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

Carla L. Saldaña; Pedro Rodriguez-Grados; Julio C. Chávez-Galarza; Shefferson Feijoo; Juan Carlos Guerrero Abad; Héctor V. Vásquez; Jorge L. Maicelo; Jorge H. Jhoncon; Carlos I. Arbizu

doi:10.20944/preprints202111.0533.v1

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preprints.org > biology and life sciences > biochemistry and molecular biology > doi: 10.20944/preprints202111.0533.v1

Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

Carla L. Saldaña

Pedro Rodriguez-Grados

Julio C. Chávez-Galarza

Shefferson Feijoo

Juan Carlos Guerrero Abad

Version 1 : Received: 26 November 2021 / Approved: 29 November 2021 / Online: 29 November 2021 (12:32:24 CET)

How to cite: 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. https://doi.org/10.20944/preprints202111.0533.v1 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. https://doi.org/10.20944/preprints202111.0533.v1

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MDPI and ACS Style

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. https://doi.org/10.20944/preprints202111.0533.v1

APA Style

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. (2021). 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. https://doi.org/10.20944/preprints202111.0533.v1

Chicago/Turabian Style

Saldaña, C.L., Jorge H. Jhoncon and Carlos I. Arbizu. 2021 "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. https://doi.org/10.20944/preprints202111.0533.v1

Abstract

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.

Keywords

chloroplast; genetic resources; genomics capirona; phylogenomics

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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