Klebsormidiophyceae sister genomes reveal multicellularity and stress adaptations.

Klebsormidium and Interfilum are two closely related genera in the charophyte group Klebsormidiophyceae. Members of Klebsormidium are usually multicellular whereas those of Interfilum are unicellular. The genome of K. nitens has been sequenced using second-generation sequencing technology, but the assembled scaffolds are frequently fragmented. In this study, we re-sequenced the genomes of K. nitens using PacBio platform and obtained 15.8 Gb long reads. We also sequenced the genome of I. paradoxum and obtained 13 Gb long reads. The I. paradoxum genome assembly (81.7 Mb) included 59 contigs with N50 of 1.9 Mb, and the K. nitens assembly (132.9 Mb) included 188 contigs with N50 of 2.1 Mb. A total of 20,425 and 15,103 protein-coding genes were annotated in K. nitens and I. paradoxum, respectively. Comparative genome analyses identified 2805 gene families specific to Klebsormidiophyceae, which are enriched in gene ontology (GO) categories related to jasmonic acid (JA) biosynthesis and rRNA catabolism. Twenty-seven gene families, enriched in RNA-DNA hybrid ribonuclease activity and transmitter-gated ion channel activity, were found to have expanded in the last common ancestor of I. paradoxum and K. nitens. Several genes related to cell wall structure, including galactosyltransferase (GALT), were absent in I. paradoxum. We also found that approximately 50% of abiotic stress-related genes (e.g., late embryogenesis abundant, LEA genes) are present in land plants. The generation of K. nitens and I. paradoxum genomes and transcriptome data provides additional resources to understand the origin and evolution of land plants.