# First Plastome Sequences of Two Endemic Taxa of Orbea Haw. from the Arabian Peninsula: Comparative Genomics and Phylogenetic Relationships Within the Tribe Ceropegieae (Asclepiadoideae, Apocynaceae)

## TL;DR

This study provides the first complete chloroplast DNA sequences for two rare Orbea plants from the Arabian Peninsula, revealing unique genetic features and evolutionary relationships.

## Contribution

The study reports the first plastome sequences of two Arabian Orbea species and identifies key genetic differences and evolutionary patterns.

## Key findings

- One Orbea species has the largest chloroplast genome in the tribe Ceropegieae with structural rearrangements.
- Six highly variable DNA regions were identified as potential barcodes for plant identification and evolutionary studies.
- Arabian Orbea species form a distinct evolutionary group separate from African species.

## Abstract

Orbea Haw. is a genus of succulent plants that grow in extremely dry regions, including parts of the Arabian Peninsula. These plants contribute to the unique biodiversity of desert ecosystems, yet their chloroplast genetic information has remained largely unstudied. This research presents the first complete chloroplast DNA sequences of two Orbea plants endemic to the Arabian Peninsula. By examining and comparing their genetic sequences with those of related species, several notable findings were revealed. One species possesses an unusually large chloroplast genome and a distinctive rearrangement of several genes, indicating a more complex evolutionary history than previously recognized. Regions of the DNA that show high levels of variation between species were also identified; these areas can support accurate plant identification and further studies on plant evolution. In addition, the relationship between the Orbea species was clarified, showing that the Arabian plants form a separate group from the African species. These results provide essential new information for understanding, conserving, and documenting the diversity of desert plants in the Arabian Peninsula.

Orbea is a morphologically diverse lineage within the subtribe Stapeliinae, yet plastome evolution in Arabian taxa remains insufficiently characterized. This study reports the first complete chloroplast genomes of Orbea sprengeri subsp. commutata and O. wissmannii var. eremastrum and investigates plastome structure, sequence variability, and phylogenetic relationships across tribe Ceropegieae. Chloroplast genomes were assembled, annotated, and compared with 13 published plastomes representing major Ceropegieae lineages. Both Arabian plastomes displayed the typical quadripartite structure and identical gene content of 114 unique genes, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. However, O. wissmannii var. eremastrum exhibited pronounced structural divergence, possessing the largest plastome recorded for the tribe (170,054 bp), an 8.9 kb expansion of the inverted repeat regions, and an 8.4 kb inversion spanning the ndhG–ndhF region. Comparative analyses revealed conserved gene order across Ceropegieae but identified six highly variable loci (accD, clpP, ndhF, ycf1, psbM–trnD, and rpl32–trnL) as potential DNA barcodes. Selection pressure analyses indicated strong purifying selection across most genes, with localized adaptive signals in accD, ndhE, ycf1, and ycf2. Phylogenomic reconstruction consistently resolved the two Arabian Orbea taxa as a distinct clade separate from the African O. variegata. This study fills a gap in Ceropegieae plastid genomics and underscores the importance of sequencing additional Orbea species to capture the full extent of genomic variation within this diverse genus.