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

<h4>Background</h4>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.<h4>Findings</h4>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.<h4>Conclusions</h4>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.