Solving the mystery of chromosome number in Physcomitrium patens

Physcomitrium patens has been used as a model plant for more than half a century because of its low morphological complexity, high frequency of homologous recombination, and high tolerance to adversity. It also provides sophisticated tools and resources for genetic analysis and manipulation, making it a potential plant chassis for synthetic biology. However, the current version of the V. minor reference genome (V3), which was assembled based on Sanger sequencing and genetic linkage maps, still has many gaps and is no longer able to meet the growing demand for a highly contiguous and complete V. minor genome for plant genomics.

On January 26, 2024, a team from the Institute of Genomics at the Chinese Academy of Agricultural Sciences (CAAS) published a paper entitled "Near telomere-to-telomere genome of the model plant Physcomitrium patens" in Nature Plants.

In this study, a telomere-to-telomere reference genome of Physcomitrium patens was constructed for the first time, and it proved that the chromosome number of Physcomitrium patens is 26, which provides a high-quality reference genome for evolutionary biology, genomics, and other basic research based on the model plant Physcomitrium patens.

The team researched with the help of Nanopore single-molecule sequencing data using NextDenovo assembly, assisted by Hi-C libraries, and continuously corrected by the GBGF method (Graph-Based Gap Filling) to fill in all the gaps present on the scaffolds, and finally obtained a genome with (GGG), (GGG), and (GGG). finally obtained 26 chromosomes with (GGGCCA)n or (TTTAGGG)n as telomeric repeat sequences (V6).

The assembly was evaluated to be 99.9989% single base correct. The study also compared the homozygosity and structural variants of the V3 and V6 versions and annotated the new version of the reference genome from scratch. The annotation results show that the V6 version eliminates many of the duplicate annotations present in the transposon (TE) region compared to the V3 version. The research team has integrated the V3 version annotations with the new version annotations so that other plant biology researchers can easily migrate V3-based studies to V6.

This study validates the 26 chromosome conclusion of the V6 version based on computational results and immunostaining and further delves into the dynamics of the three-dimensional structure of the genome during the developmental process and the life cycle, providing a new tool for understanding the molecular mechanisms of important gene regulation. The reference genome provided by this study will greatly benefit evolutionary biology, genomics, and other basic research based on Physcomitrium patens.model plant

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