dc.creatorSaldaña Serrano, Carla Lizet
dc.creatorRodriguez Grados, Pedro
dc.creatorChávez Galarza, Julio César
dc.creatorFeijoo Narvasta, Shefferson
dc.creatorGuerrero Abad, Juan Carlos
dc.creatorMaicelo Quintana, Jorge Luis
dc.creatorJhoncon, Jorge H.
dc.creatorArbizu Berrocal, Carlos Irvin
dc.date.accessioned2021-12-28T18:07:35Z
dc.date.accessioned2023-05-24T15:02:35Z
dc.date.available2021-12-28T18:07:35Z
dc.date.available2023-05-24T15:02:35Z
dc.date.created2021-12-28T18:07:35Z
dc.date.issued2021-11-29
dc.identifierSaldaña, 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.identifierhttps://hdl.handle.net/20.500.12955/1595
dc.identifierPreprints
dc.identifier10.20944/preprints202111.0533.v1
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/6441219
dc.description.abstractCapirona (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.
dc.languageeng
dc.publisherMDPI
dc.publisherSuiza
dc.relationPreprints 2021, 2021110533
dc.relationhttps://doi.org/10.20944/preprints202111.0533.v1
dc.rightshttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rightsinfo:eu-repo/semantics/openAccess
dc.sourceInstituto Nacional de Innovación Agraria
dc.sourceRepositorio Institucional - INIA
dc.subjectChloroplast
dc.subjectGenetic resources
dc.subjectGenomics capirona
dc.subjectPhylogenomics
dc.titleUnlocking 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
dc.typeinfo:eu-repo/semantics/workingPaper


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