A near chromosome-level assembly of the serpentine endemic columbine, Aquilegia eximia

Sep 29, 2026

The flowering plant genus Aquilegia contributes to biodiversity and illustrates biotic and abiotic niche adaptation across the Northern Hemisphere, particularly in California. The study reports a near-chromosome level draft genome assembly for Aquilegia eximia, a California endemic serpentine-soil specialist. Using high-throughput long reads (PacBio) and chromatin capture (Omni-C), the assembly improves contiguity over an existing North American reference. The genome supports comparative analyses, revealing shared overall structure and reciprocal translocation differences among related columbines, and enables conservation-focused genomic and trait mapping for the CCGP.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages11

Reading Time28 min

AccessFree to download

Abstract

Introduction

Genome Resources A near chromosome-level assembly of the serpentine endemic columbine, Aquilegia eximia Jason Johns1,*,, Merly Escalona2,, Courtney Miller3, Noravit Chumchim4, Oanh Nguyen4,, Mohan P. A. Marimuthu4,, Samuel Sacco5,, Colin Fairbairn5,, Eric Beraut5,, ErinToffelmier3,, H. Bradley Shaffer3, and Scott Hodges1,*, 1Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States, 2Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States, 3UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States, 4DNA Technologies and Expression Analysis Core Laboratory, University of California Davis, Davis, CA, United States, 5Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States * Corresponding author: Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States. Email: [johnswjason@gmail.com](johnswjason@gmail.com) (JJ); Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States. Email: [sahodges@ucsb.edu](sahodges@ucsb.edu) (SH) Corresponding Editor: Carolyn Wessinger Abstract The flowering plant genus Aquilegia (columbine) is an important contributor to biodiversity and an example of both biotic and abiotic niche adaptation across much of the Northern Hemisphere, especially in California. Here we report a near-chromosome level draft genome assembly for A. eximia, a California endemic species. A. eximia is a serpentine-soil specialist and is very closely related to 2 columbine species also being studied for the California Conservation Genomics Project (CCGP), A. formosa (widespread) and A. pubescens (high alpine) . Utilizing high throughput, long reads (PacBio) and chromatin capture (Omni-C), the A. eximia genome makes marked contiguity improvements compared to the existing reference genome for another North American columbine, A. coerulea “Goldsmith.”The A. eximia genome will also be more useful for aligning whole genome resequencing data from California columbines than the genomes for more distantly related columbine species, the Asian A. oxysepala var. kansuensis and the European A. vulgaris. Notably, we found evidence that A. eximia, A. coerulea “Goldsmith,” and A. vulgaris all share the same overall genome structure and differ from A. oxysepala var. kansuensis by the same reciprocal translocation. The A. eximia reference genome will be a valuable tool for identifying patterns of plant biodiversity across California for the CCGP, as well as for future population genomic and trait mapping studies. Key words: California Conservation Genomics Project, CCGP, plant, reference genome, reciprocal translocation, ultramafic Introduction Aquilegia (columbines) is a genus of flowering plants of ca. 70 species (Munz 1946), having adapted to a wide variety of habitats and pollinators across the Northern Hemisphere over a short evolutionary timespan estimated at ca. 6 to 7 My (Whittall and Hodges 2007; Bastida et al. 2010; Fior et al. 2013; Zhai et al. 2019) . In California, there are 3 predominant species, the widespread A. formosa Fish. ex DC.(Hook 1881), and 2 endemic species, A. eximia Van Houtte ex Planch (Planch 1857) and A. pubescens (Coville 1893) . Our goal here is to develop a high-quality reference genome that is suitable for assessing genetic diversity of all 3 species, allowing us to assess both a widespread species and those in extreme habitats. Aquilegia formosa is found from northern Mexico to Alaska and occurs in 10/13 USDA ecoregions across the Southern California Mountains, Northern California Coast and Interior Coast Ranges, Klamath Range, the Southern, Central,

FAQs

What genome assembly is reported for Aquilegia eximia?

A near-chromosome level draft genome assembly for Aquilegia eximia is reported, built to support conservation genetics work in California.

Which sequencing technologies were used to generate the assembly?

The assembly used high-throughput long reads from PacBio and chromatin capture data from Omni-C.

What did the study find about genome structure among related Aquilegia species?

The study reports evidence that Aquilegia eximia, Aquilegia coerulea “Goldsmith,” and Aquilegia vulgaris share the same overall genome structure, while Aquilegia oxysepala var. kansuensis differs by the same reciprocal translocation.

Sep 29, 2026

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