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synonymous substitution

Zhi-Qiang Liu, Yan-Feng Liu, Nuer Kuermanali, Deng-Feng Wang, Shi-Jun Chen, Hui-Ling Guo, Li Zhao, Jun-Wei Wang, Tao Han, Yuan-Zhi Wang, Jie Wang, Chen-Feng Shen, Zhuang-Zhi Zhang, Chuang-Fu Chen
Phylogeny of hard ticks (Ixodidae) remains unresolved. Mitochondrial genomes (mitogenomes) are increasingly used to resolve phylogenetic controversies, but remain unavailable for the entire large Hyalomma genus. Hyalomma asiaticum is a parasitic tick distributed throughout the Asia. As a result of great morphological variability, two subspecies have been recognised historically; until a morphological data-based synonymization was proposed. However, this hypothesis was never tested using molecular data. Therefore, objectives of this study were to: 1...
2018: PloS One
Alejandro A Edera, Carolina L Gandini, M Virginia Sanchez-Puerta
Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by the few editing sites identified to date. This study identified 10,217 editing sites from 17 diverse angiosperms. Our analyses confirmed the universality of certain features of RNA editing, and offer new evidence behind the loss of editing sites in angiosperms. RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at specific positions called editing sites...
May 14, 2018: Plant Molecular Biology
F Rodríguez, C Vallejos, D Ponce, N Unanue, M I Hernández, S Célis, K Arcos, F Belmar, M T López, F Cassorla
Cryptorchidism is one of the most common congenital disorders in boys, and several genetic, hormonal, and environmental factors have been proposed as possible causes for this genitourinary defect. Genetic factors have been intensively searched, but relatively few pathogenic variants have been described. Cryptorchidism is a frequent finding in patients with RASopathies, a group of syndrome caused by mutations in genes of the Ras/MAPK pathway. Our aim was to determine whether patients with isolated cryptorchidism (IC) exhibit Ras/MAPK pathway gene variants associated with RASopathies...
May 11, 2018: Andrology
Pratichi Singh, J Febin Prabhu Dass
IFNL3 gene plays a crucial role in immune defense against viruses. It induces the interferon stimulated genes (ISGs) with antiviral properties by activating the JAK-STAT pathway. In this study, we investigated the evolutionary force involved in shaping the IFNL3 gene to perform its downstream function as a regulatory gene in HCV clearance. We have selected 25 IFNL3 coding sequences with human gene as a reference sequence and constructed a phylogeny. Furthermore, rate of variation, substitution saturation test, phylogenetic informativeness and differential selection were also analysed...
May 7, 2018: Progress in Biophysics and Molecular Biology
G P Tiley, R T Kimball, E L Braun, J G Burleigh
BACKGROUND: Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Gallus gallus (Red Junglefowl, the progenitor of the chicken), we know little about the genomes of closely related species. Gallus gallus is highly sexually dichromatic and polygynous, but its sister genus, Bambusicola, is smaller, sexually monomorphic, and monogamous with biparental care...
May 8, 2018: BMC Genomics
Jia Li, Yingjuan Su, Ting Wang
The plastid accD gene encodes a subunit of the acetyl-CoA carboxylase (ACCase) enzyme. The length of accD gene has been supposed to expand in Cryptomeria japonica , Taiwania cryptomerioides , Cephalotaxus , Taxus chinensis , and Podocarpus lambertii , and the main reason for this phenomenon was the existence of tandemly repeated sequences. However, it is still unknown whether the accD gene length in other cupressophytes has expanded. Here, in order to investigate how widespread this phenomenon was, 18 accD sequences and its surrounding regions of cupressophyte were sequenced and analyzed...
2018: Frontiers in Plant Science
Tatjana Sitt, Roger Pelle, Maurine Chepkwony, W Ivan Morrison, Philip Toye
The extent of sequence diversity among the genes encoding 10 antigens (Tp1-10) known to be recognized by CD8+ T lymphocytes from cattle immune to Theileria parva was analysed. The sequences were derived from parasites in 23 buffalo-derived cell lines, three cattle-derived isolates and one cloned cell line obtained from a buffalo-derived stabilate. The results revealed substantial variation among the antigens through sequence diversity. The greatest nucleotide and amino acid diversity were observed in Tp1, Tp2 and Tp9...
May 6, 2018: Parasitology
Dongsheng Zhang, Peng Hu, Taigang Liu, Jian Wang, Shouwen Jiang, Qianghua Xu, Liangbiao Chen
BACKGROUND: Temperature adaptation of biological molecules is fundamental in evolutionary studies but remains unsolved. Fishes living in cold water are adapted to low temperatures through adaptive modification of their biological molecules, which enables their functioning in extreme cold. To study nucleotide and amino acid preference in cold-water fishes, we investigated the substitution asymmetry of codons and amino acids in protein-coding DNA sequences between cold-water fishes and tropical fishes...
May 2, 2018: BMC Genomics
Daniel Spalink, Kevin Stoffel, Genevieve K Walden, Amanda M Hulse-Kemp, Theresa A Hill, Allen Van Deynze, Lynn Bohs
The integration of genomics and phylogenetics allows new insight into the structure of gene tree discordance, the relationships among gene position, gene history, and rate of evolution, as well as the correspondence of gene function, positive selection, and gene ontology enrichment across lineages. We explore these issues using the tribe Capsiceae (Solanaceae), which is comprised of the genera Lycianthes and Capsicum (peppers). In combining the annotated genomes of Capsicum with newly sequenced transcriptomes of four species of Lycianthes and Capsicum, we develop phylogenies for 6,747 genes, and construct a backbone species tree using both concordance and explicit phylogenetic network approaches...
April 24, 2018: Molecular Phylogenetics and Evolution
Jessica Rodgers, Stuart N Peirson, Steven Hughes, Mark W Hankins
Melanopsin is a blue light-sensitive opsin photopigment involved in a range of non-image forming behaviours, including circadian photoentrainment and the pupil light response. Many naturally occurring genetic variants exist within the human melanopsin gene (OPN4), yet it remains unclear how these variants affect melanopsin protein function and downstream physiological responses to light. Here, we have used bioinformatic analysis and in vitro expression systems to determine the functional phenotypes of missense human OPN4 variants...
April 26, 2018: Cellular and Molecular Life Sciences: CMLS
Juemin Xi, Junying Chen, Miaoling Xu, Hongying Yang, Songjiao Wen, Yue Pan, Xiaodan Wang, Chao Ye, Lijuan Qiu, Qiangming Sun
BACKGROUD: Variations in HPV LCR/E6/E7 have been shown to be associated with the viral persistence and cervical cancer development. So far, there are few reports about the polymorphisms of the HPV-58 LCR/E6/E7 sequences in Southwest China. This study aims to characterize the gene polymorphisms of the HPV-58 LCR/E6/E7 sequences in women of Southwest China, and assess the effects of variations on the immune recognition of viral E6 and E7 antigens. METHODS: Twelve LCR/E6/E7 of the HPV-58 isolates were amplified and sequenced...
April 25, 2018: Virology Journal
Wanzhen Liu, Hanghui Kong, Juan Zhou, Peter W Fritsch, Gang Hao, Wei Gong
The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana , endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted...
April 25, 2018: International Journal of Molecular Sciences
Eli Eisenberg, Erez Y Levanon
Modifications of RNA affect its function and stability. RNA editing is unique among these modifications because it not only alters the cellular fate of RNA molecules but also alters their sequence relative to the genome. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Recent transcriptomic studies have identified a number of 'recoding' sites at which A-to-I editing results in non-synonymous substitutions in protein-coding sequences. Many of these recoding sites are conserved within (but not usually across) lineages, are under positive selection and have functional and evolutionary importance...
April 24, 2018: Nature Reviews. Genetics
N J Marley, Ł Kaczmarek, M Gawlak, P J Bartels, D R Nelson, M Roszkowska, Stec D, P Degma
The recent re-description of Paramacrobiotus Guidetti, Schill, Bertolani, Dandekar and Wolf, 2009 has inadvertently led to the description of an objective synonym within its subgenera nominal taxa. To resolve this issue, we have re-described both subgenera, and proposed a new substitute name for one subgenus, in line with the International Code of Zoological Nomenclature. Additionally we have confirmed the placement of two recently published Paramacrobiotus species, not included in the last revision, within the respective subgenera established herein...
April 9, 2018: Zootaxa
Catherine A Tauber, Francisco Sosa, Atilano Contreras-Ramos
The green lacewing genus name Cryptochrysa Freitas Penny 2001 is identified as a junior homonym of Cryptochrysa Hampson 1926 (Lepidoptera: Noctuidae). Moreover, Titanochrysa Sosa Freitas 2012 is determined to be an available junior synonym of Cryptochrysa Freitas Penny. Thus, Titanochrysa becomes the substitute name for the preoccupied generic name. Here, we also provide (i) new information and images for Titanochrysa chloros (Freitas Penny) comb. nov., the only species ever included in the chrysopid genus Cryptochrysa, (ii) a clarified set of diagnostic features for the reconstituted genus Titanochrysa, and (iii) a key and images for identifying the six described Titanochrysa species...
January 24, 2018: Zootaxa
Marcos C Vieira, Daniel Zinder, Sarah Cobey
High-affinity antibodies arise within weeks of infection from the evolution of B-cell receptors under selection to improve antigen recognition. This rapid adaptation is enabled by the distribution of highly mutable "hotspot" motifs in B-cell receptor genes. High mutability in antigen-binding regions (complementarity determining regions [CDRs]) creates variation in binding affinity, whereas low mutability in structurally important regions (framework regions [FRs]) may reduce the frequency of destabilizing mutations...
May 1, 2018: Molecular Biology and Evolution
Adi Yannai, Sophia Katz, Ruth Hershberg
Codon usage bias affects the genomes of organisms from all kingdoms of life, and results from both background substitution biases and natural selection. Natural selection on codon usage to increase translation accuracy and efficiency has long been known to affect gene sequences. Such selection is stronger on highly, compared to lowly expressed genes, resulting in higher levels of codon bias within genes with higher expression levels. Additionally, selection on translation accuracy affects more strongly codons encoding conserved amino acids, since these will more often affect protein folding and/or function...
April 23, 2018: Genome Biology and Evolution
Tomohide Yasunaga, Kazutaka Yamada, Jing-Fu Tsai
The fauna of plant bug subfamily Isometopinae in Taiwan and Japanese Southwest (Nansei) Islands is reviewed. Twenty-five species are recognized, including two new species of Myiomma Puton, M. austroccidens sp. nov. and M. kentingense sp. nov., which are herein diagnosed and described. In addition, Isometopus yehi Lin, 2004 is synonymized with I. bipunctatus Lin; Isometopidea yangi Lin is transferred to Kohnometopus; and a substitute name, Alcecoris linyangorum, is proposed for A. formosanus (Lin Yang) (= a junior secondary homonym of Alcecoris formosanus Lin)...
December 19, 2017: Zootaxa
Saeid Amanloo, Masoomeh Shams-Ghahfarokhi, Mohammad Ghahri, Mehdi Razzaghi-Abyaneh
BACKGROUND: Candida glabrata is a yeast that can cause hazardous fungal infections with high mortality and drug resistance. AIMS: The aim of this study was to determine the profile of drug susceptibility in clinical isolates of C. glabrata and review the resistance mechanisms to caspofungin. METHODS: A total of 50 C. glabrata clinical isolates from Iran were tested for in vitro susceptibilities to amphotericin B, caspofungin, fluconazole and voriconazole...
April 20, 2018: Revista Iberoamericana de Micología
W Tian, F M Zhu, W Y Wang, L X Li, J H Cai
A novel allelic variant in HLA-B*40 lineage, HLA-B*40:298:02, has been identified in an individual of Han ethnicity afflicted with nasopharyngeal carcinoma in Hunan province, southern China. Following polymerase chain reaction-Sanger sequence-based typing (PCR-SBT), this new variant was further confirmed by two distinct strategies of cloning and sequencing. HLA-B*40:298:02 differs from HLA-B*40:298:01 by a single synonymous cytosine substitution at nucleotide position 26 (T→C) in exon 3, which corresponds to codon 99 of the mature HLA-B mRNA molecule...
April 20, 2018: International Journal of Immunogenetics
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