Complete Chloroplast Genome Sequence and Phylogenetic Inference of the Canary Islands Dragon Tree (Dracaena draco L.)

Abstract

Dracaena draco, which belongs to the genus Dracaena, is an endemic succulent of the Canary Islands. Although it is one of the most popular and widely grown ornamental plants in the world, little is known about its genomic variability. Next generation sequencing, especially in combination with advanced bioinformatics analysis, is a new standard in taxonomic and phylogenetic research. Therefore, in this study, the complete D. draco chloroplast genome (cp) was sequenced and analyzed in order to provide new genomic information and to elucidate phylogenetic relationships, particularly within the genus Dracaena. The D. draco chloroplast genome is 155,422 bp, total guanine-cytosine (GC) content is 37.6%, and it has a typical quadripartite plastid genome structure with four separate regions, including one large single copy region of 83,942 bp length and one small single copy region of 18,472 bp length, separated by two inverted repeat regions, each 26,504 bp in length. One hundred and thirty-two genes were identified, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Seventy-seven simple sequence repeats were also detected. Comparative analysis of the sequence data of various members of Asparagales revealed mutational hotspots potentially useful for their genetic identification. Phylogenetic inference based on 16 complete chloroplast genomes of Asparagales strongly suggested that Dracaena species form one monophyletic group, and that close relationships exist between D. draco, D. cochinchinensis and D. cambodiana. This study provides new and valuable data for further taxonomic, evolutionary and phylogenetic studies within the Dracaena genus.

New Insight into Taxonomy of European Mountain Pines, Pinus mugo Complex, Based on Complete Chloroplast Genomes Sequencing

“…This result is in line with expectations because the second combination included more distant pines, not just three closely related taxa. A similar relationship was found also in the case of other species [ 49 ].…”

Characterization of the Complete Chloroplast Genome Sequence of the Socotra Dragon`s Blood Tree (Dracaena cinnabari Balf.)

“…Genome-wide evolutionary dynamics and events in Dracaena species were analyzed using the progressive MAUVE algorithm with default settings and MAUVE [33] plugin v1.1.1 available in Geneious Prime 2020.0.49.1.7 [28]. The chloroplast genome of Dracaena cinnabari as a reference sequence was used for comparisons with previously published Dracaena species, i.e., D. angustifolia [25], D. draco [26], and D. elliptica [25].…”

“…Complete chloroplast genomes were aligned with MAFFT 7.450 using default settings [35]. A General Time Reversible + Proportion Invariation + Gamma nucleotide substitution model (GTR + I + G) was used as the substitution model for the ML analysis [26]. The ML analysis was performed in RaxML v8.2.11 [36], with 1000 rapid bootstrap replicates along with a search for the best-scoring ML tree in every run and parsimony random seed set to 10.…”

“…Ye and D. elliptica Thunb. [25] or recently, D. draco (L.) L. [26]. However, no similar study has been published to date on the detailed characterization of the chloroplast genome features for D. cinnabari.…”

Dragon Trees, Tertiary Relicts in Current Reality

“…The Special Issue includes nine studies covering a broad range of research topics related to Dragon trees. Celi ński et al [28] present the complete D. draco chloroplast genome, which provides new information and helps to elucidate phylogenetic relationships, particularly within the genus Dracaena. A new approach in taxonomy with a potential for growth analysis is presented by Vahalík et al [29], who compared 3D tree models four Dragon tree species.…”