The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae)
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Genetics and Molecular Biology |
Texto Completo: | http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572022000500301 |
Resumo: | Abstract Here we sequenced and characterized the complete plastome of Bactris riparia, a species closely related to B. gasipaes and widely distributed in Western Amazonia. We performed a comparative genomic analysis with B. riparia and the other four Bactridinae species retrieved from GenBank. The plastome of B. riparia was 156,715 bp with a quadripartite structure. Gene content included 86 protein-coding genes (CDS), 38 tRNAs, and 8 rRNAs. Bactris riparia has 69 more base pairs than B. gasipaes, with identical numbers in IR, and more in LSC and SSC. The comparative analysis indicated that structure, collinearity, and IR/SSC borders of plastomes within subtribe Bactridinae are, in general, conserved. We predicted 69 SSRs in B. riparia plastome. Among them, ~80% consisted of A/T homopolymers. Among the 52 variable CDS, rbcL showed the highest non-synonymous rate, while the rps15 gene had the highest synonymous rate. Three genes (ccsA, cemA, and rpoC1) presented evidence of positive selection and 22 genes showed evidence of purifying selection. The phylogenetic tree based on plastome sequences set Bactris as more closely related to Astrocaryum than to Acrocomia. These new plastome data of B. riparia will contribute to studies about the diversity, evolutionary history, and conservation of palms. |
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Genetics and Molecular Biology |
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The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae)PalmsAmazonian floodplainsplastomemolecular evolutionAbstract Here we sequenced and characterized the complete plastome of Bactris riparia, a species closely related to B. gasipaes and widely distributed in Western Amazonia. We performed a comparative genomic analysis with B. riparia and the other four Bactridinae species retrieved from GenBank. The plastome of B. riparia was 156,715 bp with a quadripartite structure. Gene content included 86 protein-coding genes (CDS), 38 tRNAs, and 8 rRNAs. Bactris riparia has 69 more base pairs than B. gasipaes, with identical numbers in IR, and more in LSC and SSC. The comparative analysis indicated that structure, collinearity, and IR/SSC borders of plastomes within subtribe Bactridinae are, in general, conserved. We predicted 69 SSRs in B. riparia plastome. Among them, ~80% consisted of A/T homopolymers. Among the 52 variable CDS, rbcL showed the highest non-synonymous rate, while the rps15 gene had the highest synonymous rate. Three genes (ccsA, cemA, and rpoC1) presented evidence of positive selection and 22 genes showed evidence of purifying selection. The phylogenetic tree based on plastome sequences set Bactris as more closely related to Astrocaryum than to Acrocomia. These new plastome data of B. riparia will contribute to studies about the diversity, evolutionary history, and conservation of palms.Sociedade Brasileira de Genética2022-01-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572022000500301Genetics and Molecular Biology v.45 n.4 2022reponame:Genetics and Molecular Biologyinstname:Sociedade Brasileira de Genética (SBG)instacron:SBG10.1590/1678-4685-gmb-2021-0305info:eu-repo/semantics/openAccessDias,Micheli CristinaClement,Charles RolandFraga,Hugo Pacheco de FreitasSilva,Raquel Santos daRodrigues,Doriane PicançoVieira,Leila do Nascimentoeng2022-11-04T00:00:00Zoai:scielo:S1415-47572022000500301Revistahttp://www.gmb.org.br/ONGhttps://old.scielo.br/oai/scielo-oai.php||editor@gmb.org.br1678-46851415-4757opendoar:2022-11-04T00:00Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG)false |
dc.title.none.fl_str_mv |
The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae) |
title |
The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae) |
spellingShingle |
The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae) Dias,Micheli Cristina Palms Amazonian floodplains plastome molecular evolution |
title_short |
The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae) |
title_full |
The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae) |
title_fullStr |
The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae) |
title_full_unstemmed |
The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae) |
title_sort |
The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae) |
author |
Dias,Micheli Cristina |
author_facet |
Dias,Micheli Cristina Clement,Charles Roland Fraga,Hugo Pacheco de Freitas Silva,Raquel Santos da Rodrigues,Doriane Picanço Vieira,Leila do Nascimento |
author_role |
author |
author2 |
Clement,Charles Roland Fraga,Hugo Pacheco de Freitas Silva,Raquel Santos da Rodrigues,Doriane Picanço Vieira,Leila do Nascimento |
author2_role |
author author author author author |
dc.contributor.author.fl_str_mv |
Dias,Micheli Cristina Clement,Charles Roland Fraga,Hugo Pacheco de Freitas Silva,Raquel Santos da Rodrigues,Doriane Picanço Vieira,Leila do Nascimento |
dc.subject.por.fl_str_mv |
Palms Amazonian floodplains plastome molecular evolution |
topic |
Palms Amazonian floodplains plastome molecular evolution |
description |
Abstract Here we sequenced and characterized the complete plastome of Bactris riparia, a species closely related to B. gasipaes and widely distributed in Western Amazonia. We performed a comparative genomic analysis with B. riparia and the other four Bactridinae species retrieved from GenBank. The plastome of B. riparia was 156,715 bp with a quadripartite structure. Gene content included 86 protein-coding genes (CDS), 38 tRNAs, and 8 rRNAs. Bactris riparia has 69 more base pairs than B. gasipaes, with identical numbers in IR, and more in LSC and SSC. The comparative analysis indicated that structure, collinearity, and IR/SSC borders of plastomes within subtribe Bactridinae are, in general, conserved. We predicted 69 SSRs in B. riparia plastome. Among them, ~80% consisted of A/T homopolymers. Among the 52 variable CDS, rbcL showed the highest non-synonymous rate, while the rps15 gene had the highest synonymous rate. Three genes (ccsA, cemA, and rpoC1) presented evidence of positive selection and 22 genes showed evidence of purifying selection. The phylogenetic tree based on plastome sequences set Bactris as more closely related to Astrocaryum than to Acrocomia. These new plastome data of B. riparia will contribute to studies about the diversity, evolutionary history, and conservation of palms. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-01-01 |
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=S1415-47572022000500301 |
url |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572022000500301 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1590/1678-4685-gmb-2021-0305 |
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 |
Sociedade Brasileira de Genética |
publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
dc.source.none.fl_str_mv |
Genetics and Molecular Biology v.45 n.4 2022 reponame:Genetics and Molecular Biology instname:Sociedade Brasileira de Genética (SBG) instacron:SBG |
instname_str |
Sociedade Brasileira de Genética (SBG) |
instacron_str |
SBG |
institution |
SBG |
reponame_str |
Genetics and Molecular Biology |
collection |
Genetics and Molecular Biology |
repository.name.fl_str_mv |
Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG) |
repository.mail.fl_str_mv |
||editor@gmb.org.br |
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1752122390711631872 |