Changes in atmospheric CO 2 concentration have played a central role in algal and plant adaptation and evolution. The commercially important red algal genus, Pyropia (Bangiales) appears to have responded to inorganic carbon (C i ) availability by evolving alternating heteromorphic generations that occupy distinct habitats. The leafy gametophyte inhabits the intertidal zone that undergoes frequent emersion, whereas the sporophyte conchocelis bores into mollusk shells. Here, we analyze a high-quality genome assembly of Pyropia yezoensis to elucidate the interplay between C i availability and life cycle evolution. We find horizontal gene transfers from bacteria and expansion of gene families (e.g. carbonic anhydrase, anti-oxidative related genes), many of which show gametophyte-specific expression or significant up-regulation in gametophyte in response to dehydration. In conchocelis, the release of HCO 3 - from shell promoted by carbonic anhydrase provides a source of C i . This hypothesis is supported by the incorporation of 13 C isotope by conchocelis when co-cultured with 13 C-labeled CaCO 3 .

Pyropia haitanensis (Bangiales, Rhodophyta), a major economically important marine crop, is also considered as an ideal research model of Rhodophyta to address several major biological questions such as sexual reproduction and adaptation to intertidal abiotic stresses. However, comparative genomic analysis to decipher the underlying molecular mechanisms is hindered by the lack of high‐quality genome information. Therefore, we integrated sequencing data from Illumina short‐read sequencing, PacBio single‐molecule sequencing and BioNano optical genome mapping. The assembled genome was approximately 53.3 Mb with an average GC% of 67.9%. The contig N50 and scaffold N50 were 510.3 kb and 5.8 Mb, respectively. Additionally, 10 superscaffolds representing 80.9% of the total assembly (42.7 Mb) were anchored and orientated to the 5 linkage groups based on markers and genetic distance; this outcome is consistent with the karyotype of five chromosomes (n = 5) based on cytological observation in P. haitanensis. Approximately 9.6% and 14.6% of the genomic region were interspersed repeat and tandem repeat elements, respectively. Based on full‐length transcriptome data generated by PacBio, 10,903 protein‐coding genes were identified. The construction of a genome‐wide phylogenetic tree demonstrated that the divergence time of P. haitanensis and Porphyra umbilicalis was ~204.4 Ma. Interspecies comparison revealed that 493 gene families were expanded and that 449 were contracted in the P. haitanensis genome compared with those in the Po. umbilicalis genome. The genome identified is of great value for further research on the genome evolution of red algae and genetic adaptation to intertidal stresses.

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