Underwater CAM photosynthesis elucidated by Isoetes genome

Abstract

To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigated the underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identified several key differences. Notably, for carboxylation of PEP, Isoetes recruited the lesser-known "bacterial-type" PEPC, along with the "plant-type" exclusively used in other terrestrial CAM and C4 plants. Furthermore, we found that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.

Core circadian clock and light signaling genes brought into genetic linkage across the green lineage

“…For instance, almost all of the genes in the single-celled pico-algae Ostreococcus show oscillations in gene expression in a TOD fashion ( Monnier et al, 2010 ; Thommen et al, 2012 ), while 80% of genes in the model macroalga Chlamydomonas reinhardtii have TOD peak abundance ( Zones et al, 2015 ). In most plants, over 30% of genes cycle under diurnal conditions of light and temperature, while 10%–20% cycle under circadian conditions of continuous light and temperature ( Michael et al, 2008b ; Khan et al, 2010 ; Filichkin et al, 2011 ; Sato et al, 2013 ; Nose and Watanabe, 2014 ; Cronn et al, 2017 ; Ferrari et al, 2019 ; MacKinnon et al, 2019 ; Wai et al, 2019 ; Greenham et al, 2020 ; Lai et al, 2020 ; Michael et al, 2020 ; Wickell et al, 2021 ). However, there is evidence that the majority of genes in plants may have TOD expression potential since in Arabidopsis 90% of all genes have TOD expression in at least one of an array of conditions tested ( Michael et al, 2008b ).…”

“…While plants have more components, this core negative feedback circadian clock is conserved as far back as Ostreococcus , whose oscillator is made up of one sMYB– PRR loop ( Corellou et al, 2009 ; Monnier et al, 2010 ; Morant et al, 2010 ). Subsequently, several studies have explored the evolution and conservation of the core circadian clock components in bryophytes, lycophytes, and a diverse array of angiosperms finding that some genes like the sMYB and PRRs are found across the green linkage, yet others have only emerged in flowering plants ( Holm et al, 2010 ; McClung, 2010 ; Takata et al, 2010 ; Satbhai et al, 2011 ; Ryo et al, 2016 ; Linde et al, 2017 ; Wickell et al, 2021 ). However, as more nonmodel plants from distinct branches of the green lineage are analyzed, novelty in the circadian clock may become more prevalent.…”

Data_Sheet_2.PDF

“…Of these, the monogeneric Selaginellales and Isoëtales have garnered the most research attention, with the former being used extensively for studying evo-devo and desiccation tolerance (VanBuren et al, 2018;Spencer et al, 2021) and the latter for its independent origin of CAM photosynthesis and well-documented, rampant hybridization (Szovenyi et al, 2021). The recent publications of Selaginella and Isoëtes genomes has also brought these two lineages into the modern genomic era (Banks et al, 2011;VanBuren et al, 2018;Xu et al, 2018;Wickell et al, 2021). Lycopodiales, however, are both the most diverse (16 genera across three subfamilies) and least studied order, receiving relatively sparse research and completely lacking genomic resources.…”

Table_2.xlsx

“…Of these, the monogeneric Selaginellales and Isoëtales have garnered the most research attention, with the former being used extensively for studying evo-devo and desiccation tolerance (VanBuren et al, 2018;Spencer et al, 2021) and the latter for its independent origin of CAM photosynthesis and well-documented, rampant hybridization (Szovenyi et al, 2021). The recent publications of Selaginella and Isoëtes genomes has also brought these two lineages into the modern genomic era (Banks et al, 2011;VanBuren et al, 2018;Xu et al, 2018;Wickell et al, 2021). Lycopodiales, however, are both the most diverse (16 genera across three subfamilies) and least studied order, receiving relatively sparse research and completely lacking genomic resources.…”