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

Background The liverwort A. endiviifolia, a dioicous, simple thalloid species, is notable for its cryptic diversity, habitat adaptability, genomic innovation, and 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. Findings 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 (QV 47.6). The assembly consisted of nine chromosomes, which included 18 telomeres and nine centromeres (ranging from 1.9 to 5 Mbp in length). RNA-seq-based annotation identified 34,615 genes, predominantly protein-coding. The TEs comprised 12.16% LTR 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 found to be significantly enriched in centromeric regions. The average GC content ranged from 38.8% to 39.6%, with gene density varied between a value 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. Conclusions 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.