High-quality Genome Assembly of Syntrichia caninervis Reveals Copia-dominant Centromeric Structure

The Telomere-to-Telomere (T2T) genome represents the most complete reference genome for species, providing essential genetic information that aids in studies of populations and gene functions. Advancements in third-generation sequencing technologies, like PacBio and Oxford Nanopore, have greatly enhanced genomic analyses of key species.

Syntrichia caninervis, a crucial species in desert biological soil crusts, maintains ecological balance in the Gurbantunggut Desert. This moss has gained attention as a model for studying desiccation tolerance, demonstrating resilience to extreme stresses. However, assembling its high-quality genome has been challenging due to difficulties in obtaining pure strains and endosymbiotic sequence contamination.

In a study published in Plant Biotechnology Journal, Prof. ZHANG Daoyuan's team at the Xinjiang Institute of Ecology and Geography (XIEG) of the Chinese Academy of Sciences, successfully developed a monoclonal tissue culture system for Syntrichia caninervis. By employing third-generation sequencing, they obtained the complete genome sequence of its endosymbiont, Paenibacillus sp., and achieved a gapless assembly of Syntrichia caninervis's genome, totaling 323.44 Mbp with an N50 value of 24.41 Mbp and single-base accuracy over 99.999%. This makes it the highest-quality moss genome reported to date.

The T2T genome of Syntrichia caninervis surpassed the previous Mojave Desert genome by assembling over 30 Mbp of previously missing sequences, filling over 20,000 chromosomal gaps, and annotating more than 1,500 additional protein-coding genes. Notably, new structural variations were found on sex chromosomes from differing ecotypes in the Gurbantunggut and Mojave Deserts. The latest genome version also identified 677 transcription factor genes—135 more than before—and fully annotated previously unclassified factors, enriching the transcriptional regulatory gene pool.

Key desiccation-related gene families, including LEA and ELIPs, exhibited increased tandem repeat patterns, with a 10% improvement in transcriptomic mapping rates over the prior version. These enhancements provide a solid foundation for future population genomics and gene function research.

The assembly of centromeric regions, historically challenging, is now a focus for detailed structural analysis. The study confirmed the centromeric structure of Syntrichia caninervis, dominated by Copia transposons, which contrasts with angiosperms. This discovery offers valuable insights into the evolutionary patterns of centromeric structures in land plants.

Article link：https://doi.org/10.1111/pbi.14549

Contact

LONG Huaping

Xinjiang Institute of Ecology and Geography

E-mail: longhp@ms.xjb.ac.cn

Web: http://english.egi.cas.cn