DOI: 10.5061/dryad.qrfj6q5hp
title: Alignments used for phylogenetic analysis of capirona (Calycophyllum spruceanum, Rubiaceae)

description: Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily
 Ixoroideae, one of the 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), eight
 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes and
 one 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.
description: A single capirona tree was selected to be sequenced from San
 Bernardo Research Station of INIA, located in Madre de Dios department
 (2°41´8.66" N / 69° 22´49.8" E / 227.2 m.a.s.l ) in the Peruvian
 Amazon. A branch with flowers was collected and deposited at the
 Scientific Collection of the Herbarium of Universidad Nacional Mayor de
 San Marcos (UNMSM), under the voucher number No 324323. Total genomic DNA
 was extracted from fresh leaves by CTAB method with minor modiﬁcations,
 the quality was evaluated on a 1% agarose gel and the quantification was
 performed by fluorescence. 2.2. DNA Sequence and Genome Assembly
 High-quality genomic DNA was used to construct libraries. Pair-end clean
 reads were obtained by PE 150 library and the Illumina HiSeq 2500
 platform. Adapters and low-quality reads were removed using Trim Galore.
 We used clean data to assemble the chloroplast genome using the
 GetOrganelle v1.7.2 pipeline, in which SPAdes v3.11.1, bowtie2 v2.4.2 and
 BLAST+ v2.11 were employed. To gain an insight into the
 phylogenetic location of <i>Calycophyllum. sprucearum</i>, a
 maximum-likelihood (ML) tree was constructed with 1,000 nonparametric
 bootstrap replicates using RAxML v8.2.11 software under GTR+GAMMA
 nucleotide substitution model of evolution. The complete chloroplast
 genome of <i>C. sprucearum</i> was compared and aligned with
 other 19 chloroplast genomes obtained from Genbank by the MAFFT v7.475
 software. Seven species from Rubioideae, five species from Cinchonoideae,
 and six species from Ixoroideae were included in the analysis.
 <i>Lonicera hispida</i> (Caprifoliaceae) was included as an
 outgroup.
description: This file represents the complete chloroplast sequence alignments of 19
 species that belong to Rubiaceace family. Lonicera hispida
 (Caprifoliaceae) was included as an outgroup. In this work, we sequenced
 the complete chloroplast genome of Calycophyllum spruceanum. The overall
 length of the C. sprucearum chloroplast genome is 154,480 bp, exhibiting
 the circular quadripartite structure characteristic of major angiosperm
 plants. After annotation and modification, the entire chloroplast (cp)
 genome sequence was submitted to the GenBank database with accession
 number: OK326865 (https://www.ncbi.nlm.nih.gov/nuccore/OK326865.1/). The
 associated Bioproject, Biosample and SRA numbers are PRJNA760977,
 SAMN21240132, and SRR15725575, respectively.