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https://www.readbyqxmd.com/read/28642787/mutational-signatures-are-critical-for-proper-estimation-of-purifying-selection-pressures-in-cancer-somatic-mutation-data-when-using-the-dn-ds-metric
#1
Jimmy Van den Eynden, Erik Larsson
Large cancer genome sequencing initiatives have led to the identification of cancer driver genes based on signals of positive selection in somatic mutation data. Additionally, the identification of purifying (negative) selection has the potential to identify essential genes that may be of therapeutic interest. The most widely used way of quantifying selection pressures in protein-coding genes is the dN/dS metric, which compares non-synonymous to synonymous substitution rates. In this study, we examine whether and how this metric is influenced by the mutational processes that have been active during tumor evolution...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28630112/rapid-evolution-of-ovarian-biased-genes-in-the-yellow-fever-mosquito-aedes-aegypti
#2
Carrie A Whittle, Cassandra G Extavour
Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2,927, 2,013 and 4,449 coding-sequences (CDS) with ovary-biased, testis-biased and unbiased expression respectively in the yellow-fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28585043/candidate-genes-for-migration-do-not-distinguish-migratory-and-non-migratory-birds
#3
Juan S Lugo Ramos, Kira E Delmore, Miriam Liedvogel
Migratory traits in birds have been shown to have a strong heritable component and several candidate genes have been suggested to control these migratory traits. To investigate if the genetic makeup of one or a set of these candidate genes can be used to identify a general pattern between migratory and non-migratory birds, we extracted genomic sequence data for 25 hypothesised candidate genes for migration from 70 available genomes across all orders of Aves and characterised sequence divergence between migratory and non-migratory phenotypes...
June 5, 2017: Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology
https://www.readbyqxmd.com/read/28584717/calculating-site-specific-evolutionary-rates-at-the-amino-acid-or-codon-level-yields-similar-rate-estimates
#4
Dariya K Sydykova, Claus O Wilke
Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN∕dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it assigns a relative conservation score to each site in an alignment. How site-wise dN∕dS values relate to Rate4Site scores is not known. Here we elucidate the relationship between these two rate measurements. We simulate sequences with known dN∕dS, using either dN∕dS models or mutation-selection models for simulation...
2017: PeerJ
https://www.readbyqxmd.com/read/28578709/genetic-diversity-of-plasmodium-vivax-revealed-by-the-merozoite-surface-protein-1-icb5-6-fragment
#5
Wei Ruan, Ling-Ling Zhang, Yan Feng, Xuan Zhang, Hua-Liang Chen, Qiao-Yi Lu, Li-Nong Yao, Wei Hu
BACKGROUND: Plasmodium vivax remains a potential cause of morbidity and mortality for people living in its endemic areas. Understanding the genetic diversity of P. vivax from different regions is valuable for studying population dynamics and tracing the origins of parasites. The PvMSP-1 gene is highly polymorphic and has been used as a marker in many P. vivax population studies. The aim of this study was to investigate the genetic diversity of the PvMSP-1 gene icb5-6 fragment and to provide more genetic polymorphism data for further studies on P...
June 5, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/28578201/correlated-evolutionary-rates-across-genomic-compartments-in-annonaceae
#6
Paul H Hoekstra, Jan J Wieringa, Erik Smets, Rita D Brandão, Jenifer de Carvalho Lopes, Roy H J Erkens, Lars W Chatrou
The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models...
May 31, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28533181/comparative-genome-analysis-of-lactobacillus-plantarum-gb-lp3-provides-candidates-of-survival-related-genetic-factors
#7
Soomin Jeon, Jaehoon Jung, Kwondo Kim, DongAhn Yoo, Chanho Lee, Jungsun Kang, Kyungjin Cho, Dae-Kyung Kang, Woori Kwak, Sook Hee Yoon, Heebal Kim, Seoae Cho
Lactobacillus plantarum is found in various environmental niches such as in the gastrointestinal tract of an animal host or a fermented food. This species isolated from a certain environment is known to possess a variety of properties according to inhabited environment's adaptation. However, a causal relationship of a genetic factor and phenotype affected by a specific environment has not been systematically comprehended. L. plantarum GB-LP3 strain was isolated from Korean traditional fermented vegetable and the whole genome of GB-LP3 was sequenced...
May 19, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28529468/contrasting-patterns-of-nucleotide-polymorphism-suggest-different-selective-regimes-within-different-parts-of-the-pgic1-gene-in-festuca-ovina-l
#8
Yuan Li, Bengt Hansson, Lena Ghatnekar, Honor C Prentice
BACKGROUND: Phosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes. An earlier study of the PgiC1 gene, which encodes cytosolic PGI in the grass Festuca ovina L., revealed a marked difference in the levels of nucleotide polymorphism between the 5' and 3' portions of the gene. METHODS: In the present study, we characterized the sequence polymorphism in F. ovina PgiC1 in more detail and examined possible explanations for the non-uniform pattern of nucleotide polymorphism across the gene...
2017: Hereditas
https://www.readbyqxmd.com/read/28484686/impact-of-pe_pgrs33-gene-polymorphisms-on-mycobacterium-tuberculosis-infection-and-pathogenesis
#9
Serena Camassa, Ivana Palucci, Raffaella Iantomasi, Tiziana Cubeddu, Mariachiara Minerva, Flavio De Maio, Samuel Jouny, Elisa Petruccioli, Delia Goletti, Francesco Ria, Michela Sali, Maurizio Sanguinetti, Riccardo Manganelli, Stefano Rocca, Priscille Brodin, Giovanni Delogu
PE_PGRS33 is a surface-exposed protein of Mycobacterium tuberculosis (Mtb) which exerts its role in macrophages entry and immunomodulation. In this study, we aimed to investigate the polymorphisms in the pe_pgrs33 gene of Mtb clinical isolates and evaluate their impact on protein functions. We sequenced pe_pgrs33 in a collection of 135 clinical strains, genotyped by 15-loci MIRU-VNTR and spoligotyping and belonging to the Mtb complex (MTBC). Overall, an association between pe_pgrs33 alleles and MTBC genotypes was observed and a dN/dS ratio of 0...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28466060/population-genetic-analysis-of-potato-virus-x-based-on-the-cp-gene-sequence
#10
Mohammad Hajizadeh, Nemat Sokhandan-Bashir
To investigate the genetic variation and molecular evolution of potato virus X (PVX), 87 coat protein (CP) gene sequences were retrieved from GenBank and analyzed. Of the PVX isolates studied, one recombinant isolate (X3) was detected from South America population of the virus. The other isolates belonged to two lineages, Eurasia and America, with the significant FST value (0.60). Non-synonymous nucleotide diversity to synonymous nucleotide diversity (ω = dN/dS) was less than 1 indicating that the CP gene has been under negative selection or neutral evolution...
March 2017: Virusdisease
https://www.readbyqxmd.com/read/28454644/genetic-diversity-of-immune-related-antigens-in-region-of-difference-2-of-mycobacterium-tuberculosis-strains
#11
Yi Jiang, Haican Liu, Xuezhi Wang, Shiqi Xiao, Machao Li, Guilian Li, Lili Zhao, Xiuqin Zhao, Xiangfeng Dou, Kanglin Wan
Region of Difference 2 (RD2) was lost during the ongoing propagation of BCG between 1927 and 1931, a time that coincides with reports of the ongoing attenuation of the vaccine. Some data demonstrate that RD2 plays a role in mycobacterial virulence, and that its deletion from Mycobacterium tuberculosis leads to a decrease in bacterial growth in both a macrophage and a murine model. Human T-cell epitopes of M. tuberculosis are evolutionarily hyperconserved and thus it was deduced that M. tuberculosis lacks antigenic variation and immune evasion...
May 2017: Tuberculosis
https://www.readbyqxmd.com/read/28424354/less-effective-selection-leads-to-larger-genomes
#12
Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando, Christophe Jean Douady
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical data sets. Here, we tested this hypothesis using 22 de novo transcriptomes and low-coverage genomes of asellid isopods, which represent 11 independent habitat shifts from surface water to resource-poor groundwater...
June 2017: Genome Research
https://www.readbyqxmd.com/read/28423875/adaptive-selection-at-agouti-gene-inferred-breed-specific-selection-signature-within-the-indigenous-goat-populations
#13
Hafiz Ishfaq Ahmad, Guiqiong Liu, Xunping Jiang, Chenhui Liu, Xu Fangzheng, Yuqing Chong, Nabeel Ijaz, Huang Huarong
Objective: The aim of this study was to calculate selection signatures at possible loci leading to population differentiation, as well as pattern of selection of agouti gene within the local goat breeds and its correlation among other animal species to reveal molecular evolution. Methods: The high Fst outlier method corresponding to Fst distribution was used to identify the loci subject to positive selection. According to the empirical distribution of Fst estimates, we selected the SNPs having high Fst outlier corresponded to the upper 1% of the distribution as the loci under selection...
April 19, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28397003/plastome-wide-nucleotide-substitution-rates-reveal-accelerated-rates-in-papilionoideae-and-correlations-with-genome-features-across-legume-subfamilies
#14
Erika N Schwarz, Tracey A Ruhlman, Mao-Lun Weng, Mohammad A Khiyami, Jamal S M Sabir, Nahid H Hajarah, Njud S Alharbi, Samar O Rabah, Robert K Jansen
This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids...
April 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28387863/neutral-genetic-processes-influence-mhc-evolution-in-threatened-gopher-tortoises-gopherus-polyphemus
#15
Jean P Elbers, Rachel W Clostio, Sabrina S Taylor
Levels of adaptive genetic variation influence how species deal with environmental and ecological change, but these levels are frequently inferred using neutral genetic markers. Major histocompatibility complex (MHC) genes play a key role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation. Parts of the peptide binding region, sites where MHC molecules directly interact with pathogen and self-proteins, were sequenced from a MHC class I (95/441 tortoises) and class II (245/441 tortoises) gene in threatened and non-threatened populations of gopher tortoises (Gopherus polyphemus), and adaptive genetic variation at MHC genes was compared to neutral genetic variation derived from 10 microsatellite loci (441 tortoises)...
April 6, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28386078/evolution-of-full-length-genomes-of-hbv-quasispecies-in-sera-of-patients-with-a-coexistence-of-hbsag-and-anti-hbs-antibodies
#16
Tai-Cheng Zhou, Xiao Li, Long Li, Xiao-Fei Li, Liang Zhang, Jia Wei
Although the evolutionary changes of viral quasispecies are correlated to the pathological status of a disease, little is known in the coexistence of hepatitis B surface antigen (HBsAg) and antibodies to these antigens (anti-HBs). To examine evolutionary changes in hepatitis B virus (HBV) and their relationship to the coexistence of HBsAg and anti-HBs antibodies, HBV genomes in patients with a coexistence of HBsAg and anti-HBs antibodies (experimental group) and HBsAg positive without anti-HBs (control group) were assessed...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28384231/the-mitochondrial-genome-of-pin-tailed-snipe-gallinago-stenura-and-its-implications-for-the-phylogeny-of-charadriiformes
#17
Chaochao Hu, Chenling Zhang, Lei Sun, Yi Zhang, Wenli Xie, Baowei Zhang, Qing Chang
The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1...
2017: PloS One
https://www.readbyqxmd.com/read/28379613/signals-of-selection-in-conditionally-expressed-genes-in-the-diversification-of-three-horned-beetle-species
#18
Melissa H Pespeni, Jason T Ladner, Armin P Moczek
Species radiations may be facilitated by phenotypic differentiation already present within populations, such as those arising through sex-specific development or developmental processes biased toward particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the genus: horn location, polarity of sexual dimorphism, and degree of nutritional sensitivity...
April 5, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28363794/adaptive-evolution-of-insect-selective-excitatory-%C3%AE-type-sodium-channel-neurotoxins-from-scorpion-venom
#19
Wenlan Wu, Zhongjie Li, Yibao Ma
Insect selective excitatory β-type sodium channel neurotoxins from scorpion venom (β-NaScTxs) are composed of about 70-76 amino acid residues and share a common scaffold stabilized by four unique disulfide bonds. The phylogenetic analysis of these toxins was hindered by limited sequence data. In our recent study, two new insect selective excitatory β-NaScTxs, LmIT and ImIT, were isolated from Lychas mucronatus and Isometrus maculatus, respectively. With the sequences previously reported, we examined the adaptive molecular evolution of insect selective excitatory β-NaScTxs by estimating the nonsynonymous-to-synonymous rate ratio (ω=dN/dS)...
March 29, 2017: Peptides
https://www.readbyqxmd.com/read/28360388/transiently-expressed-pattern-during-myogenesis-and-candidate-mirnas-of-tmem8c-in-goose
#20
Ke He, Ting Ren, Songhui Zhu, Shiri Liang, Ayong Zhao
Transmembrane protein 8C (Tmem8C) is a muscle-specific membrane protein that controls myoblast fusion, which is essential for the formation of multinucleated muscle fibres. As most of the birds can fly, they have enormous requirement for the muscle, but there are only a few studies of Tmem8C in birds. In this study, we obtained the coding sequence (CDS) of Tmem8C in goose, predicted miRNAs that can act on the 3'UTR, analysed expression profiles of this gene in breast and leg muscles (BM and LM) during the embryonic period and neonatal stages, and identified miRNAs that might affect the targeted gene...
March 2017: Journal of Genetics
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