Comparative Chloroplast Genomics of Ten Collabieae Species Including Three Novel Genomes

Area of Science:

• Plant genomics
• Orchidaceae evolutionary biology

Background:

• Collabieae orchids, found in tropical Asia, possess significant ornamental and medicinal value.
• Habitat destruction and overharvesting threaten wild Collabieae populations.
• Chloroplast (cp) genomes are vital for understanding genetic diversity and evolutionary relationships.

Purpose of the Study:

• To characterize the chloroplast genome of the Collabieae tribe.
• To provide genomic resources for the conservation of Collabieae species.

Main Methods:

• Sequencing and analysis of three new chloroplast genomes (Acanthophippium sylhetense, Eriodes barbata, Spathoglottis plicata) and seven related species.
• Comparative analysis of genome structure, gene content, and sequence variation.

Main Results:

• All ten Collabieae cp genomes exhibit a conserved quadripartite circular structure (157,036–158,321 bp) with 136 genes.
• High consistency in gene number, order, orientation, GC content, and codon usage was observed.
• Structural divergence at plastome junctions, variations in SSRs and repetitive elements, and six hypervariable regions were identified.
• Phylogenetic analysis revealed distinct branching patterns for E. barbata, Acanthophippium, and Spathoglottis.

Conclusions:

• The phylogenetic framework supports previous findings on Collabieae evolution.
• This research offers essential cp genomic data for advancing evolutionary studies and conservation efforts for Collabieae orchids.