Alignments used for phylogenetic analysis of capirona (Calycophyllum spruceanum, Rubiaceae)

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.