Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

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16 páginas
Detalles Bibliográficos
Autores: Saldaña Serrano, Carla Lizet, Rodriguez Grados, Pedro, Chávez Galarza, Julio César, Feijoo Narvasta, Shefferson, Guerrero Abad, Juan Carlos, Maicelo Quintana, Jorge Luis, Jhoncon, Jorge H., Arbizu Berrocal, Carlos Irvin
Formato: documento de trabajo
Fecha de Publicación:2021
Institución:Instituto Nacional de Innovación Agraria
Repositorio:INIA-Institucional
Lenguaje:inglés
OAI Identifier:oai:null:20.500.12955/1595
Enlace del recurso:https://hdl.handle.net/20.500.12955/1595
Nivel de acceso:acceso abierto
Materia:Chloroplast
Genetic resources
Genomics capirona
Phylogenomics
https://purl.org/pe-repo/ocde/ford#4.04.00
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dc.title.es_PE.fl_str_mv Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species
title Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species
spellingShingle Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species
Saldaña Serrano, Carla Lizet
Chloroplast
Genetic resources
Genomics capirona
Phylogenomics
https://purl.org/pe-repo/ocde/ford#4.04.00
title_short Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species
title_full Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species
title_fullStr Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species
title_full_unstemmed Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species
title_sort Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species
author Saldaña Serrano, Carla Lizet
author_facet Saldaña Serrano, Carla Lizet
Rodriguez Grados, Pedro
Chávez Galarza, Julio César
Feijoo Narvasta, Shefferson
Guerrero Abad, Juan Carlos
Maicelo Quintana, Jorge Luis
Jhoncon, Jorge H.
Arbizu Berrocal, Carlos Irvin
author_role author
author2 Rodriguez Grados, Pedro
Chávez Galarza, Julio César
Feijoo Narvasta, Shefferson
Guerrero Abad, Juan Carlos
Maicelo Quintana, Jorge Luis
Jhoncon, Jorge H.
Arbizu Berrocal, Carlos Irvin
author2_role author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Saldaña Serrano, Carla Lizet
Rodriguez Grados, Pedro
Chávez Galarza, Julio César
Feijoo Narvasta, Shefferson
Guerrero Abad, Juan Carlos
Maicelo Quintana, Jorge Luis
Jhoncon, Jorge H.
Arbizu Berrocal, Carlos Irvin
dc.subject.es_PE.fl_str_mv Chloroplast
Genetic resources
Genomics capirona
Phylogenomics
topic Chloroplast
Genetic resources
Genomics capirona
Phylogenomics
https://purl.org/pe-repo/ocde/ford#4.04.00
dc.subject.ocde.es_PE.fl_str_mv https://purl.org/pe-repo/ocde/ford#4.04.00
description 16 páginas
publishDate 2021
dc.date.accessioned.none.fl_str_mv 2021-12-28T18:07:35Z
dc.date.available.none.fl_str_mv 2021-12-28T18:07:35Z
dc.date.issued.fl_str_mv 2021-11-29
dc.type.es_PE.fl_str_mv info:eu-repo/semantics/workingPaper
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dc.identifier.citation.es_PE.fl_str_mv Saldaña, C.L.; Rodriguez-Grados, P.; Chávez-Galarza, J.C.; Feijoo, S.; Guerrero Abad, J.C.; Vásquez, H.V.; Maicelo, J.L.; Jhoncon, J.H.; Arbizu, C.I. Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species. Preprints 2021, 2021110533 (doi: 10.20944/preprints202111.0533.v1).
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12955/1595
dc.identifier.journal.es_PE.fl_str_mv Preprints
dc.identifier.doi.none.fl_str_mv 10.20944/preprints202111.0533.v1
identifier_str_mv Saldaña, C.L.; Rodriguez-Grados, P.; Chávez-Galarza, J.C.; Feijoo, S.; Guerrero Abad, J.C.; Vásquez, H.V.; Maicelo, J.L.; Jhoncon, J.H.; Arbizu, C.I. Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species. Preprints 2021, 2021110533 (doi: 10.20944/preprints202111.0533.v1).
Preprints
10.20944/preprints202111.0533.v1
url https://hdl.handle.net/20.500.12955/1595
dc.language.iso.es_PE.fl_str_mv eng
language eng
dc.relation.ispartof.es_PE.fl_str_mv Preprints 2021, 2021110533
dc.relation.publisherversion.es_PE.fl_str_mv https://doi.org/10.20944/preprints202111.0533.v1
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dc.coverage.spatial.es_PE.fl_str_mv Perú
dc.publisher.es_PE.fl_str_mv MDPI
dc.publisher.country.es_PE.fl_str_mv Suiza
dc.source.es_PE.fl_str_mv Instituto Nacional de Innovación Agraria
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spelling Saldaña Serrano, Carla LizetRodriguez Grados, PedroChávez Galarza, Julio CésarFeijoo Narvasta, SheffersonGuerrero Abad, Juan CarlosMaicelo Quintana, Jorge LuisJhoncon, Jorge H.Arbizu Berrocal, Carlos IrvinPerú2021-12-28T18:07:35Z2021-12-28T18:07:35Z2021-11-29Saldaña, C.L.; Rodriguez-Grados, P.; Chávez-Galarza, J.C.; Feijoo, S.; Guerrero Abad, J.C.; Vásquez, H.V.; Maicelo, J.L.; Jhoncon, J.H.; Arbizu, C.I. Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species. Preprints 2021, 2021110533 (doi: 10.20944/preprints202111.0533.v1).https://hdl.handle.net/20.500.12955/1595Preprints10.20944/preprints202111.0533.v116 páginasCapirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of de major lineages in the Rubiaceae family, and is an important timber tree, with origin in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct librar-ies. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes and 01 pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotide (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than invert regions. Finally, phylogenetic analysis resolved that C. spruceanum is a sister species to Emmenopterys henryi, and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.1. Introduction. 2. Results. 3. Discussion. 4. Materials and Methods. 5. Conclusions. 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Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species
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