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https://www.readbyqxmd.com/read/28431152/insights-into-the-existence-of-isomeric-plastomes-in-cupressoideae-cupressaceae
#1
Xiao-Jian Qu, Chung-Shien Wu, Shu-Miaw Chaw, Ting-Shuang Yi
The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few cypress species have been reported to contain isomeric plastomes, but whether the existence of isomeric plastomes is ubiquitous in the family remains to be investigated with a broader taxon sampling. In this study, we sequenced the complete plastomes of ten species in Cupressoideae, the largest cypress subfamily. Cupressoideae showed relatively accelerated rates of substitutions at both nonsynonymous and synonymous sites as compared with other subfamilies of Cupressaceae...
April 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28423875/adaptive-selection-at-agouti-gene-inferred-breed-specific-selection-signature-within-the-indigenous-goat-populations
#2
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/28420808/sequence-variations-in-estrogen-receptor-1-and-2-genes-and-their-association-with-egg-production-traits-in-chinese-dagu-chickens
#3
Xiaotian Niu, Thobela Louis Tyasi, Ning Qin, Dehui Liu, Hongyan Zhu, Xiaoxia Chen, Fengwei Zhang, Shuguo Yuan, Rifu Xu
Estrogen receptors α (ESR1) and β (ESR2) play central roles in folliculogenesis, and therefore in reproductive biology. In the present study, two single nucleotide polymorphisms (SNPs) were identified in the ESR1 and ESR2 genes using PCR-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing. One of the identified SNPs, a T1101C transition located within exon 4 of the ESR1 gene, was significantly associated with hen-housed egg production (HHEP) at 30, 43, 57 and 66 weeks of age (P<0.05), and egg weight (EW) at 30 weeks (P<0...
April 15, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28419109/polymorphisms-in-the-selectin-gene-cluster-are-associated-with-fertility-and-survival-time-in-a-population-of-holstein-friesian-cows
#4
Xing Chen, Shujun Zhang, Zhangrui Cheng, Jessica S Cooke, Dirk Werling, D Claire Wathes, Geoffrey E Pollott
Selectins are adhesion molecules, which mediate attachment between leucocytes and endothelium. They aid extravasation of leucocytes from blood into inflamed tissue during the mammary gland's response to infection. Selectins are also involved in attachment of the conceptus to the endometrium and subsequent placental development. Poor fertility and udder health are major causes for culling dairy cows. The three identified bovine selectin genes SELP, SELL and SELE are located in a gene cluster. SELP is the most polymorphic of these genes...
2017: PloS One
https://www.readbyqxmd.com/read/28414099/molecular-evolution-of-the-plastid-genome-during-diversification-of-the-cotton-genus
#5
Zhiwen Chen, Corrinne E Grover, Pengbo Li, Yumei Wang, Hushuai Nie, Yanpeng Zhao, Meiyan Wang, Fang Liu, Zhongli Zhou, Xingxing Wang, Xiaoyan Cai, Kunbo Wang, Jonathan F Wendel, Jinping Hua
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and one tetraploid genomic group, namely AD. To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome duringdiversification, chloroplast genomes (cpDNA) from 6 D-genome and 2 G-genome species of Gossypium (G. armourianum D2-1, G. harknessii D2-2, G. davidsonii D3-d, G. klotzschianum D3-k, G. aridum D4, G. trilobum D8, and G. australe G2, G. nelsonii G3) were newly reported here...
April 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28411162/insights-into-evolution-in-andean-polystichum-dryopteridaceae-from-expanded-understanding-of-the-cytosolic-phosphoglucose-isomerase-gene
#6
Brendan M Lyons, Monique A McHenry, David S Barrington
Cytosolic phosphoglucose isomerase (pgiC) is an enzyme essential to glycolysis found universally in eukaryotes, but broad understanding of variation in the gene coding for pgiC is lacking for ferns. We used a substantially expanded representation of the gene for Andean species of the fern genus Polystichum to characterize pgiC in ferns relative to angiosperms, insects, and an amoebozoan; assess the impact of selection versus neutral evolutionary processes on pgiC; and explore evolutionary relationships of selected Andean species...
April 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28397003/plastome-wide-nucleotide-substitution-rates-reveal-accelerated-rates-in-papilionoideae-and-correlations-with-genome-features-across-legume-subfamilies
#7
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/28396254/mildly-deleterious-mitochondrial-dna-variants-are-less-frequent-in-healthy-older-individuals-but-not-more-prevalent-in-alzheimer-s-patients
#8
Ilse S Pienaar, Neil Howell, Joanna L Elson
Mitochondrial DNA (mtDNA) association studies have been conducted for over a decade using the haplogroup (lineage) association method, but this frequently produces conflicting results. Here we analyzed complete mtDNA sequence data of Alzheimer's disease (AD) patients and aged controls, from the United Kingdom (UK) and the United States (US), using a new "mutational load" method. We calculated a pathogenicity score for each of the non-synonymous substitutions of the mtDNA sequences to produce a "total mutational load" for each sequence, and compared the mutational loads of cases and controls...
April 7, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28391525/regsnps-splicing-a-tool-for-prioritizing-synonymous-single-nucleotide-substitution
#9
Xinjun Zhang, Meng Li, Hai Lin, Xi Rao, Weixing Feng, Yuedong Yang, Matthew Mort, David N Cooper, Yue Wang, Yadong Wang, Clark Wells, Yaoqi Zhou, Yunlong Liu
While synonymous single-nucleotide variants (sSNVs) have largely been unstudied, since they do not alter protein sequence, mounting evidence suggests that they may affect RNA conformation, splicing, and the stability of nascent-mRNAs to promote various diseases. Accurately prioritizing deleterious sSNVs from a pool of neutral ones can significantly improve our ability of selecting functional genetic variants identified from various genome-sequencing projects, and, therefore, advance our understanding of disease etiology...
April 8, 2017: Human Genetics
https://www.readbyqxmd.com/read/28388287/in-silico-analysis-of-non-synonymous-single-nucleotide-polymorphisms-in-human-dazl-gene-associated-with-male-infertility
#10
Mili Nailwal, Jenabhai B Chauhan
In living systems the most frequent type of genetic mutation is the single nucleotide polymorphism (SNP). Non-synonymous SNPs (nsSNPs) or missense mutations arise in coding regions of a particular gene. nsSNPs result in a single amino acid substitution which may have effects on the structure and/or function of proteins. Spermatogenesis is a complex process where haploid spermatozoa are formed. The deleted in azoospermia like (DAZL) gene has a relationship with male infertility and dysfunction of DAZL may decrease the sperm count which leads to oligozoospermia or azoospermia...
April 7, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28378144/development-and-genetic-characterization-of-a-novel-herbicide-imazethapyr-tolerant-mutant-in-rice-oryza-sativa-l
#11
D Shoba, M Raveendran, S Manonmani, S Utharasu, D Dhivyapriya, G Subhasini, S Ramchandar, R Valarmathi, Nitasha Grover, S Gopala Krishnan, A K Singh, Pawan Jayaswal, Prashant Kale, M K Ramkumar, S V Amitha Mithra, T Mohapatra, Kuldeep Singh, N K Singh, N Sarla, M S Sheshshayee, M K Kar, S Robin, R P Sharma
BACKGROUND: Increased water and labour scarcity in major rice growing areas warrants a shift towards direct seeded rice cultivation under which management of weeds is a major issue. Use of broad spectrum non-selective herbicides is an efficient means to manage weeds. Availability of rice genotypes with complete tolerance against broad-spectrum non-selective herbicides is a pre-requisite for advocating use of such herbicides. In the present study, we developed an EMS induced rice mutant, 'HTM-N22', exhibiting tolerance to a broad spectrum herbicide, 'Imazethapyr', and identified the mutations imparting tolerance to the herbicide...
December 2017: Rice
https://www.readbyqxmd.com/read/28361915/evolution-of-multi-drug-resistant-hcv-clones-from-pre-existing-resistant-associated-variants-during-direct-acting-antiviral-therapy-determined-by-third-generation-sequencing
#12
Haruhiko Takeda, Yoshihide Ueda, Tadashi Inuzuka, Yukitaka Yamashita, Yukio Osaki, Akihiro Nasu, Makoto Umeda, Ryo Takemura, Hiroshi Seno, Akihiro Sekine, Hiroyuki Marusawa
Resistance-associated variant (RAV) is one of the most significant clinical challenges in treating HCV-infected patients with direct-acting antivirals (DAAs). We investigated the viral dynamics in patients receiving DAAs using third-generation sequencing technology. Among 283 patients with genotype-1b HCV receiving daclatasvir + asunaprevir (DCV/ASV), 32 (11.3%) failed to achieve sustained virological response (SVR). Conventional ultra-deep sequencing of HCV genome was performed in 104 patients (32 non-SVR, 72 SVR), and detected representative RAVs in all non-SVR patients at baseline, including Y93H in 28 (87...
March 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28348854/bayesian-codon-substitution-modelling-to-identify-sources-of-pathogen-evolutionary-rate-variation
#13
Guy Baele, Marc A Suchard, Filip Bielejec, Philippe Lemey
Phylodynamic reconstructions rely on a measurable molecular footprint of epidemic processes in pathogen genomes. Identifying the factors that govern the tempo and mode by which these processes leave a footprint in pathogen genomes represents an important goal towards understanding infectious disease evolution. Discriminating between synonymous and non-synonymous substitution rates is crucial for testing hypotheses about the sources of evolutionary rate variation. Here, we implement a codon substitution model in a Bayesian statistical framework to estimate absolute rates of synonymous and non-synonymous substitution in unknown evolutionary histories...
June 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28347326/first-report-of-the-phe1534cys-kdr-mutation-in-natural-populations-of-aedes-albopictus-from-brazil
#14
Oscar Alexander Aguirre-Obando, Ademir Jesus Martins, Mário Antônio Navarro-Silva
BACKGROUND: Knockdown resistance (kdr), caused by alterations in the voltage-gated sodium channel (NaV), is one of the mechanisms responsible for pyrethroid (PY) resistance. In the Asian tiger mosquito, Aedes albopictus, at least four different mutations were described in the IIIS6 NaV segment in populations from Asia, North America and Europe. In contrast, in Aedes aegypti at least 12 non-synonymous mutations have been reported at nine different codons, mostly in the IIS6 and IIIS6 NaV segments...
March 27, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28334822/posigene-automated-and-easy-to-use-pipeline-for-genome-wide-detection-of-positively-selected-genes
#15
Arne Sahm, Martin Bens, Matthias Platzer, Karol Szafranski
Many comparative genomics studies aim to find the genetic basis of species-specific phenotypic traits. A prevailing strategy is to search genome-wide for genes that evolved under positive selection based on the non-synonymous to synonymous substitution ratio. However, incongruent results largely due to high false positive rates indicate the need for standardization of quality criteria and software tools. Main challenges are the ortholog and isoform assignment, the high sensitivity of the statistical models to alignment errors and the imperative to parallelize large parts of the software...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28332757/selective-modes-determine-evolutionary-rates-gene-compactness-and-expression-patterns-in-brassica
#16
Yue Guo, Jing Liu, Jiefu Zhang, Shengyi Liu, Jianchang Du
It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories, i.e., positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (Ka) and the synonymous substitution (Ks) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa, and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs...
March 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28299895/deep-sequencing-and-variant-analysis-of-an-italian-pathogenic-field-strain-of-equine-infectious-anaemia-virus
#17
K Cappelli, R F Cook, V Stefanetti, F Passamonti, G L Autorino, M T Scicluna, M Coletti, A Verini Supplizi, S Capomaccio
Equine infectious anaemia virus (EIAV) is a lentivirus with an almost worldwide distribution that causes persistent infections in equids. Technical limitations have restricted genetic analysis of EIAV field isolates predominantly to gag sequences resulting in very little published information concerning the extent of inter-strain variation in pol, env and the three ancillary open reading frames (ORFs). Here, we describe the use of long-range PCR in conjunction with next-generation sequencing (NGS) for rapid molecular characterization of all viral ORFs and known transcription factor binding motifs within the long terminal repeat of two EIAV isolates from the 2006 Italian outbreak...
March 15, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28295310/a-rare-case-of-plastid-protein-coding-gene-duplication-in-the-chloroplast-genome-of-euglena-archaeoplastidiata-euglenophyta
#18
Matthew S Bennett, Shin-Han Shiu, Richard E Triemer
Gene duplication is an important evolutionary process that allows duplicate functions to diverge, or, in some cases, allows for new functional gains. However, in contrast to the nuclear genome, gene duplications within the chloroplast are extremely rare. Here, we present the chloroplast genome of the photosynthetic protist Euglena archaeoplastidiata. Upon annotation it was found that the chloroplast genome contained a novel tandem direct duplication which encoded a portion of RuBisCO large subunit (rbcL) followed by a complete copy of ribosomal protein L32 (rpl32) as well as the associated intergenic sequences...
March 12, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28288365/dexd-h-box-rna-helicase-genes-are-differentially-expressed-between-males-and-females-during-the-critical-period-of-male-sex-differentiation-in-channel-catfish
#19
Changxu Tian, Suxu Tan, Lisui Bao, Qifan Zeng, Shikai Liu, Yujia Yang, Xiaoxiao Zhong, Zhanjiang Liu
DExD/H-box RNA helicases are motor proteins participating in nearly all aspects of cellular processes, especially in RNA metabolism. In this study, a total of 54 DExD/H-box RNA helicase genes including 37 DDX (DEAD-box) and 17 DHX (DEAH-box) genes were characterized in channel catfish (Ictalurus punctatus), and annotated through phylogenetic and syntenic analyses. All the catfish RNA helicases contained conserved helicase signature motifs, demonstrating that the RNA helicase gene family was highly conserved...
March 1, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28288206/an-in-vivo-system-for-directed-experimental-evolution-of-rabbit-haemorrhagic-disease-virus
#20
Robyn N Hall, Lorenzo Capucci, Markus Matthaei, Simona Esposito, Peter J Kerr, Michael Frese, Tanja Strive
The calicivirus Rabbit haemorrhagic disease virus (RHDV) is widely used in Australia as a biocontrol agent to manage wild European rabbit (Oryctolagus cuniculus) populations. However, widespread herd immunity limits the effectiveness of the currently used strain, CAPM V-351. To overcome this, we developed an experimental platform for the selection and characterisation of novel RHDV strains. As RHDV does not replicate in cell culture, variant viruses were selected by serially passaging a highly virulent RHDV field isolate in immunologically naïve laboratory rabbits that were passively immunised 18-24 hours post-challenge with a neutralising monoclonal antibody...
2017: PloS One
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