Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence

Detalhes bibliográficos
Autor(a) principal: Andrade,Mateus Chagas
Data de Publicação: 2018
Outros Autores: Perek,Matheus, Pereira,Fernanda Bortolanza, Moro,Michele, Tambarussi,Evandro Vagner
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Crop Breeding and Applied Biotechnology
Texto Completo: http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1984-70332018000100097
Resumo: Abstract In this study, we quantify and document the distribution and organization of cpSSRs in the chloroplast genome of 31 Eucalyptus species. Our sample included all previously sequenced plastomes of Eucalyptus species available from the NCBI online database. We processed the complete cpDNA sequences and identified mono-, di-, tri-, tetra-, penta-, and hexanucleotide cpSSRs, with the majority of cpSSRs classified as mononucleotide. After genome microsatellite selection, we evaluated the microsatellites for coding and non-coding regions and cpSSRs were predominantly identified in non-coding regions of cpDNA for all nucleotide types. Penta- and hexanucleotide cpSSRs were the least frequent types of microsatellites. We also developed and virtually amplified 60 primers pairs that can be used in studies of Eucalyptus species. Thus, these cpSSR regions can be used in studies assessing the ecology, breeding, and conservation of the genus.
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spelling Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequenceChloroplast DNADNA fingerprintgenetic diversityspecies differentiation.Abstract In this study, we quantify and document the distribution and organization of cpSSRs in the chloroplast genome of 31 Eucalyptus species. Our sample included all previously sequenced plastomes of Eucalyptus species available from the NCBI online database. We processed the complete cpDNA sequences and identified mono-, di-, tri-, tetra-, penta-, and hexanucleotide cpSSRs, with the majority of cpSSRs classified as mononucleotide. After genome microsatellite selection, we evaluated the microsatellites for coding and non-coding regions and cpSSRs were predominantly identified in non-coding regions of cpDNA for all nucleotide types. Penta- and hexanucleotide cpSSRs were the least frequent types of microsatellites. We also developed and virtually amplified 60 primers pairs that can be used in studies of Eucalyptus species. Thus, these cpSSR regions can be used in studies assessing the ecology, breeding, and conservation of the genus.Crop Breeding and Applied Biotechnology2018-03-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1984-70332018000100097Crop Breeding and Applied Biotechnology v.18 n.1 2018reponame:Crop Breeding and Applied Biotechnologyinstname:Sociedade Brasileira de Melhoramento de Plantasinstacron:CBAB10.1590/1984-70332018v18n1a13info:eu-repo/semantics/openAccessAndrade,Mateus ChagasPerek,MatheusPereira,Fernanda BortolanzaMoro,MicheleTambarussi,Evandro Vagnereng2018-02-28T00:00:00Zoai:scielo:S1984-70332018000100097Revistahttps://cbab.sbmp.org.br/#ONGhttps://old.scielo.br/oai/scielo-oai.phpcbabjournal@gmail.com||cbab@ufv.br1984-70331518-7853opendoar:2018-02-28T00:00Crop Breeding and Applied Biotechnology - Sociedade Brasileira de Melhoramento de Plantasfalse
dc.title.none.fl_str_mv Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence
title Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence
spellingShingle Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence
Andrade,Mateus Chagas
Chloroplast DNA
DNA fingerprint
genetic diversity
species differentiation.
title_short Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence
title_full Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence
title_fullStr Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence
title_full_unstemmed Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence
title_sort Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence
author Andrade,Mateus Chagas
author_facet Andrade,Mateus Chagas
Perek,Matheus
Pereira,Fernanda Bortolanza
Moro,Michele
Tambarussi,Evandro Vagner
author_role author
author2 Perek,Matheus
Pereira,Fernanda Bortolanza
Moro,Michele
Tambarussi,Evandro Vagner
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Andrade,Mateus Chagas
Perek,Matheus
Pereira,Fernanda Bortolanza
Moro,Michele
Tambarussi,Evandro Vagner
dc.subject.por.fl_str_mv Chloroplast DNA
DNA fingerprint
genetic diversity
species differentiation.
topic Chloroplast DNA
DNA fingerprint
genetic diversity
species differentiation.
description Abstract In this study, we quantify and document the distribution and organization of cpSSRs in the chloroplast genome of 31 Eucalyptus species. Our sample included all previously sequenced plastomes of Eucalyptus species available from the NCBI online database. We processed the complete cpDNA sequences and identified mono-, di-, tri-, tetra-, penta-, and hexanucleotide cpSSRs, with the majority of cpSSRs classified as mononucleotide. After genome microsatellite selection, we evaluated the microsatellites for coding and non-coding regions and cpSSRs were predominantly identified in non-coding regions of cpDNA for all nucleotide types. Penta- and hexanucleotide cpSSRs were the least frequent types of microsatellites. We also developed and virtually amplified 60 primers pairs that can be used in studies of Eucalyptus species. Thus, these cpSSR regions can be used in studies assessing the ecology, breeding, and conservation of the genus.
publishDate 2018
dc.date.none.fl_str_mv 2018-03-01
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1984-70332018000100097
url http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1984-70332018000100097
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 10.1590/1984-70332018v18n1a13
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv text/html
dc.publisher.none.fl_str_mv Crop Breeding and Applied Biotechnology
publisher.none.fl_str_mv Crop Breeding and Applied Biotechnology
dc.source.none.fl_str_mv Crop Breeding and Applied Biotechnology v.18 n.1 2018
reponame:Crop Breeding and Applied Biotechnology
instname:Sociedade Brasileira de Melhoramento de Plantas
instacron:CBAB
instname_str Sociedade Brasileira de Melhoramento de Plantas
instacron_str CBAB
institution CBAB
reponame_str Crop Breeding and Applied Biotechnology
collection Crop Breeding and Applied Biotechnology
repository.name.fl_str_mv Crop Breeding and Applied Biotechnology - Sociedade Brasileira de Melhoramento de Plantas
repository.mail.fl_str_mv cbabjournal@gmail.com||cbab@ufv.br
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