Giant chromosomes of a tiny plant-the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta).

The liverwort Apopellia endiviifolia, a dioicous, simple thalloid species, is notable for its cryptic diversity, habitat adaptability, and genomic innovation, and it represents a clade that is sister to all other Jungermanniopsida. These features make A. endiviifolia an essential model for exploring speciation mechanisms and the evolution of genome structures within liverworts. We present the genome assembly of a haploid A. endiviifolia isolate with a total size of 2,914,960,273 bp and an N50 of 468,157,909 bp, demonstrating high completeness (99.2% BUSCO) and a high consensus quality (quality value 47.6). The assembly consisted of 9 chromosomes, which included 18 telomeres and 9 centromeres (ranging from 1.9 to 5 Mbp in length). RNA sequencing-based annotation identified 34,615 genes, predominantly protein coding. The transposable elements comprised 12.16% long terminal repeat elements and 57 Helitrons. Among the retroelements, the Copia and Gypsy superfamilies comprised 8.94% and 2.95% of the genome, respectively. The Ty3/Gypsy superfamily was significantly enriched in centromeric regions. The average GC content ranged from 38.8% to 39.6%, with gene density varying between 5.52 and 9.78 genes per 500 kbp. Synteny analysis of related liverwort species has revealed complex chromosomal relationships, indicating extensive genome rearrangements among species. This study provides the first high-quality reference genome assembly of the haploid liverwort A. endiviifolia. Assembly and annotation offer valuable resources for investigating liverwort evolution, centromere biology, and genome expansion in simple thalloid liverworts.