Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis

Abstract

Background Calanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae. Results The complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius. Conclusion This study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.

Characterization of the Complete Chloroplast Genome and Phylogenetic Implications of Euonymus microcarpus (Oliv.) Sprague

“…It suggests that the four most frequently used codons are AAA-K (1114), AUU-I (1093), GAA-E (1058) and UUU-F (982), accounting for 4.14%, 4.07%, 3.94% and 3.65% among all codons, respectively ( Table S2 and Figure 3 ). Similar to the previous results for other angiosperms, most of the codons ending with A or T have RSCU values greater than 1, while, most of those ending with C or G have RSCU values of less than 1 [ 25 , 26 , 27 ].…”

Complete Chloroplast Genome of a Montane PlantSpathoglottis aureaLindl.: Comparative Analyses and Phylogenetic Relationships among members of Tribe Collabieae

“…Compared to other Collabieae species, the S. aurea cp genome shows a highly conserved structure without any gene loss. The quadripartite structure and gene compositions are consistent with previously reported Collabieae species (9,10,40). In Figure 5, gene inversion was observed in the Collabium formosanum cp genome because of its different orientation submitted in the GenBank (41).…”

“…In the present study, S. aurea shows a further relationship with other species (Clade A); in particular, Cephalantheropsis and Phaius also reside in the same clade as Calanthe . Despite several differences in morphological characteristics, a number of molecular studies (9,44) including the present study have consistently shown that these two genera are positioned within the Calanthe clade. For the Phaius species, the morphological characteristic differences are minimal compared to those of the Calanthe species.…”

“…Despite this, based on a revision by Chase (7), among the Collabieae tribe the chloroplast genome has been reported for several taxa, such as Calanthe (8)(9)(10)(11) and Tainia (12)(13)(14). Although the group has approximately 450-500 known species, scarce genomic data are available and there are few reports of taxonomic conflicts (9,15,16).…”

Un synopsis du genre Calanthe R.Br. (Collabieae, Orchidaceae) en Nouvelle-Calédonie, avec la caractérisation de deux nothoespèces

“…et Styloglossum Breda au niveau générique. Récemment, l'analyse du plastome de huit espèces de l'alliance Calanthe confirme la polyphylie (Chen et al 2020; Nanjala et al 2022).…”