A Universal Target-Enrichment Probe Set for Cycads Enables Standardised Phylogenomic and Population-Genomic Analyses

Full description

Cycads are among the most threatened plant lineages, yet genomic resources for resolving species boundaries, conservation units, and management priorities remain limited by large genomes, paralogy, and the lack of a standardised marker system across Cycadales. We present Cycad629, a target-enrichment probe set designed to generate comparable phylogenomic and population-genomic data across the order. Cycad629 was developed from transcriptomes representing 140 cycad species across all genera, as well as the published Cycas panzhihuaensis genome. Orthology screening identified 629 putatively single-copy genes present in at least 75% of taxa, supplemented by 129 genus-specific loci, yielding 758 candidate loci and 38,209 retained probes. We evaluated performance across 141 individuals representing 59 cycad taxa and population-level sampling of Encephalartos horridus and E. trispinosus. Cycad629 recovered high numbers of loci across genera despite variation in sequencing depth and enrichment efficiency. A 371-gene phylogenomic dataset produced a well-resolved species tree, and population-scale analyses yielded more than 52,000 high-quality SNPs per species before linkage pruning. These results show that Cycad629 provides a scalable and repeatable marker system for phylogenomics, conservation genetics, species delimitation, and landscape genomics in cycads.

Cycad629 target sequences for HybPiper assembly of cycad target-enrichment data
The Cycad629 target file is a FASTA-formatted reference sequence set used as input to HybPiper software for read mapping and locus assembly. It contains representative orthologous coding sequences for the full 758-locus Cycad629 panel, comprising 629 putatively single-copy nuclear loci shared across Cycadales and 129 additional genus-specific loci. Targets were developed using transcriptomic data representing 140 cycad species across all genera, together with the Cycas panzhihuaensis genome, and were screened for orthology, taxon occupancy and phylogenetic informativeness.

This target file is an analytical reference and does not contain raw or sample-specific sequencing reads. It enables reproducible assembly and comparison of paired-end Illumina target-capture reads associated with NCBI Sequence Read Archive submission SUB16333679. The libraries were enriched using the custom Cycad629 probe kit and sequenced on an Illumina NovaSeq 6000.

SUB16333679 is the temporary NCBI submission identifier. Once processing is complete, add the permanent BioProject and SRA/SRR accession numbers to the university record.