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Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to plants and animals

ABSTRACT: Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to plants and animals

PROVIDER: PRJNA481378 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7528100_1.fastq.gz	Fastqsanger.gz
	SRR7528100_2.fastq.gz	Fastqsanger.gz
	SRR7528101_1.fastq.gz	Fastqsanger.gz
	SRR7528101_2.fastq.gz	Fastqsanger.gz
	SRR7528102_1.fastq.gz	Fastqsanger.gz

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Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to plants and animals

Project description:Kelp are the largest photosynthetic organisms in the ocean with tissue differentiation and complex life cycles. Other multicellular organisms with similar complexity such as plants and animals are well known to posses epigenetic mechanisms such as DNA methylation to control development and morphogenesis. Despite plant-like body plans and the presence of different life-cycle stages, the kelp species Saccharina japonica has only a very low level of DNA methylation, yet we have found strong evidence for differential methylation of regulatory elements and protein-coding genes which seem to contribute to the formation of life-cycle stages, tissue differentiation, growth and halogen metabolism. Thus, DNA methylation seems to play an important role in kelp, which has not been reported before.

2018-07-17 | GSE117191 | GEO

Temperature dependent sex-biased gene expression in the gametophytes of the kelp Saccharina latissima

Project description:We performed a laboratory experiment with vegetative gametophytes of the kelp Saccharina latissima and exposed the gametophytes to three temperatures (4°C, 12°C and 20°C) by sex (female, male) for 14 days.

2019-09-25 | E-MTAB-8267 | biostudies-arrayexpress

Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants.

Project description:Brown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. This contribution provides the first single-base methylome profiles of haploid gametophytes and diploid sporophytes of a multicellular alga. Although only c. 1.4% of cytosines in Saccharina japonica were methylated mainly at CHH sites and characterized by 5-methylcytosine (5mC), there were significant differences between life-cycle stages. DNA methyltransferase 2 (DNMT2), known to efficiently catalyze tRNA methylation, is assumed to methylate the genome of S. japonica in the structural context of tRNAs as the genome does not encode any other DNA methyltransferases. Circular and long noncoding RNA genes were the most strongly methylated regulatory elements in S. japonica. Differential expression of genes was negatively correlated with DNA methylation with the highest methylation levels measured in both haploid gametophytes. Hypomethylated and highly expressed genes in diploid sporophytes included genes involved in morphogenesis and halogen metabolism. The data herein provide evidence that cytosine methylation, although occurring at a low level, is significantly contributing to the formation of different life-cycle stages, tissue differentiation and metabolism in brown algae.

| S-EPMC6916402 | biostudies-literature

A partially sex-reversed giant kelp sheds light into the mechanisms of sexual differentiation in UV sexual system

Project description:In UV sexual systems, sex is determined during the haploid phase of the life cycle and males have a V chromosome whereas females have a U chromosome. Previous work in the model Ectocarpus revealed that the V chromosome has a dominant role in male sex determination and the female developmental program being a ‘default’ program, triggered in the absence of the male master sex determination gene(s). Here, we describe the identification of a genetically male giant kelp strain presenting phenotypic features typical of a female, despite lacking the U-specific region. The conversion to the female developmental program is however incomplete, because gametes of this feminised male are unable to produce the sperm-attracting pheromone lamoxiren. We identify the transcriptomic pathways underlying the male and female specific developmental programs and show that the phenotypic feminisation of the variant strain is associated with both feminisation and de-masculinisation of gene expression patterns. Importantly, the feminisation phenotype was associated with the dramatic downregulation of two V-specific genes including a candidate sex-determining gene on the V-specific region. Our results reveal the transcriptional changes associated with sexual differentiation in a UV system with extensive sexual dimorphism, disentangling the role of sex-linked genes and autosomal gene expression in the initiation of the male and female developmental programs. Overall, the data presented here imply that the U-specific region in the giant kelp is not required to initiate the female developmental program, but is critical to produce fully functional eggs, arguing against the idea that female is the ‘default’ sex in this species.

2022-04-28 | GSE165423 | GEO

Transcriptomic responses of two population strains of the kelp Saccharina latissima to temperature and salinity changes

Project description:The data is a result of a large laboratory experiment targeting interactive effects of salinity and temperature on the transcriptomic level in algae from two populations of an ecologically relevant kelp species (Laminariales), Saccharina latissima. Research interest in S. latissima has recently been increasing given its importance as ecosystem engineer along temperate rocky shores in the Atlantic Ocean, and its growing potential in industrial applications such as aquaculture, pharmaceutics, food and feed. Young sporophytes of S. latissima were raised from stock cultures of clonal male and female gametophytes at the Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research. Cultures originated from sporophyte collected at Kongsfjorden (79°N, 11°E; Spitsbergen, Norway) and at Roscoff (48° 43′ 39″ N, 3° 59′ 13.2″ W; Brittany, France). Sporophytes of both populations were grown aerated in glass beakers at 8°C and under a photon fluence rate of 20 µmol photons m–2 s–1 of photosynthetically active radiation with a 18 h light: 6 h dark photoperiod and were cultivated in sterile seawater enriched with Provasoli (Starr & Zeikus 1993) with an absolute salinity (SA) of ~30 during three months. At the start of the experiment, sporophytes were either kept at 8°C (or transferred to 0°C and 15°C) in temperature controlled rooms. After one week, per each temperature, sporophytes were divided into a low salinity treatment of SA 20 or kept at the control salinity (SA 30).

2019-07-08 | E-MTAB-7348 | biostudies-arrayexpress

Transcriptome sequencing and comparative expression profiling analysis of Saccharina japonica under blue light

Project description:Saccharina japonica is one of the most important marine economic crops worldwide. Blue light usually plays a significant role in the lives of Saccharina that may be beneficial to the culture system. Here we applied high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of Saccharina japonica with blue light and dark exposure respectively. Comparative analysis of gene expression was conducted to understand the underlying molecular mechanisms. RNA-seq analysis yielded 70,497 non-redundant unigenes. 25,924 unigenes of them had good comparability with known gene sequences in existing species. Based on the values of RPKM, 11,660 differentially expressed unigenes were detected in expression profiles between blue light and dark exposed samples. Our results provide clues to potential genes identification in the species and lay the foundation for future functional genomics study.

2012-10-02 | GSE33853 | GEO

Saccharina latissima gametogenesis

Project description:Male and female gametogenesis in the kelp Saccharina latissima (Laminariales, Laminariaceae)

| PRJEB32911 | ENA

Temperature dependent sex-biased gene expression in the gametophytes of the kelp Saccharina latissima

Project description:Temperature dependent sex-biased gene expression in the gametophytes of the kelp Saccharina latissima

| PRJEB34090 | ENA

Transcriptome sequencing and comparative expression profiling analysis of Saccharina japonica under blue light

2012-10-02 | E-GEOD-33853 | biostudies-arrayexpress

Saccharina

Project description:Saccharina sp. overview

| PRJNA376629 | ENA