Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Acta Scientiarum. Animal Sciences (Online) |
Texto Completo: | https://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/34352 |
Resumo: | This study was realized to determine the genetic variation of Central Javanese duck based on the D-Loop mtDNA gene. D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method with ABI automatic sequencer. ClustalW from MEGA-6.06 software program was employed for multiple alignments of nucleotide sequences. Nucleotide sequences of D-loop gene of mtDMA from the Central Javanese duck were aligned together with other Anas isolates from Genbank using ClustalW of MEGA-6.06 program. The estimation of genetic distance and phylogenetic tree construction were analyzed by Neighbor-Joining method, whereas the calculation of distance matrix was performed using Kimura 2-parameter. Multiple alignments obtained were 720 nucleotides at position 56 to 779 at the 5 'end. The results of the polymorphism analysis on D-loop sequences produced 23 haplotypes. However, this haplotype information does not represent the relationship among the geographical origins of duck with the certain duck species name. Moreover, a total number of 32 variable sites were identified. Insertions were detected in four sequences (126, 155, 771 and 779 nucleotide number). In the phylogenetic analysis, it is safe to conclude that the Central Javanese duck is closely related to Anas platyrhynchos and Anas zonorynchos. |
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Acta Scientiarum. Animal Sciences (Online) |
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|
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Mitochondrial D-loop sequence variation among Central Javanese Duck in IndonesiamtDNAD-loopCentral Javanese duckgenetic variation. This study was realized to determine the genetic variation of Central Javanese duck based on the D-Loop mtDNA gene. D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method with ABI automatic sequencer. ClustalW from MEGA-6.06 software program was employed for multiple alignments of nucleotide sequences. Nucleotide sequences of D-loop gene of mtDMA from the Central Javanese duck were aligned together with other Anas isolates from Genbank using ClustalW of MEGA-6.06 program. The estimation of genetic distance and phylogenetic tree construction were analyzed by Neighbor-Joining method, whereas the calculation of distance matrix was performed using Kimura 2-parameter. Multiple alignments obtained were 720 nucleotides at position 56 to 779 at the 5 'end. The results of the polymorphism analysis on D-loop sequences produced 23 haplotypes. However, this haplotype information does not represent the relationship among the geographical origins of duck with the certain duck species name. Moreover, a total number of 32 variable sites were identified. Insertions were detected in four sequences (126, 155, 771 and 779 nucleotide number). In the phylogenetic analysis, it is safe to conclude that the Central Javanese duck is closely related to Anas platyrhynchos and Anas zonorynchos. Editora da Universidade Estadual de Maringá2017-09-22info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionlaboratory workapplication/pdfhttps://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/3435210.4025/actascianimsci.v39i4.34352Acta Scientiarum. Animal Sciences; Vol 39 No 4 (2017); 449-456Acta Scientiarum. Animal Sciences; v. 39 n. 4 (2017); 449-4561807-86721806-2636reponame:Acta Scientiarum. Animal Sciences (Online)instname:Universidade Estadual de Maringá (UEM)instacron:UEMenghttps://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/34352/pdfCopyright (c) 2017 Acta Scientiarum. Animal Sciencesinfo:eu-repo/semantics/openAccessSusanti, RIswari, Retno SriFibriana, FidiaSari, Retno Ika2022-02-17T21:49:54Zoai:periodicos.uem.br/ojs:article/34352Revistahttp://www.periodicos.uem.br/ojs/index.php/ActaSciAnimSciPUBhttp://www.periodicos.uem.br/ojs/index.php/ActaSciAnimSci/oaiactaanim@uem.br||actaanim@uem.br|| rev.acta@gmail.com1807-86721806-2636opendoar:2022-02-17T21:49:54Acta Scientiarum. Animal Sciences (Online) - Universidade Estadual de Maringá (UEM)false |
dc.title.none.fl_str_mv |
Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia |
title |
Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia |
spellingShingle |
Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia Susanti, R mtDNA D-loop Central Javanese duck genetic variation. |
title_short |
Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia |
title_full |
Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia |
title_fullStr |
Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia |
title_full_unstemmed |
Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia |
title_sort |
Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia |
author |
Susanti, R |
author_facet |
Susanti, R Iswari, Retno Sri Fibriana, Fidia Sari, Retno Ika |
author_role |
author |
author2 |
Iswari, Retno Sri Fibriana, Fidia Sari, Retno Ika |
author2_role |
author author author |
dc.contributor.author.fl_str_mv |
Susanti, R Iswari, Retno Sri Fibriana, Fidia Sari, Retno Ika |
dc.subject.por.fl_str_mv |
mtDNA D-loop Central Javanese duck genetic variation. |
topic |
mtDNA D-loop Central Javanese duck genetic variation. |
description |
This study was realized to determine the genetic variation of Central Javanese duck based on the D-Loop mtDNA gene. D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method with ABI automatic sequencer. ClustalW from MEGA-6.06 software program was employed for multiple alignments of nucleotide sequences. Nucleotide sequences of D-loop gene of mtDMA from the Central Javanese duck were aligned together with other Anas isolates from Genbank using ClustalW of MEGA-6.06 program. The estimation of genetic distance and phylogenetic tree construction were analyzed by Neighbor-Joining method, whereas the calculation of distance matrix was performed using Kimura 2-parameter. Multiple alignments obtained were 720 nucleotides at position 56 to 779 at the 5 'end. The results of the polymorphism analysis on D-loop sequences produced 23 haplotypes. However, this haplotype information does not represent the relationship among the geographical origins of duck with the certain duck species name. Moreover, a total number of 32 variable sites were identified. Insertions were detected in four sequences (126, 155, 771 and 779 nucleotide number). In the phylogenetic analysis, it is safe to conclude that the Central Javanese duck is closely related to Anas platyrhynchos and Anas zonorynchos. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-09-22 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion laboratory work |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/34352 10.4025/actascianimsci.v39i4.34352 |
url |
https://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/34352 |
identifier_str_mv |
10.4025/actascianimsci.v39i4.34352 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
https://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/34352/pdf |
dc.rights.driver.fl_str_mv |
Copyright (c) 2017 Acta Scientiarum. Animal Sciences info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Copyright (c) 2017 Acta Scientiarum. Animal Sciences |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Editora da Universidade Estadual de Maringá |
publisher.none.fl_str_mv |
Editora da Universidade Estadual de Maringá |
dc.source.none.fl_str_mv |
Acta Scientiarum. Animal Sciences; Vol 39 No 4 (2017); 449-456 Acta Scientiarum. Animal Sciences; v. 39 n. 4 (2017); 449-456 1807-8672 1806-2636 reponame:Acta Scientiarum. Animal Sciences (Online) instname:Universidade Estadual de Maringá (UEM) instacron:UEM |
instname_str |
Universidade Estadual de Maringá (UEM) |
instacron_str |
UEM |
institution |
UEM |
reponame_str |
Acta Scientiarum. Animal Sciences (Online) |
collection |
Acta Scientiarum. Animal Sciences (Online) |
repository.name.fl_str_mv |
Acta Scientiarum. Animal Sciences (Online) - Universidade Estadual de Maringá (UEM) |
repository.mail.fl_str_mv |
actaanim@uem.br||actaanim@uem.br|| rev.acta@gmail.com |
_version_ |
1799315361829486592 |