expression patterns of this gene family are still lacking in Solanum tuberosum (potato). RESULTS: In this study, a comprehensive analysis of the TPS gene family was conducted in potato. A total of eight putative potato TPS genes (StTPSs) were identified by searching the latest potato genome sequence...
December 1, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29183841/prevalence-and-genetic-diversity-of-human-diarrhoeagenic-escherichia-coli-isolates-by-multilocus-sequence-typing
#14
Fei Yu, Xiao Chen, Shufa Zheng, Dongsheng Han, Yiyin Wang, Ruonan Wang, Baohong Wang, Yu Chen
BACKGROUND: The population structure of human diarrheagenic Escherichia coli (DEC) isolates derived from worldwide collections remains undefined. METHODS: A total of 1,196 clinical isolates obtained from multilocus sequence typing (MLST) database. Genetic diversity analysis, MLST analysis and phylogenetic analysis combined with different pathotypes were performed through a variety of calculation softwares. RESULTS: All isolates were categorized as one of 579 different sequence types (STs)...
November 25, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/29172233/stronger-selective-constraint-on-downstream-genes-in-the-oxidative-phosphorylation-pathway-of-cetaceans
#15
Ran Tian, Shixia Xu, Simin Chai, Daiqing Yin, Harold Zakon, Guang Yang
The oxidative phosphorylation (OXPHOS) pathway is an efficient way to produce energy via adenosine triphosphate (ATP), which is critical for sustaining an energy supply for cetaceans in a hypoxic environment. Several studies have shown that natural selection may shape the evolution of the genes involved in OXPHOS. However, how network architecture drives OXPHOS protein sequence evolution remains poorly explored. Here, we investigated the evolutionary patterns of genes in the OXPHOS pathway across six cetacean genomes within the framework of a functional network...
November 24, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29167739/measuring-evolutionary-rates-of-proteins-in-a-structural-context
#16
Dariya K Sydykova, Benjamin R Jack, Stephanie J Spielman, Claus O Wilke
We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations, one based on relative amino-acid rates and the other based on site-specific codon rates measured as dN/dS. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses...
2017: F1000Research
https://www.readbyqxmd.com/read/29162445/the-neuromorphological-caudate-putaminal-clustering-of-neostriate-interneurons-kohonen-self-organizing-maps-and-supervised-artificial-neural-networks-with-multivariate-analysis
#17
Ivan Grbatinić, Nebojša Milošević, Bojana Krstonošić
AIMS: The objective of this study is to investigate the possibility of the neuromorphotopological clustering of neostriate interneurons (NSIN) and their consequent classification into caudate (CIN) and putaminal neuron type (PIN), according to the nuclear localization of the neurons. It tends to discover whether these two topological neuron types are morphologically different. MATERIAL AND METHODS: The binary images of adult human NSIN are used for the purposes of the analysis...
November 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29128519/genetic-structure-of-two-erythrocyte-binding-antigens-of-plasmodium-falciparum-reveals-a-contrasting-pattern-of-selection
#18
Pramita Chowdhury, Srikanta Sen, Sumana Datta Kanjilal, Sanghamitra Sengupta
Erythrocyte binding antigens 175 (EBA-175) and 140 (EBA-140) play key roles in erythrocyte invasion by binding to glycophorin A (GPA) and C (GPC) respectively in human malaria. Since antigenic variation in malaria endemic region is a major barrier to development of effective vaccine, we explore the nature and pattern of sequence diversity of these two vaccine candidates in Kolkata, India. Population genetic parameters based on parasite sequences representing region II of Pfeba-175 and Pfeba-140 genes were estimated using DnaSP V...
November 8, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29126243/faster-evolving-primate-genes-are-more-likely-to-duplicate
#19
Áine N O'Toole, Laurence D Hurst, Aoife McLysaght
An attractive and long-standing hypothesis regarding the evolution of genes after duplication posits that the duplication event creates new evolutionary possibilities by releasing a copy of the gene from constraint. Apparent support was found in numerous analyses, particularly the observation of higher rates of evolution in duplicated as compared to singleton genes. Could it, instead, be that more duplicable genes (owing to mutation, fixation or retention biases) are intrinsically faster evolving? To uncouple the measurement of rates of evolution from the determination of duplicate or singleton status, we measure the rates of evolution in singleton genes in outgroup primate lineages but classify these genes as to whether they have duplicated or not in a crown group of great apes...
November 7, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29109707/genomic-comparisons-reveal-microevolutionary-differences-in-mycobacterium-abscessus-subspecies
#20
Joon L Tan, Kee P Ng, Chia S Ong, Yun F Ngeow
Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear...
2017: Frontiers in Microbiology
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