Genomewide transcriptional reprogramming in the seagrass Cymodocea nodosa under experimental ocean acidification

Abstract

Here, we report the first use of massive-scale RNA-sequencing to explore seagrass response to CO -driven ocean acidification (OA). Large-scale gene expression changes in the seagrass Cymodocea nodosa occurred at CO levels projected by the end of the century. C. nodosa transcriptome was obtained using Illumina RNA-Seq technology and de novo assembly, and differential gene expression was explored in plants exposed to short-term high CO /low pH conditions. At high pCO , there was a significant increased expression of transcripts associated with photosynthesis, including light reaction functions and CO fixation, and also to respiratory pathways, specifically for enzymes involved in glycolysis, in the tricarboxylic acid cycle and in the energy metabolism of the mitochondrial electron transport. The upregulation of respiratory metabolism is probably supported by the increased availability of photosynthates and increased energy demand for biosynthesis and stress-related processes under elevated CO and low pH. The upregulation of several chaperones resembling heat stress-induced changes in gene expression highlighted the positive role these proteins play in tolerance to intracellular acid stress in seagrasses. OA further modifies C. nodosa secondary metabolism inducing the transcription of enzymes related to biosynthesis of carbon-based secondary compounds, in particular the synthesis of polyphenols and isoprenoid compounds that have a variety of biological functions including plant defence. By demonstrating which physiological processes are most sensitive to OA, this research provides a major advance in the understanding of seagrass metabolism in the context of altered seawater chemistry from global climate change.

Elevated trace elements in Posidonia oceanica and Cymodocea nodosa at six Mediterranean volcanic seeps

“…Saying that, studies on seagrass eco-physiology at these CO 2 seeps have provided mixed results, for example, Posidonia oceanica antioxidant stress related genes are more expressed near volcanic seeps (at Panarea and Ischia Islands, Italy), whereas the expression of genes involved in photosynthesis and growth responses of Cymodocea nodosa near a seep off Vulcano islands, Italy were contrary to the expected beneficial effects of CO 2 (Olivé et al, 2017). On the other hand, under experimental CO 2 enrichment there was a significant increased expression of C. nodosa transcripts associated with photosynthesis, as expected (Ruocco et al, 2017).…”

m6A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms

“…Here, we provided a first inventory of these genes in marine plants in terms of the presence/absence and expression patterns across species and under different conditions. We screened the protein complement of the Z. marina genome, the first seagrass species for which a full genome sequence has been obtained [ 51 ], and the one of a previously published transcriptome of C. nodosa [ 58 ], together with the protein complement of Arabidopsis thaliana and Oryza sativa genomes, to identify writer and eraser proteins through a comparative approach. The comparative analysis of all the considered species led to the construction of networks of ortholog and paralog proteins.…”

“…Dedicated analyses (by multiple alignments, data not shown) confirmed that similar copies from C. nodosa sequences included in the considered networks have to be considered as products of alternative transcripts that are worth being further investigated as a result of the already published transcriptome assembly [ 58 ].…”

“…Protein collections for C. nodosa , A. thaliana , O. sativa, and Z. marina were downloaded from ENA [ 58 ], TAIR [ 63 ], TIGR [ 64 ], and ORCAE [ 50 ] databases, respectively. The networks of orthologs and paralogs were predicted by using a python software developed according to the pipeline described in two works that were already published [ 65 , 66 ].…”

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.

“…Although only one (of the TAR/Tork lineage) over 180 LTR-REs resulted significantly over-expressed in heat-treated than in control plants, it cannot be excluded that retrotransposon expression in meadows subjected to environmental constraints can increase, since environmental stresses often induce transposable element transcription, as observed in another seagrass, Cymodocea nodosa, under experimental acidification [72]. Such an activity might produce genetic and epigenetic variations, which could be selected in those environments.…”