Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira
The complete mitochondrial genome of the brown brocket deer Mazama gouazoubira and a set of polymorphic microsatellite markers were identified by 454-pyrosequencing. De novo genome assembly recovered 98% of the mitochondrial genome with a mean coverage of 9-fold. The mitogenome consisted of 16,356 b...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Sociedade Brasileira de Genética
2015-09-01
|
| Series: | Genetics and Molecular Biology |
| Subjects: | |
| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572015000300338&lng=en&tlng=en |
| _version_ | 1811213013274853376 |
|---|---|
| author | Renato Caparroz Aline M.B. Mantellatto David J. Bertioli Marina G. Figueiredo José Maurício B. Duarte |
| author_facet | Renato Caparroz Aline M.B. Mantellatto David J. Bertioli Marina G. Figueiredo José Maurício B. Duarte |
| author_sort | Renato Caparroz |
| collection | DOAJ |
| description | The complete mitochondrial genome of the brown brocket deer Mazama gouazoubira and a set of polymorphic microsatellite markers were identified by 454-pyrosequencing. De novo genome assembly recovered 98% of the mitochondrial genome with a mean coverage of 9-fold. The mitogenome consisted of 16,356 base pairs that included 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and the control region, as found in other deer. The genetic divergence between the mitogenome described here and a previously published report was ∼0.5%, with the control region and ND5 gene showing the highest intraspecific variation. Seven polymorphic loci were characterized using 15 unrelated individuals; there was moderate genetic variation across most loci (mean of 5.6 alleles/locus, mean expected heterozygosity = 0.70), with only one locus deviating significantly from Hardy-Weinberg equilibrium, probably because of null alleles. Marker independence was confirmed with tests for linkage disequilibrium. The genetic variation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the phylogeography and population genetic patterns in M. gouazoubira, particularly in the context of habitat fragmentation in South America. |
| first_indexed | 2024-04-12T05:40:11Z |
| format | Article |
| id | doaj.art-9ba767fa7a6f420caeacf46591e3e66f |
| institution | Directory Open Access Journal |
| issn | 1678-4685 |
| language | English |
| last_indexed | 2024-04-12T05:40:11Z |
| publishDate | 2015-09-01 |
| publisher | Sociedade Brasileira de Genética |
| record_format | Article |
| series | Genetics and Molecular Biology |
| spelling | doaj.art-9ba767fa7a6f420caeacf46591e3e66f2022-12-22T03:45:42ZengSociedade Brasileira de GenéticaGenetics and Molecular Biology1678-46852015-09-0138333834510.1590/S1415-475738320140344S1415-47572015000300338Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubiraRenato CaparrozAline M.B. MantellattoDavid J. BertioliMarina G. FigueiredoJosé Maurício B. DuarteThe complete mitochondrial genome of the brown brocket deer Mazama gouazoubira and a set of polymorphic microsatellite markers were identified by 454-pyrosequencing. De novo genome assembly recovered 98% of the mitochondrial genome with a mean coverage of 9-fold. The mitogenome consisted of 16,356 base pairs that included 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and the control region, as found in other deer. The genetic divergence between the mitogenome described here and a previously published report was ∼0.5%, with the control region and ND5 gene showing the highest intraspecific variation. Seven polymorphic loci were characterized using 15 unrelated individuals; there was moderate genetic variation across most loci (mean of 5.6 alleles/locus, mean expected heterozygosity = 0.70), with only one locus deviating significantly from Hardy-Weinberg equilibrium, probably because of null alleles. Marker independence was confirmed with tests for linkage disequilibrium. The genetic variation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the phylogeography and population genetic patterns in M. gouazoubira, particularly in the context of habitat fragmentation in South America.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572015000300338&lng=en&tlng=enconservationmicrosatellitesmitogenomepopulation genetics454-pyrosequencing |
| spellingShingle | Renato Caparroz Aline M.B. Mantellatto David J. Bertioli Marina G. Figueiredo José Maurício B. Duarte Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira Genetics and Molecular Biology conservation microsatellites mitogenome population genetics 454-pyrosequencing |
| title | Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira |
| title_full | Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira |
| title_fullStr | Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira |
| title_full_unstemmed | Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira |
| title_short | Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira |
| title_sort | characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next generation sequencing for the brown brocket deer mazama gouazoubira |
| topic | conservation microsatellites mitogenome population genetics 454-pyrosequencing |
| url | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572015000300338&lng=en&tlng=en |
| work_keys_str_mv | AT renatocaparroz characterizationofthecompletemitochondrialgenomeandasetofpolymorphicmicrosatellitemarkersthroughnextgenerationsequencingforthebrownbrocketdeermazamagouazoubira AT alinembmantellatto characterizationofthecompletemitochondrialgenomeandasetofpolymorphicmicrosatellitemarkersthroughnextgenerationsequencingforthebrownbrocketdeermazamagouazoubira AT davidjbertioli characterizationofthecompletemitochondrialgenomeandasetofpolymorphicmicrosatellitemarkersthroughnextgenerationsequencingforthebrownbrocketdeermazamagouazoubira AT marinagfigueiredo characterizationofthecompletemitochondrialgenomeandasetofpolymorphicmicrosatellitemarkersthroughnextgenerationsequencingforthebrownbrocketdeermazamagouazoubira AT josemauriciobduarte characterizationofthecompletemitochondrialgenomeandasetofpolymorphicmicrosatellitemarkersthroughnextgenerationsequencingforthebrownbrocketdeermazamagouazoubira |