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Luís Bernardo Pina-Cabral, Miguel Carneiro, Begoña Criado, Pedro José Esteves
Platelet integrin αIIbβ3 is crucial for platelet aggregation. Although structural and functional characteristics of this protein have been extensively studied, the evolutionary pattern studies of this protein complex in mammals are scarce. Here, we addressed this question using maximum likelihood approaches to identify codons that are evolving under positive selection. Likelihood of positive selection was estimated using CODEML implemented in PAML software applied to integrin αIIbβ3 derived from nucleotide sequences of 10 different mammalian species...
April 4, 2018: Platelets
Xiao-Yong Zhan, Qing-Yi Zhu
Methicillin-resistant Staphylococcus aureus (S. aureus) (MRSA) represents more and more S. aureus infections. MecA, the novel coding gene of penicillin-binding protein (PBP) 2a of MRSA, is the key resistance factor of β-lactam, but little is known about the evolution of this gene. Given the crucial role of mecA in S. aureus physiology and β-lactam resistance, the selective forces may contribute to adaptation of the bacteria to the special environments such as its host or antibiotics. To understand the evolution of this gene, we screened GenBank database and analyzed mecA of 249 S...
April 2018: Infection, Genetics and Evolution
Noé Vázquez, Cristina P Vieira, Bárbara S R Amorim, André Torres, Hugo López-Fernández, Florentino Fdez-Riverola, José L R Sousa, Miguel Reboiro-Jato, Jorge Vieira
When changes at few amino acid sites are the target of selection, adaptive amino acid changes in protein sequences can be identified using maximum-likelihood methods based on models of codon substitution (such as codeml). Although such methods have been employed numerous times using a variety of different organisms, the time needed to collect the data and prepare the input files means that tens or hundreds of coding regions are usually analyzed. Nevertheless, the recent availability of flexible and easy to use computer applications that collect relevant data (such as BDBM) and infer positively selected amino acid sites (such as ADOPS), means that the entire process is easier and quicker than before...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
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...
February 2018: Marine Genomics
Anders Gonçalves da Silva
In this chapter, I review the basic algorithm underlying the CODEML model implemented in the software package PAML. This is intended as a companion to the software's manual, and a primer to the extensive literature available on CODEML. At the end of this chapter, I hope that you will be able to understand enough of how CODEML operates to plan your own analyses.
2017: Methods in Molecular Biology
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...
February 2017: Molecular Genetics and Genomics: MGG
Maira Ferreira Cicero, Nathalia Mantovani Pena, Luiz Claudio Santana, Rafael Arnold, Rafael Gonçalves Azevedo, Élcio de Souza Leal, Ricardo Sobhie Diaz, Shirley Vasconcelos Komninakis
BACKGROUND: The Hepatitis Delta Virus (HDV) can increase the incidence of fulminant hepatitis. For this infection occurs, the host must also be infected with Hepatitis B Virus. Previous studies demonstrated the endemicity and near exclusivity of this infection in the Amazon region, and as a consequence of the difficulty in accessing this area we used dried blood spots (DBS) in sample collection. The aims of this study were to investigate the presence of recombination, to analyze the epidemiology, ancestry and evolutionary pressures on HDV in Brazil...
September 29, 2016: BMC Infectious Diseases
Kevin N Chesmore, Jacquelaine Bartlett, Chao Cheng, Scott M Williams
Pleiotropy has been claimed to constrain gene evolution but specific mechanisms and extent of these constraints have been difficult to demonstrate. The expansion of molecular data makes it possible to investigate these pleiotropic effects. Few classes of genes have been characterized as intensely as human transcription factors (TFs). We therefore analyzed the evolutionary rates of full TF proteins, along with their DNA binding domains and protein-protein interacting domains (PID) in light of the degree of pleiotropy, measured by the number of TF-TF interactions, or the number of DNA-binding targets...
October 23, 2016: Genome Biology and Evolution
S Ahlawat, P Sharma, R Sharma, R Arora, N K Verma, B Brahma, P Mishra, S De
Meiotic recombination contributes to augmentation of genetic diversity, exclusion of deleterious alleles and proper segregation of chromatids. PRDM9 has been identified as the gene responsible for specifying the location of recombination hotspots during meiosis and is also the only known vertebrate gene associated with reproductive isolation between species. PRDM9 encodes a protein with a highly variable zinc finger (ZF) domain that varies between as well as within species. In the present study, the ZF domain of PRDM9 on chromosome 1 was characterized for the first time in 15 goat breeds and 25 sheep breeds of India...
December 2016: Animal Genetics
Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vitor Vasconcelos, Agostinho Antunes
BACKGROUND: Uncovering how phenotypic diversity arises and is maintained in nature has long been a major interest of evolutionary biologists. Recent advances in genome sequencing technologies have remarkably increased the efficiency to pinpoint genes involved in the adaptive evolution of phenotypes. Reliability of such findings is most often examined with statistical and computational methods using Maximum Likelihood codon-based models (i.e., site, branch, branch-site and clade models), such as those available in codeml from the Phylogenetic Analysis by Maximum Likelihood (PAML) package...
September 6, 2016: BMC Bioinformatics
Joseph P Bielawski, Jennifer L Baker, Joseph Mingrone
This unit provides protocols for using the CODEML program from the PAML package to make inferences about episodic natural selection in protein-coding sequences. The protocols cover inference tasks such as maximum likelihood estimation of selection intensity, testing the hypothesis of episodic positive selection, and identifying sites with a history of episodic evolution. We provide protocols for using the rich set of models implemented in CODEML to assess robustness, and for using bootstrapping to assess if the requirements for reliable statistical inference have been met...
June 20, 2016: Current Protocols in Bioinformatics
Akhtar Rasool Asif, Sumayyah Qadri, Nabeel Ijaz, Ruheena Javed, Abdur Rahman Ansari, Muhammd Awais, Muhammad Younus, Hasan Riaz, Xiaoyong Du
OBJECTIVE: Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL)-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene...
July 2017: Asian-Australasian Journal of Animal Sciences
Caroline Daigle, Daniel P Matton
BACKGROUND: Members of the plant MAP Kinases superfamily have been mostly studied in Arabidopsis thaliana and little is known in most other species. In Solanum chacoense, a wild species close to the common potato, it had been reported that members of a specific group in the MEKK subfamily, namely ScFRK1 and ScFRK2, are involved in male and female reproductive development. Apart from these two kinases, almost nothing is known about the roles of this peculiar family. METHODS: MEKKs were identified using BLAST and hidden Markov model (HMM) to build profiles using the 21 MEKKs from A...
2015: BMC Genomics
Andrew Ndhlovu, Pierre M Durand, Scott Hazelhurst
The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry...
2015: Database: the Journal of Biological Databases and Curation
Yu Fan, Dandan Yu, Yong-Gang Yao
The tree shrew (Tupaia belangeri) is a small mammal with a close relationship to primates and it has been proposed as an alternative experimental animal to primates in biomedical research. The recent release of a high-quality Chinese tree shrew genome enables more researchers to use this species as the model animal in their studies. With the aim to making the access to an extensively annotated genome database straightforward and easy, we have created the Tree shrew Database (TreeshrewDB). This is a web-based platform that integrates the currently available data from the tree shrew genome, including an updated gene set, with a systematic functional annotation and a mRNA expression pattern...
November 21, 2014: Scientific Reports
Daniel C Jeffares, Bartłomiej Tomiczek, Victor Sojo, Mario dos Reis
The ratio of non-synonymous to synonymous substitutions (dN/dS) is a useful measure of the strength and mode of natural selection acting on protein-coding genes. It is widely used to study patterns of selection on protein genes on a genomic scale-from the small genomes of viruses, bacteria, and parasitic eukaryotes to the largest eukaryotic genomes. In this chapter we describe all the steps necessary to calculate the dN/dS of all the genes using at least two genomes. We include a brief discussion on assigning orthologs, and of codon-aware alignment of orthologs...
2015: Methods in Molecular Biology
Emanuel Maldonado, Kartik Sunagar, Daniela Almeida, Vitor Vasconcelos, Agostinho Antunes
Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins...
2014: PloS One
Patamarerk Engsontia, Unitsa Sangket, Wilaiwan Chotigeat, Chutamas Satasook
Lepidoptera (comprised of butterflies and moths) is one of the largest groups of insects, including more than 160,000 described species. Chemoreception plays important roles in the adaptation of these species to a wide range of niches, e.g., plant hosts, egg-laying sites, and mates. This study investigated the molecular evolution of the lepidopteran odorant (Or) and gustatory receptor (Gr) genes using recently identified genes from Bombyx mori, Danaus plexippus, Heliconius melpomene, Plutella xylostella, Heliothis virescens, Manduca sexta, Cydia pomonella, and Spodoptera littoralis...
August 2014: Journal of Molecular Evolution
Mario Valle, Hannes Schabauer, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Nicolas Salamin
MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML...
April 15, 2014: Bioinformatics
Ana Pinheiro, Jenny M Woof, Laurent Abi-Rached, Peter Parham, Pedro J Esteves
IgA is the predominant immunoglobulin isotype in mucosal tissues and external secretions, playing important roles both in defense against pathogens and in maintenance of commensal microbiota. Considering the complexity of its interactions with the surrounding environment, IgA is a likely target for diversifying or positive selection. To investigate this possibility, the action of natural selection on IgA was examined in depth with six different methods: CODEML from the PAML package and the SLAC, FEL, REL, MEME and FUBAR methods implemented in the Datamonkey webserver...
2013: PloS One
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