First Draft Genome Assembly of the Seaweed Sargassum fusiforme

Wang, Shengqin; Lin, Lidong; Shi, Yijiang; Qian, Weiguo; Li, Nan; Zou, Huixi; Wu, Mingjiang

doi:10.3389/fgene.2020.590065

Cited by 15 publications

(13 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…So far, seven brown seaweed species had complete or draft genome sequences released, including Ectocarpus siliculosus ( Cock et al, 2010 ; Cormier et al, 2017 ), Saccharina japonica ( Ye et al, 2015 ), Cladosiphon okamuranus ( Nishitsuji et al, 2016 , 2020 ), Nemacystus decipiens ( Nishitsuji et al, 2019 ), Macrocystis pyrifera (NCBI Bioproject: PRJNA605694 ), Sargassum fusiforme ( Wang et al, 2020 ), and Undaria pinnatifida ( Shan et al, 2020 ; Graf et al, 2021 ). The alginate- and fucoidan-relevant genes in these genomes are listed in Supplementary Table 1 .…”

Section: Alginatementioning

confidence: 99%

The Cell Wall Polysaccharides Biosynthesis in Seaweeds: A Molecular Perspective

Shao

Duan

2022

Front. Plant Sci.

View full text Add to dashboard Cite

Cell wall polysaccharides (CWPS) of seaweeds play crucial roles in mechanical shear resistance, cell-cell adhesion and the interactions with changeable marine environments. They have diverse applications in food, cosmetics, agriculture, pharmaceuticals and therapeutics. The recent boost of multi-omics sequence analysis has rapidly progressed the mining of presumed genes encoding enzymes involved in CWPS biosynthesis pathways. In this review, we summarize the biosynthetic pathways of alginate, fucoidan, agar, carrageenan and ulvan in seaweeds referred to the literatures on published genomes and biochemical characterization of encoded enzymes. Some transcriptomic data were briefly reported to discuss the correlation between gene expression levels and CWPS contents. Mannuronan C-5 epimerase (MC5E) and carbohydrate sulfotransferase (CST) are crucial enzymes for alginate and sulfated CWPS, respectively. Nonetheless, most CWPS-relevant genes were merely investigated by gene mining and phylogenetic analysis. We offer an integrative view of CWPS biosynthesis from a molecular perspective and discuss about the underlying regulation mechanism. However, a clear understanding of the relationship between chemical structure and bioactivities of CWPS is limited, and reverse genetic manipulation and effective gene editing tools need to be developed in future.

show abstract

Section: Alginatementioning

confidence: 99%

The Cell Wall Polysaccharides Biosynthesis in Seaweeds: A Molecular Perspective

Shao

Duan

2022

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…The ddRAD-seq reads were filtered using process_radtags (parameters as follows: --clean --quality --rescue --renz_1 ecoRI --renz_2 nlaIII) to remove Illumina adapters and to eliminate low-quality regions. The clean data were then mapped to the S. fusiforme reference genome assembly using bowtie 2 [16]. SNP calling was carried out using ref_map.pl pipeline of Stacks program with PCR duplicates removed [15].…”

Section: Read Mapping and Snp Callingmentioning

confidence: 99%

ddRAD Sequencing-Based Scanning of Genetic Variants in Sargassum fusiforme

Lin

Wang

et al. 2022

JMSE

Self Cite

View full text Add to dashboard Cite

Sargassum fusiforme is a commercially important brown seaweed that has experienced significant population reduction both from heavy exploitation and degradation of the environment. Cultivated breed strains are also in a state of population mixing. These population stressors make it necessary to investigate the population genetics to discover best practices to conserve and breed this seaweed. In this study, the genetic diversity and population structure of S. fusiforme were investigated by the genome-wide SNP data acquired from double digest restriction site-associated DNA sequencing (ddRAD-seq). We found a low genetic diversity and a slight population differentiation within and between wild and cultivated populations, and the effective population size of S. fusiforme had experienced a continuous decline. Tajima’s D analysis showed the population contraction in wild populations may be related to copper pollution which showed a consistent trend with the increase of the sea surface temperature. The potential selection signatures may change the timing or level of gene expression, and further experiments are needed to investigate the effect of the mutation on relevant pathways. These results suggest an urgent need to manage and conserve S. fusiforme resources and biodiversity considering the accelerating change of the environment.

show abstract

“…Genomes have been published for six brown macroalgae: Ectocarpus sp. (Cock et al, 2010), S. japonica (Ye et al, 2015), Undaria pinnatifida (Shan et al, 2020), Cladosiphon okamuranus (Nishitsuji et al, 2016), Nemacystus decipiens (Nishitsuji et al, 2019), and Sargassum fusiforme (Wang et al, 2020). Published seagrass genomes include Z. marina (Olsen et al, 2016), Z. muelleri (Lee et al, 2016), and Halophila ovalis .…”

Section: Integrative Analysesmentioning

confidence: 99%

Priming of Marine Macrophytes for Enhanced Restoration Success and Food Security in Future Oceans

et al. 2021

View full text Add to dashboard Cite

Marine macrophytes, including seagrasses and macroalgae, form the basis of diverse and productive coastal ecosystems that deliver important ecosystem services. Moreover, western countries increasingly recognize macroalgae, traditionally cultivated in Asia, as targets for a new bio-economy that can be both economically profitable and environmentally sustainable. However, seagrass meadows and macroalgal forests are threatened by a variety of anthropogenic stressors. Most notably, rising temperatures and marine heatwaves are already devastating these ecosystems around the globe, and are likely to compromise profitability and production security of macroalgal farming in the near future. Recent studies show that seagrass and macroalgae can become less susceptible to heat events once they have been primed with heat stress. Priming is a common technique in crop agriculture in which plants acquire a stress memory that enhances performance under a second stress exposure. Molecular mechanisms underlying thermal priming are likely to include epigenetic mechanisms that switch state and permanently trigger stress-preventive genes after the first stress exposure. Priming may have considerable potential for both ecosystem restoration and macroalgae farming to immediately improve performance and stress resistance and, thus, to enhance restoration success and production security under environmental challenges. However, priming methodology cannot be simply transferred from terrestrial crops to marine macrophytes. We present first insights into the formation of stress memories in both seagrasses and macroalgae, and research gaps that need to be filled before priming can be established as new bio-engineering technique in these ecologically and economically important marine primary producers.

show abstract

First Draft Genome Assembly of the Seaweed Sargassum fusiforme

Cited by 15 publications

References 35 publications

The Cell Wall Polysaccharides Biosynthesis in Seaweeds: A Molecular Perspective

The Cell Wall Polysaccharides Biosynthesis in Seaweeds: A Molecular Perspective

ddRAD Sequencing-Based Scanning of Genetic Variants in Sargassum fusiforme

Priming of Marine Macrophytes for Enhanced Restoration Success and Food Security in Future Oceans

Contact Info

Product

Resources

About