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The filamentous algal endophyte Laminarionema elsbetiae is highly prevalent in European populations of the brown alga Saccharina latissima, but has also been found occasionally in the other kelp species Laminaria digitata. The presence of L. elsbetiae coincides with morphological changes in the hosts such as twisted stipes and deformed blades, however, little is known about the molecular bases of these algal host-endophyte interactions. Using a co-cultivation experiment, we showed that physiological and gene regulation responses, and later endophyte prevalences are different between the main and the occasional host. The contact with the endophyte L. elsbetiae induced a stronger and faster transcriptomic regulation in the occasional host L. digitata after 24 h, from which growth rate was later affected. During the first two days of co-cultivation, only 21 differentially expressed genes (DEGs) were common in both kelps, indicating a crucial difference between the molecular responses of the two hosts. By functional annotation, we identified DEGs related to host-endophyte recognition, defense response and cell wall modification. Our results suggest that expression pattern differences between the two kelps related to the recognition of the endophyte and later defense reactions could explain the variability of observed physiological responses and host-endophyte specificity in kelp natural populations.

International audience; Ulva compressa, a green tide-forming species, can adapt to hypo-salinity conditions, such as estuaries and brackish lakes. To understand the underlying molecular mechanisms of hypo-salinity stress tolerance, transcriptome-wide gene expression profiles in U. compressa were created using digital gene expression profiles. The RNA-seq data were analyzed based on the comparison of differently expressed genes involved in specific pathways under hypo-salinity and recovery conditions. The up-regulation of genes in photosynthesis and glycolysis pathways may contribute to the recovery of photosynthesis and energy metabolism, which could provide sufficient energy for the tolerance under long-term hyposaline stress. Multiple strategies, such as ion transportation and osmolytes metabolism, were performed to maintain the osmotic homeostasis. Additionally, several long noncoding RNA were differently expressed during the stress, which could play important roles in the osmotolerance. Our work will serve as an essential foundation for the understanding of the tolerance mechanism of U. compressa under the fluctuating salinity conditions.

Saccharina latissima, known as sugar kelp, is a brown macroalga with huge ecological and economic values. In marine intertidal environment, S. latissima has to cope with both biotic and abiotic stress, which can cause the reduction of the yield during cultivation. To better understand the physiological responses of S. latissima under different stress conditions, large-scale transcriptomic analyses are useful to explore global metabolic pathway regulations. In addition, real-time quantitative polymerase chain reaction (RT-qPCR) is a powerful and rapid method for further quantifying changes in gene expression, and for targeting specific defense-related gene pathways. However, its level of accuracy is highly related to the expression stability of reference genes used for normalization and those still need to be evaluated in S. latissima. In this study, we therefore experimentally tested eight candidate reference genes identified from in silico screening of public transcriptomic datasets of S. latissima from different abiotic and biotic stress treatments. The stability analysis using complementary statistical approaches showed that EIF5B and ATPase are the most stable reference genes under biotic stress, whereas, under temperature and light stress, their combination with NDH gene is the best choice for RT-qPCR normalization. The validated reference genes were used to monitor the expression of target genes, related to oxidative responses, such as those involved in oxylipin pathways, in S. latissima plantlets submitted to different stress in laboratory-controlled conditions.

Background: Ulva compressa, known as the green tide forming species, was reported that can adapt to hypo-salinity conditions such as estuaries and brackish lakes. To understand the underlying molecular mechanisms of hypo-salinity stress tolerance, a genome-wide gene expression profiles in U. compressa was performed using digital gene expression profile (DGE). Results: The RNA-seq data were analyzed based on the comparison of differently expressed genes involved in specific pathways under hypo-salinity and recovery conditions. Under the long-term hypo-salinity stress, the recovery of photosynthesis and energy metabolism could provide sufficient energy for the tolerance under long-term hypo-saline stress. Multiple strategies were performed to maintain the osmotic homeostasis. Additionally, several long non-coding RNA were detected as differently expressed genes during the stress, which could play important roles in the osmotolerance. Conclusions: Our work will serve as an essential foundation for the understanding of the tolerance mechanism of U. compressa under the fluctuating salinity conditions.

Alexandrium catenella is a cosmopolitan harmful algal bloom (HAB) forming dinoflagellate. To comprehend its mechanisms of bloom formation, gene expression analysis is indispensable. Quantitative real-time reverse transcription PCR (qRT-PCR) is an ideal method for swift and precise quantification of gene expression analysis that greatly relies on selection of apposite reference genes for data normalization. To date, limited studies have focused on the screening of reference genes in dinoflagellates. The unavailability of valid reference gene for normalizing poses hindrances in the appliance of qRT-PCR to the HAB forming group. The work presented here evaluated 12 reference genes for their expression stability using qRT-PCR under diverse nutritional conditions together with high light. Statistical algorithm such as RefFinder was used that analyze data using geNorm and NormFinder, comparative delta-CT method along with a combination approach that declares comprehensive ranking contingent upon the geometric mean of the results procured from other methods. Comprehensive analysis across all condition by geNorm showed ACT, IPP, and GAPDH as genes possessing highest stability followed by Tubα and ICDH. Comprehensive analysis by Normfinder declared that IPP is the most stable gene followed by ACT, CYC, GAPDH, and GTEF. Combination approach using comparative delta CT, geNorm and NormFinder analysis programs through RefFinder as well as ranking by standard deviation of delta CT declared IPP as the most stable gene followed by ACT and GAPDH. IPP, ACT, and GAPDH represented the top 4 listed stable reference genes among all the analysis methods used. The results of pairwise variation by geNorm showed that V2/V3 value under all the tested conditions was below the cut-off value of 0.15 which shows that two genes are sufficient for normalization. Our results in accord with other widely conducted studies emphasize the significance of reference gene validation in precise experimental setup before appliance to avoid serious misinterpretation of the results. It is highly expected that the procedures and outcome of the report may be helpful for future studies in the gene expression analysis of A. catenella and to screen out reference genes for other algae.

Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multiple sequence alignment. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multiple sequence alignment in a few hours. In addition, HomBlocks supports organelle genomes without annotation and makes adjustment to different taxon datasets, thereby enabling the inclusion of as many common genes as possible. Topology comparison of trees built by conventional multi-gene and HomBlocks alignments implemented in different taxon categories shows that the same efficiency can be achieved by HomBlocks as when using the traditional method. The availability of Homblocks makes organelle phylogenetic analyses more accessible to non-bioinformaticians, thereby promising to lead to a better understanding of phylogenic relationships at an organelle genome level. Availability and implementation HomBlocks is implemented in Perl and is supported by Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download from https://github.com/fenghen360/HomBlocks.git , and documentation and tutorials are available at https://github.com/fenghen360/HomBlocks . Contact: yxmao@ouc.edu.cn or fenghen360@126.com

Zostera marina a kind of seagrass with high wildlife value, is threatened by human activities in the coastal area of China and Indonesia. In this study, we obtained the complete chloroplast genome sequence of Zostera marina, of which the length is 143,877 bp. It contained a pair of IR regions (25,915 bp) separated by a small single copy region (8823 bp) and a large single copy region (83,224 bp). The overall GC contents of the chloroplast genome were 35.5%. This circular genome contains 116 annotated genes, including 78 protein-coding genes, 30 tRNAs and 8 rRNA. By phylogenetic analysis using maximum likelihood (ML) and neighbor-joining (NJ) method, Z. marina showed the closest relationship with Elodea canadensis and Potamogeton perfoliatus. This complete chloroplast genomes can be subsequently used for population genomic studies of Z. marina and provide valuable insight into in situ and ex situ conservation for this valuable species.

Bangia fuscopurpurea is a traditional mariculture crop having high nutritional value, eicosapntemacnioc acid (EPA) production, and protein content. As an intertidal species, it can tolerate drastic changes in abiotic factors such as temperature, hydration, and light radiation; however, genomic information on the evolutionary aspect and mechanism of EPA enrichment in B. fuscopurpurea and the role of EPA in cold tolerance in this species remain elusive. We conducted transcriptome profile analysis in B. fuscopurpurea to investigate the biological functions of genes associated with resistance to various environment factors. We identified 41,935 unigenes that were assembled and applied to public databases to define their functional annotation (NR, GO, KEGG, KOG, and SwissProt). We further identified genes that encoded key enzymes in EPA biosynthesis; five paralogous genes encoding delta5 desaturase were detected in B. fuscopurpurea. Fatty acid profiling and gene expression analysis of B. fuscopurpurea grown under cold stress were simultaneously performed. The EPA content was increased by 29.8% in the samples grown at 4°C, while the total amount of fatty acids remained unchanged. Moreover, all the EPA biosynthesis-related desaturase and elongase genes were upregulated under cold stress. Thus, we hypothesized that diverse EPA biosynthesis pathways and significant increase in gene copy numbers of fatty acid desaturases, together with the concomitant elevation in the transcriptional level of genes associated with fatty acid metabolism, lead to EPA accumulation and subsequently affect membrane fluidity, contributing to cold stress resistance in B. fuscopurpurea. Our findings not only provide a fundamental genetic background for further research in B. fuscopurpurea, but also have important implications for screening and genetic engineering of algae and plants for EPA production.