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A multi-gene phylogeny of Lactifluus (Basidiomycota, Russulales) translated into a new infrageneric classification of the genus Naturalis
Crop, E. de; Nuytinck, J.; Putte, K. van de; Wisitrassameewong, K.; Hackel, J.; Stubbe, D.; Hyde, K.D.; Roy, M.; Halling, R.E.; Moreau, P.-A.; Eberhardt, U.; Verbeken, A..
Infrageneric relations of the genetically diverse milkcap genus Lactifluus (Russulales, Basidiomycota) are poorly known. Currently used classification systems still largely reflect the traditional, mainly morphological, characters used for infrageneric delimitations of milkcaps. Increased sampling, combined with small-scale molecular studies, show that this genus is underexplored and in need of revision. For this study, we assembled an extensive dataset of the genus Lactifluus, comprising 80 % of all known species and 30 % of the type collections. To unravel the infrageneric relationships within this genus, we combined a multi-gene molecular phylogeny, based on nuclear ITS, LSU, RPB2 and RPB1, with a morphological study, focussing on five important...
Tipo: Article / Letter to the editor Palavras-chave: Milkcaps; Molecular evolution; Morphology; Taxonomy.
Ano: 2017 URL: http://www.repository.naturalis.nl/record/615530
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Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network ArchiMer
Meng, Arnaud; Corre, Erwan; Probert, Ian; Gutierrez-rodriguez, Andres; Siano, Raffaele; Annamale, Anita; Alberti, Adriana; Da Silva, Corinne; Wincker, Patrick; Le Crom, Stephane; Not, Fabrice; Bittner, Lucie.
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional...
Tipo: Text Palavras-chave: Genomics; Proteomics; Microbial biology; Molecular evolution; Protists; Transcriptomics.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00444/55550/57209.pdf
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Changes in G+C content of a neutrally evolving gene under a non-reversible dynamics measured by computer simulations based on experimental evolution data Genet. Mol. Biol.
Brunstein,Adriana; Varuzza,Leonardo; Sanson,Gerdine F. O.; Briones,Marcelo R. S..
To evaluate the effects of non-reversibility on compositional base changes and the distribution of branch lengths along a phylogeny, we extended, by means of computer simulations, our previous sequential PCR in vitro evolution experiment. In that study a 18S rRNA gene evolved neutrally for 280 generations and a homogeneous non-stationary model of base substitution based on a non-reversible dynamics was built from the in vitro evolution data to describe the observed pattern of nucleotide substitutions. Here, the process was extended to 840 generations without selection, using the model parameters calculated from the in vitro evolution experiment. We observed that under a non-reversible model the G+C content of the sequences significantly increases when...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Molecular evolution; Experimental phylogenetics; Neutral theory; Mathematical models of nucleotide substitutions.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400026
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Divergent evolution and purifying selection of the H (FUT1) gene in New World monkeys (Primates, Platyrrhini) Genet. Mol. Biol.
Borges,Bárbara do Nascimento; Harada,Maria Lúcia.
In the present study, the coding region of the H gene was sequenced and analyzed in fourteen genera of New World primates (Alouatta, Aotus, Ateles, Brachyteles, Cacajao, Callicebus, Callithrix, Cebus, Chiropotes, Lagothrix, Leontopithecus, Pithecia, Saguinus, and Saimiri), in order to investigate the evolution of the gene. The analyses revealed that this coding region contains 1,101 nucleotides, with the exception of Brachyteles, the callitrichines (Callithrix, Leontopithecus, and Saguinus) and one species of Callicebus (moloch), in which one codon was deleted. In the primates studied, the high GC content (63%), the nonrandom distribution of codons and the low evolution rate of the gene (0.513 substitutions/site/MA in the order Primates) suggest the action...
Tipo: Info:eu-repo/semantics/article Palavras-chave: H gene; Molecular evolution; Purifying selection; Divergent evolution; New World monkeys.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000300007
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Evolution of species-specific major seminal fluid proteins in placental mammals by gene death and positive selection Naturalis
Meslin, C.; Laurin, M.; Callebaut, I.; Druart, X.; Monget, P..
The seminal fluid is a complex substance composed of a variety of secreted proteins and has been shown to play an important role in the fertilisation process in mammals and also in Drosophila. Several genes under positive selection have been documented in some rodents and primates. Our study documents this phenomenon in several other mammalian taxa. We study the evolution of genes that encode for 20 proteins that are quantitatively predominant in the seminal fluid of at least one out of seven domestic animal species. We analyse the amino acid composition of these proteins for positive selection and for the presence of pseudogenes. Genes that disappeared through pseudogenisation include KLK2 in cattle, horse and mice. Traces of positive selection are found...
Tipo: Article / Letter to the editor Palavras-chave: Molecular evolution; Multivariate phylogenetic pairwise comparisons; Reproductive isolation; Speciation; Comparative biology; Pseudogenisation; 42.64; 42.13; 42.70.
Ano: 2015 URL: http://www.repository.naturalis.nl/record/575180
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Evolutionary change - patterns and processes Anais da ABC (AABC)
Salzano,Francisco M..
The present review considered: (a) the factors that conditioned the early transition from non-life to life; (b) genome structure and complexity in prokaryotes, eukaryotes, and organelles; (c) comparative human chromosome genomics; and (d) the Brazilian contribution to some of these studies. Understanding the dialectical conflict between freedom and organization is fundamental to give meaning to the patterns and processes of organic evolution.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Molecular evolution; Principles of evolution; Evolution; Plants; Human evolution.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652005000400006
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FOXP in Tetrapoda: Intrinsically Disordered Regions, Short Linear Motifs and their evolutionary significance Genet. Mol. Biol.
Viscardi,Lucas Henriques; Tovo-Rodrigues,Luciana; Paré,Pamela; Fagundes,Nelson Jurandi Rosa; Salzano,Francisco Mauro; Paixão-Côrtes,Vanessa Rodrigues; Bau,Claiton Henrique Dotto; Bortolini,Maria Cátira.
Abstract The FOXP subfamily is probably the most extensively characterized subfamily of the forkhead superfamily, playing important roles in development and homeostasis in vertebrates. Intrinsically disorder protein regions (IDRs) are protein segments that exhibit multiple physical interactions and play critical roles in various biological processes, including regulation and signaling. IDRs in proteins may play an important role in the evolvability of genetic systems. In this study, we analyzed 77 orthologous FOXP genes/proteins from Tetrapoda, regarding protein disorder content and evolutionary rate. We also predicted the number and type of short linear motifs (SLIMs) in the IDRs. Similar levels of protein disorder (approximately 70%) were found for...
Tipo: Info:eu-repo/semantics/article Palavras-chave: FOXP2; Intrinsically disordered protein regions; Forkhead superfamily; Short linear motif; Molecular evolution.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000100181
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Genotypic diversity of the Killer Cell Immunoglobulin-like Receptors (KIR) and their HLA class I Ligands in a Saudi population Genet. Mol. Biol.
Omar,Suliman Y. Al; Alkuriji,Afrah; Alwasel,Saleh; Dar,javid Ahmed; Alhammad,Alwaleed; Christmas,Stephen; Mansour,Lamjed.
Abstract Killer Cell Immunoglobulin-like Receptors (KIR) have been used as good markers for the study of genetic predisposition in many diseases and in human genetic population dynamics. In this context, we have investigated the genetic diversity of KIR genes and their main HLA class I ligands in Saudi population and compared the data with other studies of neighboring populations. One hundred and fourteen randomly selected healthy Saudi subjects were genotyped for the presence or absence of 16 KIR genes and their HLA-C1, -C2, -Bw4Thr80 and Bw4Ile80 groups, using a PCR-SSP technique. The results show the occurrence of the framework genes (3DL2, 3DL3 and 2DL4) and the pseudogenes (2DP1 and 3DP1) at highest frequencies. All inhibitory KIR (iKIR) genes...
Tipo: Info:eu-repo/semantics/article Palavras-chave: KIR diversity; Gene polymorphism; Molecular evolution; PCR SSP; Population viability analysis.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000100014
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MHC-restricted antigen presentation and recognition: constraints on gene, recombinant and peptide vaccines in humans BJMBR
Cunha-Neto,E..
The target of any immunization is to activate and expand lymphocyte clones with the desired recognition specificity and the necessary effector functions. In gene, recombinant and peptide vaccines, the immunogen is a single protein or a small assembly of epitopes from antigenic proteins. Since most immune responses against protein and peptide antigens are T-cell dependent, the molecular target of such vaccines is to generate at least 50-100 complexes between MHC molecule and the antigenic peptide per antigen-presenting cell, sensitizing a T cell population of appropriate clonal size and effector characteristics. Thus, the immunobiology of antigen recognition by T cells must be taken into account when designing new generation peptide- or gene-based vaccines....
Tipo: Info:eu-repo/semantics/article Palavras-chave: Vaccines; MHC; Antigen recognition; Antigen processing; T cells; Molecular evolution.
Ano: 1999 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X1999000200008
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Molecular characterization of SSS139, a new satellite DNA family in sibling species of the Drosophila buzzatii cluster Genet. Mol. Biol.
Franco,Fernando F.; Sene,Fabio M.; Manfrin,Maura H..
We characterized sequences of a novel SSS139 RsaI satellite DNA family in Drosophila gouveai and Drosophila seriema, two members of the Drosophila buzzatii cluster (D. repleta group). The sequences were AT-rich (69%) with a monomer unit length of about 139 bp and contained two direct subrepeats of 14 bp and 16 bp, suggesting that it might have originated by the duplication of smaller sequences. Southern and dot-blot hybridization analyses also detected SSS139 in other Drosophila buzzatii cluster species (D. koepferae, D. antonietae, D. borborema and D. serido) but not in D. buzzatii. These results agree with the marginal phylogenetic position of D. buzzatii within the D. buzzatii cluster.
Tipo: Info:eu-repo/semantics/other Palavras-chave: Drosophila buzzatii cluster; Molecular evolution; Repetitive DNA; Satellite DNA; SSS139 satellite DNA.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000100026
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Molecular evolution and functional divergence of alcohol dehydrogenases in animals, fungi and plants Genet. Mol. Biol.
Thompson,Claudia E.; Freitas,Loreta B.; Salzano,Francisco M..
Abstract Alcohol dehydrogenases belong to the large superfamily of medium-chain dehydrogenases/reductases, which occur throughout the biological world and are involved with many important metabolic routes. We considered the phylogeny of 190 ADH sequences of animals, fungi, and plants. Non-class III Caenorhabditis elegans ADHs were seen closely related to tetrameric fungal ADHs. ADH3 forms a sister group to amphibian, reptilian, avian and mammalian non-class III ADHs. In fishes, two main forms are identified: ADH1 and ADH3, whereas in amphibians there is a new ADH form (ADH8). ADH2 is found in Mammalia and Aves, and they formed a monophyletic group. Additionally, mammalian ADH4 seems to result from an ADH1 duplication, while in Fungi, ADH formed clusters...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Glycolytic proteins; Molecular evolution; Alcohol dehydrogenase; Functional diversification; Positive selection.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200341
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Molecular evolution in bacteria: cell division Rev. Microbiol.
Trevors,J.T..
Molecular evolution in bacteria is examined with an emphasis on the self-assembly of cells capable of primitive division and growth during early molecular evolution. Also, the possibility that some type of encapsulation structure preceeded biochemical pathways and the assembly of genetic material is examined. These aspects will be considered from an evolutionary perspective.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Cell division; Molecular evolution; Bacteria; Self-assembly.
Ano: 1998 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37141998000400001
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Novel 12S mtDNA findings in sloths (Pilosa, Folivora) and anteaters (Pilosa, Vermilingua) suggest a true case of long branch attraction Genet. Mol. Biol.
Barros,Maria Claudene; Sampaio,Iracilda; Schneider,Horacio.
We sequenced 12S RNA mtDNA for the majority of the extant species of sloths and anteaters and compared our results with previous data obtained by our group using 16S RNA mtDNA in the same specimens and to GenBank sequences of the extinct giant sloth Mylodon. Our results suggest that pigmy-anteaters may be a case of the long-branch attraction phenomenon and also show the large genetic difference between the Amazonian and Atlantic forest three-toed sloths, contrasting with the small differences observed between the two non-Atlantic forest forms of sloths. These results have important implications for the taxonomy of sloths and anteaters and strongly suggest the placement of pigmy anteaters in their own family (Cyclopidae) and raising the taxonomic status of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Anteaters; Molecular evolution; Mylodont; Sloths; Xenarthra.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000400029
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Nucleotide diversity and molecular evolution of the WAG-2 gene in common wheat (Triticum aestivum L) and its relatives Genet. Mol. Biol.
Wei,Shuhong; Peng,Zhengsong; Zhou,Yonghong; Yang,Zaijun; Wu,Kai; Ouyang,Zhongming.
In this work, we examined the genetic diversity and evolution of the WAG-2 gene based on new WAG-2 alleles isolated from wheat and its relatives. Only single nucleotide polymorphisms (SNP) and no insertions and deletions (indels) were found in exon sequences of WAG-2 from different species. More SNPs and indels occurred in introns than in exons. For exons, exons+introns and introns, the nucleotide polymorphism Π decreased from diploid and tetraploid genotypes to hexaploid genotypes. This finding indicated that the diversity of WAG-2 in diploids was greater than in hexaploids because of the strong selection pressure on the latter. All dn/ds ratios were < 1.0, indicating that WAG-2 belongs to a conserved gene affected by negative selection. Thirty-nine of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Copy number variation; Genetic diversity; Molecular evolution; Triticum; WAG-2.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000400013
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Organization and variation of mitochondrial DNA control region in pleurodiran turtles Rev. Bras. Zool.
Wang,Ling; Zhou,Xuming; Nie,Liuwang.
Three complete mitochondrial DNA (mtDNA) control regions (CRs) of Chelodina rugosa (Ogilby, 1890), Chelus fimbriata (Schneider, 1783), and Podocnemis unifilis (Troschel, 1848) were firstly determined using Long-PCR method and the length were 1,016 bp, 1,149 bp, and 985bp, respectively. Together with CRs of Pelomedusa subrufa (Bonnaterre, 1789) and nearly complete CR of Podocnemis expansa (Schweigger, 1812) obtained from GenBank, the structural and evolutionary characteristics of mtDNA CRs in pleurodiran turtle were analyzed in this study. We identified three functional domains (TAS, CD, and CSB domains) as well as their conservation sequences (TAS, CSB-F, and CSB-1) according to their homology to those of other turtles. Within the TAS domain, an...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Control region; CSB; Mitochondrial DNA; Molecular evolution; Pleurodira.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1984-46702011000400011
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Oxytocin and arginine vasopressin receptor evolution: implications for adaptive novelties in placental mammals Genet. Mol. Biol.
Paré,Pamela; Paixão-Côrtes,Vanessa R.; Tovo-Rodrigues,Luciana; Vargas-Pinilla,Pedro; Viscardi,Lucas Henriques; Salzano,Francisco Mauro; Henkes,Luiz E.; Bortolini,Maria Catira.
Abstract Oxytocin receptor (OXTR) and arginine vasopressin receptors (AVPR1a, AVPR1b, and AVPR2) are paralogous genes that emerged through duplication events; along the evolutionary timeline, owing to speciation, numerous orthologues emerged as well. In order to elucidate the evolutionary forces that shaped these four genes in placental mammals and to reveal specific aspects of their protein structures, 35 species were selected. Specifically, we investigated their molecular evolutionary history and intrinsic protein disorder content, and identified the presence of short linear interaction motifs. OXTR seems to be under evolutionary constraint in placental mammals, whereas AVPR1a, AVPR1b, and AVPR2 exhibit higher evolutionary rates, suggesting that they...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Oxytocin receptor; Arginine vasopressin receptors; Molecular evolution; Protein disorder; Interaction motifs.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000400646
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Oxytocin and arginine vasopressin systems in the domestication process Genet. Mol. Biol.
Fam,Bibiana S.O.; Paré,Pamela; Felkl,Aline B.; Vargas-Pinilla,Pedro; Paixão-Côrtes,Vanessa R.; Viscardi,Lucas Henriques; Bortolini,Maria Cátira.
Abstract Domestication is of unquestionable importance to the technological revolution that has given rise to modern human societies. In this study, we analyzed the DNA and protein sequences of six genes of the oxytocin and arginine vasopressin systems (OXT-OXTR; AVP-AVPR1a, AVPR1b and AVPR2) in 40 placental mammals. These systems play an important role in the control of physiology and behavior. According to our analyses, neutrality does not explain the pattern of molecular evolution found in some of these genes. We observed specific sites under positive selection in AVPR1b (ω = 1.429, p = 0.001) and AVPR2 (ω= 1.49, p = 0.001), suggesting that they could be involved in behavior and physiological changes, including those related to the domestication...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Oxytocin and receptors; Vasopressin and receptors; Animal domestication; Molecular evolution; Positive selection.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200235
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Unraveling the evolutionary scenario of the hobo element in populations of Drosophila melanogaster and D. simulans in South America using the TPE repeats as markers Genet. Mol. Biol.
Ragagnin,Geovani T.; Bernardo,Larissa P.; Loreto,Elgion L. S..
Abstract Transposable elements (TEs) are nucleotide sequences found in most studied genomes. These elements are highly diversified and have a large variation in nucleotide structure and mechanisms of transposition. hobo is a member of class II, belonging to hAT superfamily, described inDrosophila melanogaster, and it presents in its Open Reading Frame, a repetitive region encoding the amino acids threonine-proline-glutamic acid (TPE), which shows variability in the number of repeats in some regions of the world. Due to this variability some evolutionary scenarios of the hobo element are discussed, such as the scenario of the invasion of hobo element in populations ofD. melanogaster. In the present study, we investigated 22 DNA sequences of D. melanogaster...
Tipo: Info:eu-repo/semantics/other Palavras-chave: Transposable elements; Transposons; HAT; Genomic evolution; Molecular evolution.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000100145
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