Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment
Ma, Xiao; Vanneste, Steffen; Chang, Jiyang; Ambrosino, Luca; Barry, Kerrie; Bayer, Till; Bobrov, Alexander A.; Boston, LoriBeth; Campbell, Justin E.; Chen, Hengchi; Chiusano, Maria Luisa; Dattolo, Emanuela; Grimwood, Jane; He, Guifen; Jenkins, Jerry; Khachaturyan, Marina; Marin-Guirao, Lazaro; Mesterhazy, Attila; Muhd, Danish-Daniel; Pazzaglia, Jessica; Plott, Chris; Rajasekar, Shanmugam; Rombauts, Stephane; Ruocco, Miriam; Scott, Alison; Tan, Min Pau; Van de Velde, Jozefien; Vanholme, Bartel; Webber, Jenell; Wong, Li Lian; Yan, Mi; Sung, Yeong Yik; Novikova, Polina; Schmutz, Jeremy; Reusch, Thorsten B.H.; Procaccini, Gabriele; Olsen, Jeanine L.; Van de Peer, Yves
Date:
2024-03
Abstract:
We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the ‘savannahs of the sea’ are of major concern in times of climate change and loss of biodiversity.
Description:
DATA AVAILABILITY : The DNA sequencing data for the C. nodosa genome assembly have been deposited in the NCBI database under BioProject PRJNA1041560 via the link https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1041560. All assemblies and annotations for all seagrass species discussed in the current paper can be found at https://bioinformatics.psb.ugent.be/gdb/seagrasses/. The transcriptome data (including raw data and clean data) and sequencing QC reports for C. nodosa can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Cymnodnscriptome_2, the transcriptome data and sequencing QC reports for P. oceanica can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Posocenscriptome_2, the transcriptome data and sequencing QC reports for T. testudinum can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Thatesnscriptome_4 and the transcriptome data for Z. marina are from ref. 15. For the public databases, the RFAM database v.14.7 can be downloaded at https://ftp.ebi.ac.uk/pub/databases/Rfam/14.7/, the UniProt database can be accessed from the web at http://www.uniprot.org and downloaded from http://www.uniprot.org/downloads and the NCBI nucleotide database can be accessed via https://www.ncbi.nlm.nih.gov/.