Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci

Area of Science:

• Botany
• Genomics
• Conservation Biology

Background:

• Understanding orchid species relationships is vital for conservation efforts.
• Target sequence capture is a powerful phylogenomic tool but is often limited by high design costs.
• Developing accessible methods for genetic analysis is crucial for orchid research.

Purpose of the Study:

• To design and test a cost-effective target capture kit for sequencing hundreds of orthologous loci across orchid lineages.
• To facilitate broader application of next-generation sequencing in orchid systematics and conservation.

Main Methods:

• A target capture bait set (Orchidaceae963) was designed using 963 single-copy genes from published orchid genomes.
• The bait set was tested on genomic libraries from 28 orchid species representing three subfamilies: Cypripedioideae, Orchidoideae, and Epidendroideae.

Main Results:

• High-throughput sequencing generated millions of reads for target-enriched libraries.
• An average of 812 genes were assembled per library for Epidendroideae and 501 genes for Orchidoideae and Cypripedioideae species.
• The kit successfully captured an average of 107 genes from the widely used Angiosperms353 bait set, enabling cross-study comparisons.

Conclusions:

• The Orchidaceae963 kit significantly enhances the accessibility and utility of next-generation sequencing for orchid research.
• This tool supports advancements in orchid systematics, population genetics, and the identification of illegally traded orchids.