The Genome of the Charophyte AlgaPenium margaritaceumBears Footprints of the Evolutionary Origins of Land Plants

Abstract

30The colonization of land by plants was a pivotal event in the history of the biosphere, and yet the 31 underlying evolutionary features and innovations of the first land plant ancestors are not well 32 understood. Here we present the genome sequence of the unicellular alga Penium margaritaceum, 33 a member of the Zygnematophyceae, the sister lineage to land plants. The P. margaritaceum 34 genome has a high proportion of repeat sequences, which are associated with massive segmental 35 gene duplications, likely facilitating neofunctionalization. Compared with earlier diverging plant 36 lineages, P. margaritaceum has uniquely expanded repertoires of gene families, signaling 37 networks and adaptive responses, supporting its phylogenetic placement and highlighting the 38 evolutionary trajectory towards terrestrialization. These encompass a broad range of physiological 39 processes and cellular structures, such as large families of extracellular polymer biosynthetic and 40 modifying enzymes involved in cell wall assembly and remodeling. Transcriptome profiling of 41 cells exposed to conditions that are common in terrestrial habitats, namely high light and 42 desiccation, further elucidated key adaptations to the semi-aquatic ecosystems that are home to the 43 Zygnematophyceae. Such habitats, in which a simpler body plan would be advantageous, likely 44 provided the evolutionary crucible in which selective pressures shaped the transition to land. 45 Earlier diverging charophyte lineages that are characterized by more complex land plant-like 46 anatomies have either remained exclusively aquatic, or developed alternative life styles that allow 47 109 of 116.1 kb. The nuclear assembly captured most of the k-mers in the Illumina reads and low 110 frequency k-mers representing sequencing errors were absent ( Supplementary Fig. 1B). In addition, 111 the mapping rates of genomic and RNA-Seq reads against the nuclear assembly were 97.5% and 112 5 96.8%, respectively (Supplementary Table 2). The single nucleotide polymorphism (SNP) 113 frequency distribution on the 100 longest scaffolds was consistent with a haploid genome 114 ( Supplementary Fig. 1C). The mitochondrial and chloroplast genomes were also fully assembled, 115 and comprised 95,332 and 145,411 nucleotides, respectively ( Supplementary Fig. 2). 116The assembly contains a large proportion (80.6%) of repeat sequences (Supplementary 117 Table 3), particularly long terminal repeat (LTR) retrotransposons and simple repeats ( Fig. 2A). 118Unlike land plants and C. braunii, in which gypsy is the predominant LTR family, the P. 119 margaritaceum genome has a large proportion of copia retrotransposons, which are rare in other 120 green algae and absent from C. braunii (Nishiyama et al. 2018). An estimation of divergence time 121 indicated that the copia expansion in the P. margaritaceum genome was relatively recent, around 122 2.1 Mya (Fig. 2B). Retrotransposons carrying tyrosine recombinases, such as the DIRS and Ngaro 123 families, which are found in some chlorophyte...

Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily

“…By contrast, Zygnematophyceae zygospores contain algaenan that differs from pollen grains in its chemical position and the biochemical pathway (acetate-malate pathway) leading to its production (97). Furthermore, to our knowledge, the presence of type III PKS-like enzymes in the genomes of Charophyta is not reported with the exception of Penium margaritaceum (36). The adaption of a sporopollenin-containing protecting spore wall is considered a synapomorphy of the embryophytes to colonize the land, but appears to be pre-adaptive given that it is present in the Charophyceae, the proposed sister group to the embryophytes (7,(94)(95)(96)98).If LAP5/6 evolved first, the syntenic clusters 1/27 and/or 3/11 duplicated and formed the cluster that later the syntenic cluster that contain 'R-4-C'-type PKS genes followed by a loss of synteny between the clusters 1/27 and 3/11.…”

“…The PKSs from Ectocarpus siliculosus fall within the range of generic PKS sequences found in These findings suggest that a lateral gene transfer of type III PKS, possibly by an ancestral actinobacterium, occurred following the separation of the diatoms from other members of the Ochrophyta, but before the brown algae diverged from the Pelagophytes and Dictyochophytes(51). Similarly, genes of other pathways, including the genes for mannitol, alginate and hemicellulose biosynthesis, are present in brown algae but absent in diatoms, suggesting a lateral gene transfer from an ancestral actinobacterium to Ectocarpus siliculosus(51,56,57).It was previously stated that land plants originated from the Streptophytes of the Penium margaritaceum was reported to contain eleven copies of type III PKS(36). This indicates that type III PKS appeared earliest with the Zygnematophyceae, but not with the earlier appearing…”

Evolutionary analysis of a billion years of auxin biology

“…Nevertheless, it was suggested that the majority of the orthologs of land plant auxin pathways were found in charophytes, but absent in chlorophytes. Indeed, recently published charophyte genomes confirmed the presence of orthologs of various pathways that were earlier thought to be specific to land plants (Jiao et al, 2019;. In Chapter 3, we also found that the single homologs of auxin biosynthetic gene families (TAA and YUC) were found in charophytes but not in the chlorophytes.…”

“…On the other hand, two-component histidine kinase signaling components of cytokinin and ethylene pathways evolved prior to land plants, representing system that is more ancient than the nuclear auxin pathway (Bowman et al, 2017;Jiao et al, 2019;. In contrast, despite the presence of some ABA synthesis pathway components in charophytes, the ABAdependent responses were found only in land plants and further enhanced in vascular plants by gaining additional receptors .…”

The Phylogeny of Class B Flavoprotein Monooxygenases and the Origin of the YUCCA Protein Family

“…This suggests the absence of the functional canonical auxin biosynthetic pathway in K. nitens and implies that this pathway is a land plant innovation [ 23 ]. Recent projects on the genome sequencing of charophytes Penium Margaritaceum (Zygnematales) [ 57 ], Chara braunii [ 57 , 58 ], and Nitella [ 28 ] (Charophyceae) support this hypothesis: neither TAA nor YUCCA homologs were identified in these genomes. These data are consistent with experimental results by Ai et al [ 59 ], who demonstrated that Klebsormidium TAA homologs could not restore the wild-type phenotype of taa mutants in Arabidopsis.…”