# Decoding the genome of Brainea insignis reveals insights into fern evolution and conservation

## TL;DR

The genome of Brainea insignis is decoded to reveal evolutionary insights and guide conservation efforts for this endangered fern.

## Contribution

A chromosome-level genome assembly of Brainea insignis is presented, offering new insights into fern evolution and conservation.

## Key findings

- The genome reveals an ancient whole-genome duplication and recent repeat accumulation contributing to its large size.
- Three geographically structured lineages shaped by Quaternary refugia and limited postglacial expansion are identified.
- Genomic erosion and climate-associated local adaptation are detected, with southwestern Indochina populations at highest risk.

## Abstract

Ferns are an ancient lineage of vascular plants, yet limited genomic resources constrain both evolutionary and conservation inference. Here, we generate a chromosome-level genome assembly for the endangered cycad fern Brainea insignis (8.62 Gb), the sole species in its genus within eupolypods II, and integrate comparative and population genomics to resolve its evolutionary history and vulnerability. The genome retains the ancient whole-genome duplication shared by leptosporangiate ferns; however, its exceptional size is driven primarily by recent repeat accumulation and further shaped by lineage-specific evolutionary signatures linked to functional specialization. Resequencing across the range identifies three geographically and environmentally structured lineages shaped by Quaternary refugia, limited postglacial expansion and localized admixture. Recently reduced populations show pronounced genomic erosion, including inbreeding and elevated genetic load, due to insufficient time for purging. We detect climate-associated local adaptation and project substantial future genetic offsets, with southwestern Indochina populations at highest risk. Our results expand fern genomics and support spatially tailored conservation strategies that maintains habitat connectivity and promotes adaptive gene flow.

Limited genomic resources constrain our understanding of fern evolution and conservation. Here, the authors present the genome of Brainea insignis, a monotypic endangered fern, and identify evolutionary signatures to guide conservation strategies from comparative and population genomic analyses.