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Registro Completo |
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Biblioteca(s): |
Embrapa Semiárido. |
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Data corrente: |
03/10/2022 |
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Data da última atualização: |
17/11/2022 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
MEDEIROS, F. L. B.; SANTOS, C. A. F.; COSTA, A. E. S. |
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Afiliação: |
F. L. B. MEDEIROS, UFRPE; CARLOS ANTONIO FERNANDES SANTOS, CPATSA; A. E. S. COSTA, UFRPE. |
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Título: |
In silico microsatellite transferability from Psidium guajava to Eucalyptus globulus validated by PCR. |
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Ano de publicação: |
2021 |
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Fonte/Imprenta: |
Genetics and Molecular Research, v. 20, n. 4, gmr18985, 2021. |
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DOI: |
http://dx.doi.org/10.4238/gmr18985 |
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Idioma: |
Inglês |
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Conteúdo: |
BLAST is a genomic local alignment search tool used to identify homology between genotypes and possible orthologous genes. In vitro microsatellite transferability is a strategy to enable or increase species molecular fingerprinting, but it is dependent on PCR technique. An initial in silico step using BLAST for transferability can be helpful to save resources in pre-selecting markers more likely to amplify. We aligned and transfered SSR sequences from Psidium guajava to Eucalyptus globulus using BLAST. Twenty-three SSR clone sequences from P. guajava (query) were retrieved from the NCBI website and aligned against the whole genome of E. globulus (subject) using a cut-off e-value<1.00e?20. Another 140 loci retrieved from the GuavaMap project were analyzed using as parameters e-values<1.7 and a maximum distance of 300 nucleotides between forward and reverse sequences. All loci were analyzed using BLASTN with MEGABLAST optimization. DNA extraction of four eucalypt trees was performed with the 2x CTAB protocol containing a sorbitol initial step. Validation of the SSR selected via BLASTN was performed by PCR reactions with 12 loci (seven selected on Blast hits and five without hits) and posterior visualization on polyacrylamide gel. Nine out of 23 microsatellite loci were transferable in the in silico, with a mean identity of 87%. With regard to the GuavaMap microsatellite loci, only three showed significant alignments, among the 140 tested, with the forward and reverse mean identity of 100% and 95%, respectively. All seven SSR with e- values<1.00e?20 (mPgCIR001, mPgCIR005, mPgCIR007, mPgCIR009, mPgCIR018, mPgCIR020, and mPgCIR026) showed easy-to-score amplicons on the polyacrylamide gel when using the in silico transferability strategy. However, the other five, without significant e- values or hits, showed no amplification. These results highlight the effectiveness of in silico transferability for full-length SSR loci, constituting a valid alternative to save time and costs in transferability studies between species. MenosBLAST is a genomic local alignment search tool used to identify homology between genotypes and possible orthologous genes. In vitro microsatellite transferability is a strategy to enable or increase species molecular fingerprinting, but it is dependent on PCR technique. An initial in silico step using BLAST for transferability can be helpful to save resources in pre-selecting markers more likely to amplify. We aligned and transfered SSR sequences from Psidium guajava to Eucalyptus globulus using BLAST. Twenty-three SSR clone sequences from P. guajava (query) were retrieved from the NCBI website and aligned against the whole genome of E. globulus (subject) using a cut-off e-value<1.00e?20. Another 140 loci retrieved from the GuavaMap project were analyzed using as parameters e-values<1.7 and a maximum distance of 300 nucleotides between forward and reverse sequences. All loci were analyzed using BLASTN with MEGABLAST optimization. DNA extraction of four eucalypt trees was performed with the 2x CTAB protocol containing a sorbitol initial step. Validation of the SSR selected via BLASTN was performed by PCR reactions with 12 loci (seven selected on Blast hits and five without hits) and posterior visualization on polyacrylamide gel. Nine out of 23 microsatellite loci were transferable in the in silico, with a mean identity of 87%. With regard to the GuavaMap microsatellite loci, only three showed significant alignments, among the 140 tested, with the forward and reverse mean iden... Mostrar Tudo |
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Palavras-Chave: |
BLAST; Microssatélites in silico; SSR. |
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Thesagro: |
Goiaba; Psidium Guajava; Recurso Genético. |
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Thesaurus Nal: |
Spondias. |
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Categoria do assunto: |
G Melhoramento Genético |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/241070/1/In-silico-microsatellite-transferability-from-Psidium-guajava-to-Eucalyptus-2021.pdf
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Marc: |
LEADER 02789naa a2200241 a 4500
001 2147079
005 2022-11-17
008 2021 bl uuuu u00u1 u #d
024 7 $ahttp://dx.doi.org/10.4238/gmr18985$2DOI
100 1 $aMEDEIROS, F. L. B.
245 $aIn silico microsatellite transferability from Psidium guajava to Eucalyptus globulus validated by PCR.$h[electronic resource]
260 $c2021
520 $aBLAST is a genomic local alignment search tool used to identify homology between genotypes and possible orthologous genes. In vitro microsatellite transferability is a strategy to enable or increase species molecular fingerprinting, but it is dependent on PCR technique. An initial in silico step using BLAST for transferability can be helpful to save resources in pre-selecting markers more likely to amplify. We aligned and transfered SSR sequences from Psidium guajava to Eucalyptus globulus using BLAST. Twenty-three SSR clone sequences from P. guajava (query) were retrieved from the NCBI website and aligned against the whole genome of E. globulus (subject) using a cut-off e-value<1.00e?20. Another 140 loci retrieved from the GuavaMap project were analyzed using as parameters e-values<1.7 and a maximum distance of 300 nucleotides between forward and reverse sequences. All loci were analyzed using BLASTN with MEGABLAST optimization. DNA extraction of four eucalypt trees was performed with the 2x CTAB protocol containing a sorbitol initial step. Validation of the SSR selected via BLASTN was performed by PCR reactions with 12 loci (seven selected on Blast hits and five without hits) and posterior visualization on polyacrylamide gel. Nine out of 23 microsatellite loci were transferable in the in silico, with a mean identity of 87%. With regard to the GuavaMap microsatellite loci, only three showed significant alignments, among the 140 tested, with the forward and reverse mean identity of 100% and 95%, respectively. All seven SSR with e- values<1.00e?20 (mPgCIR001, mPgCIR005, mPgCIR007, mPgCIR009, mPgCIR018, mPgCIR020, and mPgCIR026) showed easy-to-score amplicons on the polyacrylamide gel when using the in silico transferability strategy. However, the other five, without significant e- values or hits, showed no amplification. These results highlight the effectiveness of in silico transferability for full-length SSR loci, constituting a valid alternative to save time and costs in transferability studies between species.
650 $aSpondias
650 $aGoiaba
650 $aPsidium Guajava
650 $aRecurso Genético
653 $aBLAST
653 $aMicrossatélites in silico
653 $aSSR
700 1 $aSANTOS, C. A. F.
700 1 $aCOSTA, A. E. S.
773 $tGenetics and Molecular Research$gv. 20, n. 4, gmr18985, 2021.
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Registro original: |
Embrapa Semiárido (CPATSA) |
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 | Acesso ao texto completo restrito à biblioteca da Embrapa Pantanal. Para informações adicionais entre em contato com cpap.biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Pantanal. |
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Data corrente: |
27/03/2002 |
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Data da última atualização: |
30/03/2017 |
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Autoria: |
PELLEGRIN, A. O.; LEITE, R. C.; LAGE, A. P.; FIGUEIREDO; SERENO, J. R. B. |
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Afiliação: |
Escola de Veterinaria/Curso de Pos Graduacao em Medicina Veterinaria Preventiva. |
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Título: |
Diagnostico da Campilobacteriose Genital Bovina pelo ELISA IgA. |
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Ano de publicação: |
2002 |
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Fonte/Imprenta: |
In: SEMANA DA POS-GRADUACAO DA UFMG, 3., 2002, Belo Horizonte. Anais... Belo Horizonte: UFMG, 2002. nao paginado. |
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Idioma: |
Português |
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Conteúdo: |
Um ensaio imunoenzimatico do tipo indireto para deteccao de imunoglobulinas A (ELISA IgA) anti-Campylobacter fetus foi avaliado em 311 amostras de muco cervici-vaginal de matrizes provenientes de 18 rebanhos de corte do Pantanal Mato-grossense. A especificidade do Elisa IgA foi estimada em 94,4% com base no teste de 143 controles negativos, representados por amostras de muco cervico-vaginal coletadas em 5 rebanhos leiteiros sem historico da doenca e com manejo reprodutivo por inseminacaoa artificial. Nos 18 rebanhos testados no Pantanal, 23,8% (74 animais) (IC 95%: 19,5% - 28,1%) das amostras foram positivas ao Campylobacter fetus venerealis pelo teste de ELISA- IgA para C. fetus subs. venerealis e 5,59% dentre as femeas testadas provenientes de rebanhos negativos. As medias das leituras de DO450 nos rebanhos testados no Pantanal variaram de 0,072 e 0,563 e nos rebanhos negativos variaram de 0,111 a 0,202. |
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Palavras-Chave: |
Bovine; Diagnostic; Parasita; Parasite. |
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Thesagro: |
Bovino; Campylobacter Fetus; Diagnostico; Elisa. |
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Thesaurus NAL: |
Brazil; Pantanal. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 01696naa a2200289 a 4500
001 1784433
005 2017-03-30
008 2002 bl --- 0-- u #d
100 1 $aPELLEGRIN, A. O.
245 $aDiagnostico da Campilobacteriose Genital Bovina pelo ELISA IgA.
260 $c2002
520 $aUm ensaio imunoenzimatico do tipo indireto para deteccao de imunoglobulinas A (ELISA IgA) anti-Campylobacter fetus foi avaliado em 311 amostras de muco cervici-vaginal de matrizes provenientes de 18 rebanhos de corte do Pantanal Mato-grossense. A especificidade do Elisa IgA foi estimada em 94,4% com base no teste de 143 controles negativos, representados por amostras de muco cervico-vaginal coletadas em 5 rebanhos leiteiros sem historico da doenca e com manejo reprodutivo por inseminacaoa artificial. Nos 18 rebanhos testados no Pantanal, 23,8% (74 animais) (IC 95%: 19,5% - 28,1%) das amostras foram positivas ao Campylobacter fetus venerealis pelo teste de ELISA- IgA para C. fetus subs. venerealis e 5,59% dentre as femeas testadas provenientes de rebanhos negativos. As medias das leituras de DO450 nos rebanhos testados no Pantanal variaram de 0,072 e 0,563 e nos rebanhos negativos variaram de 0,111 a 0,202.
650 $aBrazil
650 $aPantanal
650 $aBovino
650 $aCampylobacter Fetus
650 $aDiagnostico
650 $aElisa
653 $aBovine
653 $aDiagnostic
653 $aParasita
653 $aParasite
700 1 $aLEITE, R. C.
700 1 $aLAGE, A. P.
700 1 $aFIGUEIREDO
700 1 $aSERENO, J. R. B.
773 $tIn: SEMANA DA POS-GRADUACAO DA UFMG, 3., 2002, Belo Horizonte. Anais... Belo Horizonte: UFMG, 2002. nao paginado.
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Embrapa Pantanal (CPAP) |
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