Chromosome-scale reference genome of Pectocarya recurvata, the species with the smallest reported genome size in Boraginaceae

Abstract

Premise

Pectocarya recurvata (Boraginaceae, subfamily Cynoglossoideae), a species native to the Sonoran Desert (North America), has served as a model system for a suite of ecological and evolutionary studies. However, no reference genomes are currently available in Cynoglossoideae. A high-quality reference genome for P. recurvata would be valuable for addressing questions in this system and across broader taxonomic scales.

Methods

Using PacBio HiFi sequencing, we assembled a reference genome for P. recurvata and annotated coding regions with full-length transcripts from an Iso-Seq library. We assessed genome completeness with BUSCO and k-mer analysis, and estimated the genome size of six individuals using flow cytometry.

Results

The chromosome-scale genome assembly for P. recurvata was 216.0 Mbp long (N50 = 12.1 Mbp). Previous observations indicated P. recurvata is 2n = 24. Our assembly included 12 primary contigs (158.3 Mbp) containing 30,655 genes with telomeres at 23 out of 24 ends. Flow cytometry measurements from the same population included two plants with 1C = 196.9 Mbp, the smallest measured for Boraginaceae, and four with 1C = 385.8 Mbp, which is consistent with tetraploidy in this population.

Discussion

The P. recurvata genome assembly and annotation provide a high-quality genomic resource in a sparsely represented area of the angiosperm phylogeny. This new reference genome will facilitate answering open questions in ecophysiology, biogeography, and systematics.