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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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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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Phylogeny and biogeography of the Ergasilidae (Copepoda, Poecilostomatoida), with reconsideration of the taxonomic status of the Vaigamidae Naturalis
Pinto da Motta Amado, Maria Auxiliadora; Ho, Ju-Shey; Falavigna da Rocha, Carlos Eduardo.
Nineteen genera are currently considered valid in the Ergasilidae. A cladistic analysis was conducted on these genera and the five genera composing the closely allied Vaigamidae. Nineteen morphological characters were selected and polarized using Anthessius (Anthessiidae) as the outgroup. The most parsimonious cladogram (tree length = 60, Consistency Index = 0.50, Retention Index = 0.71), obtained through the use of the BB command in Hennig 86, is composed of eight major clades, with the five vaigamid genera composing the most derived clade. Based on Wiley’s (1981) “sequencing” convention, the five vaigamid genera cannot be placed in a family separate from the Ergasilidae. The biogeography of the ergasilid genera is discussed. Vaigamus spinicephalus is...
Tipo: Article / Letter to the editor Palavras-chave: Phylogenetic analysis; Biogeography; Copepoda; Poecilostomatoida; Ergasilidae; Vaigamidae; Pseudovaigamus gen. n.
Ano: 1995 URL: http://www.repository.naturalis.nl/record/503932
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Taxonomic revision and phylogenetic relationships of Dasyloricaria Isbrücker & Nijssen, 1979 (Siluriformes: Loricariidae), with description of a new species Neotropical Ichthyology
Londoño-Burbano,Alejandro; Reis,Roberto E..
ABSTRACT A taxonomic revision and phylogenetic analysis were completed for Dasyloricaria . The genus includes three valid species: D . filamentosa and D . latiura previously included in the genus, and a new species described herein. Dasyloricaria have a restricted trans-Andean distribution, with D . filamentosa occurring at the lower and middle Magdalena, lower Cauca, and Sinu in Colombia, and lago Maracaibo basin in Colombia and Venezuela; D . latiura in the Atrato and the Tuyra basins in Colombia and Panama, respectively; and the new species in the upper and middle Magdalena basin in Colombia. New synonyms for D . filamentosa and D . latiura are proposed, and a lectotype is designated for the latter. Dasyloricaria is herein recognized as monophyletic,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Armored catfishes; Identification key; Loricariinae; Northwestern South America; Phylogenetic analysis.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252016000100217
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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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Phylogenetic and Pathotypic Characterization of a Newcastle Disease Virus Strain Isolated from Ducks and Pigeons in Hubei, China Rev. Bras. Ciênc. Avic.
Wang,Y; Zhang,H; Gu,C; Cheng,G; Zhang,W; Mehmood,K; Hu,X.
ABSTRACT Newcastle disease is a highly contagious disease responsible for major outbreaks and considerable economic losses in the poultry industry in China. There is still little information available regarding gene characterization of the NDV, especially in ducks and pigeons. Therefore, the aim of this study was to investigate NDV isolated from ducks and pigeons in Hubei, China. In this study, three NDVs from ducks and pigeons were isolated between 2013 and 2015.The fusion protein (F) gene of the NDV isolates was sequenced and phylogenetically analyzed. The clinical signs and gross histopathological lesions were examined. Phylogenetic analysis of these strains indicated that all the sequences are classified as genotype II. The isolates shared a 112...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Newcastle disease virus; Phylogenetic analysis; Pathology; Ducks; Pigeons..
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2018000100145
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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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Molecular Identification of Trichoderma spp. in Garlic and Onion Fields and In Vitro Antagonism Trials on Sclerotium cepivorum Rev. Bras. Ciênc. Solo
and,Luis Alvarado-Marchena; Rivera-Méndez,William.
ABSTRACT Trichoderma species are non-pathogenic microorganisms that protect against fungal diseases and contribute to increased crop yields. However, not all Trichoderma species have the same effects on crop or a pathogen, whereby the characterization and identification of strains at the species level is the first step in the use of a microorganism. The aim of this study was the identification – at species level – of five strains of Trichoderma isolated from soil samples obtained from garlic and onion fields located in Costa Rica, through the analysis of the ITS1, 5.8S, and ITS2 ribosomal RNA regions; as well as the determination of their individual antagonistic ability over S. cepivorum Berkeley. In order to distinguish the strains, the amplified products...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Ribosomal RNA; Antagonistic test; Phylogenetic analysis.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-06832016000100404
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Morphological and molecular characterization of Pisolithus in soil under eucalyptus plantations in Brazil Rev. Bras. Ciênc. Solo
Kasuya,Maria Catarina Megumi; Coelho,Irene da Silva; Campos,Daniela Tiago da Silva; Araújo,Elza Fernandes de; Tamai,Yutaka; Miyamoto,Toshizumi.
Eighteen Pisolithus basidiomes were collected from Eucalyptus plantations in the state of Minas Gerais, Brazil. These basidiomes were characterized morphologically and molecularly. The basidiomes varied in shape, color and size. One of them was found underground, indicating a hypogeous fungus. The main morphological distinctive characteristic was spore ornamentation, which distinguished two groups. One group with short and erect spines was identified as Pisolithus microcarpus, and the other with long and curved spines as Pisolithus marmoratus, after analyzing the cladogram obtained by phylogenetic relationship based on internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA of these isolates.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Ectomycorrhizal fungus; Phylogenetic analysis; Internal transcribed spacer (ITS); Nuclear ribosomal DNA; Taxonomy.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-06832010000600013
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Molecular cloning and expression patterns of the Vasa gene from Rana nigromaculata (Amphibia: Anura) Rev. Bras. Zool.
Jia,Rui; Nie,Liu-Wang; Wang,Ning; Wang,Jingjing.
The Vasa protein is a member of the DEAD (Asp-Glu-Alu-Asp) box family of ATP-dependent RNA helicases. The Vasa gene is specifically expressed in germ-line cells of many metazoans and is known to play a critical role in gametogenesis and reproductive regulation. In this paper, we isolate the full length cDNA sequence of the Vasa gene from the frog Rana nigromaculata Hallowell, 1861. The open reading frame (ORF) encoding 398 amino acid residues has nine conserved motifs. According to the similarities at the amino acid sequenceythe phylogenetic analysis of Vasa gene was consistent with the evolution relationships from chordates to mammals. Furthermore, the expression pattern analysis of RnVasa mRNA, using the technique of Reverse Transcriptase-Polymerase...
Tipo: Info:eu-repo/semantics/article Palavras-chave: DEAD-box; Phylogenetic analysis; RT-PCR.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1984-46702009000200014
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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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Sequences of the coat protein gene from brazilian isolates of Papaya ringspot virus Trop. Plant Pathol.
LIMA,ROBERTO C. A.; SOUZA JR.,MANOEL T.; PIO-RIBEIRO,GILVAN; LIMA,J. ALBERSIO A..
Papaya ringspot virus (PRSV) is the causal agent of the main papaya (Carica papaya) disease in the world. Brazil is currently the world's main papaya grower, responsible for about 40% of the worldwide production. Resistance to PRSV on transgenic plants expressing the PRSV coat protein (cp) gene was shown to be dependent on the sequence homology between the cp transgene expressed in the plant genome and the cp gene from the incoming virus, in an isolate-specific fashion. Therefore, knowledge of the degree of homology among the cp genes from distinct PRSV isolates which are present in a given area is important to guide the development of transgenic papaya for the control of PRSV in that area. The objective of the present study was to assess the degree of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Potyvirus; Carica papaya; PRSV; Phylogenetic analysis.
Ano: 2002 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-41582002000200009
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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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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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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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Virus isolation and genotype identification of human respiratory syncytial virus in Guizhou Province, China BJID
Zhao,Ting; Ye,Zhixu; Wang,Binlin; Cui,Yuxia; Nie,Yingjie; Yang,Bin; Chen,Kun; Zhang,Hua; Hu,Fangfang; Yu,Fuxun.
ABSTRACT To investigate the genetic variation and molecular epidemiology characteristics of Human Respiratory Syncytial Virus (HRSV) in Guizhou Province, nasopharyngeal aspirates were collected from patients with acute respiratory infection (ARI) in Guizhou Provincial People's Hospital, from December 2017 to March 2018, and inoculated to Hep-2 cells to isolate HRSV. Cells that showed cytopathic effect (CPE) were then confirmed by indirect immunofluorescence assay and reverse transcription. The sequence of the PCR products was determined for HRSV isolates, and the genetic variation was analyzed. Out of 196 nasopharyngeal aspirate samples, HRSV were isolated in 39. The second hypervariable region at the 3' terminal of glycoprotein gene (HVR2) sequence...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Human respiratory syncytial virus; Virus isolation; RT-PCR; HVR2; Phylogenetic analysis; Molecular epidemiology.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702019000600427
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Phylogenetic analysis of the emergence of main hepatitis C virus subtypes in São Paulo, Brazil BJID
Nishiya,Anna Shoko; Almeida-Neto,César de; Romano,Camila Malta; Alencar,Cecília Salete; Ferreira,Suzete Cleusa; Di-Lorenzo-Oliveira,Claudia; Levi,José Eduardo; Salles,Nanci Alves; Mendrone-Junior,Alfredo; Sabino,Ester Cerdeira.
ABSTRACTBACKGROUND: It is recognized that hepatitis C virus subtypes (1a, 1b, 2a, 2b, 2c and 3a) originated in Africa and Asia and spread worldwide exponentially during the Second World War (1940) through the transfusion of contaminated blood products, invasive medical and dental procedures, and intravenous drug use. The entry of hepatitis C virus subtypes into different regions occurred at distinct times, presenting exponential growth rates of larger or smaller spread. Our study estimated the growth and spread of the most prevalent subtypes currently circulating in São Paulo.METHODS:A total of 465 non-structural region 5B sequences of hepatitis C virus covering a 14-year time-span were used to reconstruct the population history and estimate the population...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Growth rate; HCV; Phylogenetic analysis; Subtypes.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702015000500473
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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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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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Streptococcus iniae outbreaks in Brazilian Nile tilapia (Oreochromis niloticus L: ) farms BJM
Figueiredo,H. C. P.; Nobrega Netto,L.; Leal,C. A. G.; Pereira,Ulisses P.; Mian,Glaúcia F..
This is the first report of outbreaks of Streptococcus iniae in Nile tilapia farms in South America. Seven isolates were identified by biochemical, serological and molecular tests. Their 16S rRNA gene sequences showed 100% similarity with S. iniae ATCC 29178 and two distinct PFGE patterns were observed for Brazilian isolates.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Brazil; Infection; MIC; PFGE; Phylogenetic analysis; Tilapia.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822012000200019
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