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A morphology-based phylogeny of Phymaturus (Iguania: Liolaemidae) with the description of four new species from Argentina Pap. Avulsos de Zool. (São Paulo)
Lobo,Fernando; Quinteros,Sebastián.
Phylogenetic relationships within the liolaemid lizard genus Phymaturus were studied using parsimony analysis of morphological data. The data set includes 133 characters: 28 described in the literature as apomorphies of the three genera of Liolaemidae (Ctenoblepharys, Liolaemus, and Phymaturus), 21 published characters of allozymes and karyology, 53 characters taken from external morphology across all terminals of Phymaturus, and 31 from the skeletal anatomy. This data set includes representatives of 10 of the 12 species currently recognized in the literature plus twelve other terminals considered in this study and representing independent lineages assigned to patagonicus or palluma. Four of these terminals are described in the present study as new...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Liolaemidae; Phymaturus; New species; Morphology; Phylogenetic analysis.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0031-10492005001300001
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Analysis of the nucleotide sequence of the coat protein and 3'-untranslated region of two Brazilian Potato virus Y isolates Trop. Plant Pathol.
INOUE-NAGATA,ALICE K.; FONSECA,M. ESTHER N.; LOBO,TATIANA O.T.A.; ÁVILA,ANTÔNIO C. DE; MONTE,DAMARES C..
Two Brazilian Potato virus Y (PVY) isolates were biologically characterized as necrotic (PVY-NBR) and common (PVY-OBR) based upon symptoms on test plants. Additional characterization was performed by sequencing a cDNA corresponding to the 3' terminal region of the viral genome. The sequence consisted of 195 nucleotides (nt) coding part of the nuclear inclusion body b (NIb) gene, 804 nt of the coat protein (CP) gene, and 328 nt (PVY-OBR) or 326 nt (PVY-NBR) of the 3'-untranslated region (UTR). Translation of the sequence resulted in one single open reading frame with part of the NIb and a CP of 267 amino acids. The two isolates shared 95.1% similarity in the CP amino acid sequence. The CP and the 3'-UTR sequence of the Brazilian isolates were compared to...
Tipo: Info:eu-repo/semantics/article Palavras-chave: PVY; Potyvirus; Phylogenetic analysis; Taxonomy; Coat protein.
Ano: 2001 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-41582001000100008
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Biological and molecular characterization of two Brazilian isolates of Apple stem grooving virus. Repositório Alice
SOUZA, E. B.; NICKEL, O.; FAJARDO, T. V. M.; SILVA, J. M. F.; BARROS, D. R..
Abstract Apple stem grooving virus (ASGV, genus Capillovirus) is disseminated worldwide, usually causing a latent infection in most commercial apple cultivars. However, infected scions grafted onto sensitive material display reduction of yield, loss of fruit quality and tree decline. In Brazil ASGV is associated with severe phloem necrosis, xylem pitting and decline of apple trees on Maruba-kaido (Malus prunifolia cv. Ringo) rootstocks usually in a complex with other latent viruses. Two Brazilian ASGV isolates from a mixed infection causing differing reactions on apple cv. Fuji on Maruba-kaido rootstocks, i.e., normal growth vs. tree decline, have been completely sequenced. The differing intensity of symptoms they co-induced on several woody indicator...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Apple virus; ASGV (Apple stem grooving virus); Recombination; Phylogenetic analysis.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1071609
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Characterization and expression analysis of WOX2 homeodomain transcription factor in Aegilops tauschii Genet. Mol. Biol.
Zhao,Shan; Jiang,Qian-Tao; Ma,Jian; Wang,Ji-Rui; Liu,Ya-Xi; Chen,Guo-Yue; Qi,Peng-Fei; Pu,Zhi-En; Lu,Zhen-Xiang; Zheng,You-Liang; Wei,Yu-Ming.
The WUSCHEL (WUS)-related homeobox (WOX) gene family coordinates transcription during the early phases of embryogenesis. In this study, a putative WOX2 homolog was isolated and characterized from Aegilops tauschii, the donor of D genome of Triticum aestivum. The sequence consisted of 2045 bp, and contained an open reading frame (ORF), encoded 322 amino acids. The predicted protein sequence contained a highly conserved homeodomain and the WUS-box domain, which is present in some members of the WOX protein family. The full-length ORF was subcloned into prokaryotic expression vector pET-30a, and an approximately 34-kDa protein was expressed in Escherichia coli BL21 (DE3) cells with IPTG induction. The molecular mass of the expressed protein was identical to...
Tipo: Info:eu-repo/semantics/article Palavras-chave: WOX2; Aegilops tauschii; Phylogenetic analysis; Real-time quantitative PCR.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572015000100079
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Cladistic analysis of the family Stenothoidae (Amphipoda, Crustacea) Naturalis
Krapp-Schickel, T.; Koenemann, S..
The amphipod family Stenothoidae contains more than 200 species in about 40 genera; these genera are at present often defined not by the presence, but by the absence of synapomorphies, thus defining grades rather than clades. Our phylogenetic analyses yielded 4 groups of stenothoids: a basic proboloidid clade; an advanced and always clearly separated Austral-Antarctic thaumatelsonid clade, with a possibly related Arctic mesometopid clade; and finally a poorly resolved group, the stenothoids sensu stricto, including the large and probably polyphyletic genera Stenothoe and Metopa, each with more than 50 species. It is proposed to study and analyse these groups separately in future, based on better redescriptions of the individual species. Our analyses...
Tipo: Article / Letter to the editor Palavras-chave: Taxonomy; Amphipoda; Stenothoidae; Thaumatelsonidae; Phylogenetic analysis; 42.74.
Ano: 2006 URL: http://www.repository.naturalis.nl/record/214545
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Comparative analysis of the genes UL1 through UL7 of the duck enteritis virus and other herpesviruses of the subfamily Alphaherpesvirinae Genet. Mol. Biol.
Li,Huixin; Liu,Shengwang; Han,Zongxi; Shao,Yuhao; Chen,Shuhong; Kong,Xiangang.
The nucleotide sequences of eight open reading frames (ORFs) located at the 5' end of the unique long region of the duck enteritis virus (DEV) Clone-03 strain were determined. The genes identified were designated UL1 , UL2 , UL3 , UL4 , UL5 , UL6 and UL 7 homologues of the herpes simplex virus 1 (HSV-1). The DEV UL3.5 located between UL3 and UL4 had no homologue in the HSV-1. The arrangement and transcription orientation of the eight genes were collinear with their homologues in the HSV-1. Phylogenetic trees were constructed based on the alignments of the deduced amino acids of eight proteins with their homologues in 12 alpha-herpesviruses. In the UL1, UL3, UL3.5, UL5 and UL7 proteins trees, the branches were more closely related to the genus...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Duck enteritis virus; UL1-UL7 genes; Phylogenetic analysis.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000100018
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Deep-sea Hydrothermal Vent Bacteria as a Source of Glycosaminoglycan-Mimetic Exopolysaccharides ArchiMer
Zykwinska, Agata; Marchand, Laetitia; Bonnetot, Sandrine; Sinquin, Corinne; Colliec-jouault, Sylvia; Delbarre-ladrat, Christine.
Bacteria have developed a unique strategy to survive in extreme environmental conditions through the synthesis of an extracellular polymeric matrix conferring upon the cells a protective microenvironment. The main structural component of this complex network constitutes high-molecular weight hydrophilic macromolecules, namely exopolysaccharides (EPS). EPS composition with the presence of particular chemical features may closely be related to the specific conditions in which bacteria evolve. Deep-sea hydrothermal vent bacteria have already been shown to produce EPS rich in hexosamines and uronic acids, frequently bearing some sulfate groups. Such a particular composition ensures interesting functional properties, including biological activities mimicking...
Tipo: Text Palavras-chave: Exopolysaccharide; Glycosaminoglycan; Uronic acid; Hexosamine; Phylogenetic analysis.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00506/61756/65728.pdf
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Discovery and partial characterization of a novel virus, tentatively named Grapevine virgalike virus. Repositório Alice
SILVA, J. M. F.; PEREIRA, B. R. de M.; AI RWAHNÍH, M.; BLAWID, R.; BLAWID, R.; NAGATA, T.; FAJARDO, T. V. M..
The families Bromoviridae and Virgaviridae are composed of viruses with a single-stranded positive sense RNA genome possessing an alpha-like replication complex and a 3'-t-RNA-like structure.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Grapevine virgalike virus; Phylogenetic analysis; High-throughput sequencing (HTS); Bromoviridae; Virgaviridae; Nucleotides; Viruses.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1090655
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Disentangling the Trichoderma viridescens complex Naturalis
Jaklitsch, W.M.; Samuels, G.J.; Ismaiel, A.; Voglmayr, H..
Trichoderma viridescens is recognised as a species complex. Multigene analyses based on the translation elongation factor 1-alpha encoding gene (tef1), a part of the rpb2 gene, encoding the second largest RNA polymerase subunit and the larger subunit of ATP citrate lyase (acl1) reveals 13 phylogenetic species with little or no phenotypic differentiation. This is the first use of acl1 in Trichoderma phylogenetics. The typification of T. viridescens s.str. is clarified and Hypocrea viridescens is replaced by the new name T. paraviridescens. Besides these two species, eleven are phylogenetically recognised and T. olivascens, T. viridarium, T. virilente, T. trixiae, T. viridialbum, T. appalachiense, T. neosinense, T. composticola, T. nothescens and T....
Tipo: Article / Letter to the editor Palavras-chave: Acl1; Hypocrea; Hypocreaceae; Phylogenetic analysis; Rpb2; Systematics; Tef1.
Ano: 2013 URL: http://www.repository.naturalis.nl/record/532266
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Distribution of human immunodeficiency virus type 1 subtypes in the state of Amazonas, Brazil, and subtype C identification BJMBR
Cunha,L.K.H.; Kashima,S.; Amarante,M.F.C.; Haddad,R.; Rodrigues,E.S.; Silva,K.L.T.; Lima,T.A.; Castro,D.B.; Brito,F.C.; Almeida,E.G.; Covas,D.T.; Malheiro,A..
Few studies have reported the molecular epidemiological characterization of HIV-1 in the Northern region of Brazil. The present study reports the molecular and epidemiological characterization of 31 HIV-1 isolates from blood donors from the State of Amazonas who donated blood between April 2006 and March 2007. Serum/plasma samples from all donors were screened for HIV antibodies by ELISA and the results confirmed by Western blot analysis. Genomic DNA was extracted from the buffy coat using the Super Quik-Gene-DNA Isolation kit. Nested PCR was performed on the env, gag, and pol regions of HIV-1 using the Gene Amp PCR System 9700. Sequencing reactions were performed using the inner PCR primers and the DYEnamic™ ET Dye Terminator Kit, and phylogenetic...
Tipo: Info:eu-repo/semantics/article Palavras-chave: HIV-1; Subtypes; Phylogenetic analysis; Blood donors; Molecular and epidemiological characterization.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2012000200003
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Diversity analysis of Bemisia tabaci biotypes: RAPD, PCR-RFLP and sequencing of the ITS1 rDNA region Genet. Mol. Biol.
Rabello,Aline R.; Queiroz,Paulo R.; Simões,Kenya C.C.; Hiragi,Cássia O.; Lima,Luzia H.C.; Oliveira,Maria Regina V.; Mehta,Angela.
The Bemisia tabaci complex is formed by approximately 41 biotypes, two of which (B and BR) occur in Brazil. In this work we aimed at obtaining genetic markers to assess the genetic diversity of the different biotypes. In order to do that we analyzed Bemisia tabaci biotypes B, BR, Q and Cassava using molecular techniques including RAPD, PCR-RFLP and sequencing of the ITS1 rDNA region. The analyses revealed a high similarity between the individuals of the B and Q biotypes, which could be distinguished from the BR individuals. A phylogenetic tree based on ITS1 rDNA sequence was constructed. This is the first report of the ITS1 rDNA sequence of Bemisia tuberculata and of the BR biotype of B. tabaci.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Whitefly; ITS rDNA; Genetic diversity; Phylogenetic analysis.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000300029
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Diversity of foliar endophytic fungi from the medicinal plant Sapindus saponaria L . and their localization by scanning electron microscopy Biol. Res.
García,Adriana; Rhoden,Sandro A; Rubin Filho,Celso J; Nakamura,Celso V; Pamphile,João A.
Endophytic fungi inhabit vegetable tissues or organs, without causing them any harm. Endophytes can co-evolve with plant hosts and possess species-specific interactions. They can protect the plant from insect attacks and diseases, and are also able to produce substances of biotechnological interest. In folk medicine, the bark, roots and fruits of Sapindus saponaria is used to produce substances with anxiolytic, astringent, diuretic and expectorant properties, as well as tonics, blood depuratives and cough medicine. This study evaluated the diversity of endophytic fungi present in the leaves of S. saponaria L. and observed the colonization of host plants by endophytes, using light and scanning electron microscopy. We verified that these fungi are found in...
Tipo: Journal article Palavras-chave: Endophyte; Light microscopy; Phylogenetic analysis; SEM.
Ano: 2012 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602012000200006
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Four new species in Habenaria (Orchidaceae) from the Espinhaço Range, Brazil. Repositório Alice
BATISTA, J. A. N.; VALE, A. A.; CARVALHO, B. M.; PROITE, K.; RAMALHO, A. J.; MUNHOZ, A. C. D.; BERG, C. van den; BIANCHETTI, L. B..
bitstream/item/180665/1/036364416x691858.pdf
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Campo rupestre; Endemism; Minas Gerais; Phylogenetic analysis.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1059112
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Full-Length Genomic Characterization of Chicken Anemia Virus in Turkey Rev. Bras. Ciênc. Avic.
Aşkar,S.
ABSTRACT Chicken infectious anemia (CIA) is an immune-suppressive disease caused by chicken anemia virus (CAV). It is characterized by lymphoid atrophy, aplastic anemia, especially in chicks. In this study, full-length genomic characterization of CAV DNA from the broiler flocks in Turkey and phylogenetic analysis were aimed. In the study, CAV DNA were found positive for 37 (53%) flocks with PCR studies from thymus tissues of each 70 broiler flocks. And 17 purified CAV DNA PCR products from these 37 CAV isolates were full length sequenced with the NGS method (Illumina MiSeq). Also with the phylogenetic analyses, full length PCR products of 17 purified CAV isolates have been determined as 2298bp genome size and 99% similarity with each other. The highest...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Broiler; Chicken Infectious Anemia; Phylogenetic analysis.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2019000300323
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Genetic analysis of the porcine group B rotavirus NSP2 gene from wild-type Brazilian strains BJMBR
Médici,K.C.; Barry,A.F.; Alfieri,A.F.; Alfieri,A.A..
Group B rotaviruses (RV-B) were first identified in piglet feces, being later associated with diarrhea in humans, cattle, lambs, and rats. In human beings, the virus was only described in China, India, and Bangladesh, especially infecting adults. Only a few studies concerning molecular analysis of the RV-B NSP2 gene have been conducted, and porcine RV-B has not been characterized. In the present study, three porcine wild-type RV-B strains from piglet stool samples collected from Brazilian pig herds were used for analysis. PAGE results were inconclusive for those samples, but specific amplicons of the RV-B NSP2 gene (segment 8) were obtained in a semi-nested PCR assay. The three porcine RV-B strains showed the highest nucleotide identity with the human WH1...
Tipo: Info:eu-repo/semantics/other Palavras-chave: Piglets; Diarrhea; Group B rotavirus; NSP2 gene; Phylogenetic analysis.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2010000100003
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Genetic diversity and phylogenetic relationships of annual and perennial Glycine species. Repositório Alice
HWANG, E.-Y.; WEI, H.; SCHROEDER, S. G.; FICKUS, E. W.; QUIGLEY, C. V.; ELIA, P.; ARAYA, S.; DONG, F.; COSTA, L.; FERREIRA, M. E.; CREGAN, P. B.; SONG, Q..
bitstream/item/202511/1/2325.full.pdf
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Divergence; Nucleotide diversity; Perennial crop relatives; Phylogenetic analysis; Trans-specific polymorphism; Soybeans.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1112726
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Genome-wide Analysis of LBD (LATERAL ORGAN BOUNDARIES Domain) Gene Family in Brassica rapa BABT
Huang,Xiaoyun; Liu,Gang; Zhang,Weiwei.
ABSTRACT LOB (lateral organ boundaries)-domain proteins define a family of plant-specific transcription factors involved in developmental process from embryogenesis to seed production. They play a crucial role in shaping the plant architecture through coordinating cell fate at meristem to organ boundaries. Identification of LBD genes from Brassica rapa genome, and analysis of phylogeny,gene structure, chromosome location, phylogenetic and tissue expression pattern analysis of LBD family genes in Chinese cabbage will be useful to the functions identification of plant LBD genes. Based on Brassica rapa genome database and bioinformatic method, Chinese cabbage LBD family genes were identified and the genes were sequenced. A phylogenetic tree was created using...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Brassica rapa; LBD; Phylogenetic analysis; Gene expression; Genome-wide.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132018000100439
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Genome-wide characterization of the NRAMP gene family in Phaseolus vulgaris provides insights into functional implications during common bean development Genet. Mol. Biol.
Ishida,Juliane Karine; Caldas,Danielle G.G.; Oliveira,Lucas Roberto; Frederici,Gabriela Campos; Leite,Lucas Margato Pereira; Mui,Tsai Siu.
Abstract Transporter proteins play an essential role in the uptake, trafficking and storage of metals in plant tissues. The Natural Resistance-Associated Macrophage Protein (NRAMP) family plays an essential role in divalent metal transport. We conducted bioinformatics approaches to identify seven NRAMP genes in the Phaseolus vulgaris genome, investigated their phylogenetic relation, and performed transmembrane domain and gene/protein structure analyses. We found that the NRAMP gene family forms two distinct groups. One group included the PvNRAMP1, -6, and -7 genes that share a fragmented structure with a numerous exon/intron organization and encode proteins with mitochondrial or plastidial localization. The other group is characterized by few exons that...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Phaseolus vulgaris; Transporter; NRAMP; Gene family; Phylogenetic analysis.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000500820
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Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers Genet. Mol. Biol.
Hu,Lifang; Liu,Shiqiang.
Members of the ERF transcription-factor family participate in a number of biological processes, viz., responses to hormones, adaptation to biotic and abiotic stress, metabolism regulation, beneficial symbiotic interactions, cell differentiation and developmental processes. So far, no tissue-expression profile of any cucumber ERF protein has been reported in detail. Recent completion of the cucumber full-genome sequence has come to facilitate, not only genome-wide analysis of ERF family members in cucumbers themselves, but also a comparative analysis with those in Arabidopsis and rice. In this study, 103 hypothetical ERF family genes in the cucumber genome were identified, phylogenetic analysis indicating their classification into 10 groups, designated I to...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Cucumis sativus L.; ERF; Phylogenetic analysis; Transcription factor; Genome sequence.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000400015
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Identification and characterization of Fusarium mangiferae as pathogen of mango malformation in India BABT
Kumar,Pradeep; Kamle,Madhu; Misra,Asok Kumar; O'Donovan,Anthonia; Pagano,Marcela; Modi,Dinesh Raj.
ABSTRACT Fusarium mangiferae (=F. subglutinans) isolates collect from malformed samples from major mango-growing area of North India. Molecular identification and characterization of eleven most virulent isolates of F. mangiferae, based on pathogenicity tests used for the present study. Species-specific, genus specific ITS-PCR and PCR-RFLP performed for the accurate and easy detection of F. mangiferae. The rDNA-ITS 28S region sequences used for phylogenetic analysis of Fusarium isolates from India and other countries for homology search between them. The phylogenetic tree divided the isolates into three clades (i.e., American, Asian and African) and showed the high level of sequence based similarity (69-99%) among all Fusarium sequences from Asia. Thus,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Fusarium mangiferae; Detection; Phylogenetic analysis; Vegetative malformation; Floral malformation..
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132016000100204
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