Seagrasses colonized the sea1 on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet2. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes3, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae4 and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming5, 6, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants7.
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Extended data figures and tables
Extended Data Figures
- Extended Data Figure 1: Number of genes expressed in five tissues of Z. marina. (336 KB)
a, Venn diagram of genes with expression values (FPKM) higher than 1 are considered as expressed in the tissue. b, Pairwise differential gene expression analysis between tissues. The male flower shows the highest number of differentially expressed genes.
- Extended Data Figure 2: Circos plot of the ten largest scaffolds of Z. marina. (676 KB)
Tracks from outside to inside. GC percentage, gene density, and transposable element (TE) density (density measured in 20-Kb sliding windows and gene expression profiles from five tissues (root, leaf, male flower, female flower early and female flower late) presented as log2 FPKM values.
- Extended Data Figure 3: Potential impact of transposable elements (TEs) on Z. marina evolution. (151 KB)
a, Frequency distribution of pairwise sequence identity values between copies of Copia- and Gypsy-type LTR retrotransposons and DNA transposons, and their cognate consensus sequences (younger repeats share higher sequence similarity). Two peaks are detectable for Copia-type elements. b, Distance to the closest TE for the set of Z. marina single-copy genes and the set of Z. marina accessory genes. TE-proximal accessory genes are more frequent than TE-proximal single-copy genes. c, Frequency of pairwise sequence identity between accessory gene-proximal Ty3-Gypsy elements and their cognate consensus sequences. A number of high-identity copies (that is, putatively young duplicate genes) is observed.
- Extended Data Figure 4: Unrooted maximum likelihood tree of genes encoding light-harvesting complex A (LHCA) and LHCB proteins of Z.marina, Spirodela polyrhiza and Arabidopsis thaliana. (229 KB)
The analysis was carried out on protein sequences using PhyML 3 with LG substitution model and 100 bootstrap replicates. Supplementary Note 7.1, Supplementary Table 7.3.
- Extended Data Figure 5: Alignment of metallothionein (MT) and half-metallothionein (HMT) genes in Z. marina as compared with other plants. (954 KB)
Alignments were performed in ClustalW on the Lyon PBIL web server and edited manually. The upper alignments are for type 1–3 MTs and HMTs; the lower alignment is for type 4 EcMTs where there is no Zostera homologue. Conserved residues are shown in red and residues in the same amino acid group in blue. Cys and His residues, putatively involved in binding metals, are highlighted in green and yellow, respectively. Aromatic amino acids absent in canonical animal MTs are highlighted in grey. MTs and MT-like proteins were obtained from: Arabidopsis thaliana (ARATH), Japanese rice (ORYSJ), Cicer arietinum (CICAR), banana (MUSAC), wheat (WHEAT), potato (SOLTU), Setaria Italica (SETIT), Vitis vinifera (VITVI) and the alismatids: Posidonia oceanica (POSOC) highlighted in grey, Spirodela polyrhiza (SPIPO) highlighted in blue, and Zostera marina (ZOSMA) highlighted in yellow. See Supplementary Note 8.2.
- Extended Data Figure 6: Conceptual summary of physiological and structural adaptations made by Z. marina in its return to the sea. (631 KB)
Ecosystem services shown in blue. Physical processes related to salinity, light and CO2 availability shown in white within light-green boxes. Gene losses and gains associated with morphological and physiological processes shown in white within the dark-green box on the right.