Por favor, use este identificador para citar o enlazar este ítem: https://hdl.handle.net/20.500.12955/1595
Título : 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
Autor : Saldaña, Carlos L.
Rodriguez Grados, Pedro
Chávez Galarza, Julio C.
Feijoo, Shefferson
Guerrero Abad, Juan Carlos
Maicelo, Jorge L.
Jhoncon, Jorge H.
Arbizu, Carlos I.
Fecha de publicación : 29-nov-2021
Resumen : Capirona (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.
Palabras clave : Chloroplast
Genetic resources
Genomics capirona
Phylogenomics
Editorial : MDPI
Citación : 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).
Descripción : 16 páginas
URI : https://hdl.handle.net/20.500.12955/1595
metadata.dc.identifier.doi: 10.20944/preprints202111.0533.v1
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