Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species

Abstract

Epidendrum, one of the three largest genera of Orchidaceae, exhibits significant horticultural and ornamental value and serves as an important research model in conservation, ecology, and evolutionary biology. Given the ambiguous identification of germplasm and complex evolutionary relationships within the genus, the complete plastome of this genus (including five species) were firstly sequenced and assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. The lengths of the plastomes ranged from 147,902 bp to 150,986 bp, with a GC content of 37.16% to 37.33%. Gene annotation revealed the presence of 78–82 protein-coding genes, 38 tRNAs, and 8 rRNAs. A total of 25–38 long repeats and 130–149 SSRs were detected. Analysis of relative synonymous codon usage (RSCU) indicated that leucine (Leu) was the most and cysteine (Cys) was the least. The consistent and robust phylogenetic relationships of Epidendrum and its closely related taxa were established using a total of 43 plastid genomes from the tribe Epidendreae. The genus Epidendrum was supported as a monophyletic group and as a sister to Cattleya. Meanwhile, four mutational hotspots (trnCGCA–petN, trnDGUC–trnYGUA, trnSGCU–trnGUCC, and rpl32–trnLUAG) were identified for further phylogenetic studies. Our analysis demonstrates the promising utility of plastomes in inferring the phylogenetic relationships of Epidendrum.

The Complete Chloroplast Genome of an Epiphytic Leafless Orchid, Taeniophyllum complanatum: Comparative Analysis and Phylogenetic Relationships

“…Furthermore, the amino acid frequency for leucine (Leu) was the highest, while the frequency for cysteine (Cys) was the lowest in the encoded amino acids of the T. complanatum chloroplast. Our results matched well with previous studies on codon preferences in the Orchidaceae [25,63]. These findings also suggest a high similarity in codon usage frequency in orchid plants, further demonstrating the high conservation of the T. complanatum chloroplast genome (Table S4).…”

“…Similarly, for the genus Paraphalaenopsis, regions such as psbB, ccsA, trnK UUU , trnS GCU -trnG UCC , and rps16-trnQ UUG show substantial differences [47]. In the case of Epidendrum, areas like trnC GCA -petN, trnD GUC -trnY GUA , trnS GCU -trnG UCC , and rpl32-trnL UAG are known for their maximum differences [63]. Furthermore, regions like atpI-atpH, matK, psbA-trnH, and trnL-F are typically used as marker genes to detect the evolution relationships within Aeridinae [66].…”

Characteristics and Comparative Analysis of the Complete Plastomes of Apostasia fujianica and Neuwiedia malipoensis (Apostasioideae)

“…Additionally, the quantity of long repeats varies among different genera of orchids. For instance, Aerides has 49-65 long repeats [53], Trichoglottis has 33-46 [54], and Epidendrum has 25-38 [55]. We believe these results could serve as valuable molecular resources for DNA marker development.…”

Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids

“…Within the smaller SC region, genes such as accD and clpP shared similarities with the LSC regions of other Orchidaceae plastomes; genes within the larger SC region, particularly the four rRNA genes, exhibited similarity to the IR regions of other Orchidaceae plastomes. Previous studies reported nucleotide diversity values (Pi) of 0.14 for five Epidendrum plastomes and 0.129 for seven Trichoglottis plastomes [26,27]. In the case of E. roseum, the high intraspecific plastome polymorphism is manifested by Pi values reaching up to 0.146.…”