“…This includes a recently published, highly fragmented genome that merely encompass 11 completed stramenopile BUSCO genes, as well as a limited set of gene models that underwent reciprocal blast against Ectocarpus siliculosus and encompassed 78 complete BUSCO genes (Fig. 2 ) [ 32 , 33 ]. Fig.…”
Section: Resultsmentioning
confidence: 99%
“…This giant kelp reference genome compares favorably to the three published major brown macroalgae genomes, Ectocarpus siliculosus , Saccharina japonica , and Undaria pinnatifida , with similar N50 values (genome contiguity) and BUSCO scores (genome completeness) [ 25 – 27 , 43 ]. Additionally, our study presents a comprehensive analysis of whole genome linkage disequilibrium, nucleotide diversity and Tajima’s D. Compared to previous giant kelp genomes, the giant kelp assembly presented here vastly improves on genome contiguity and completeness, in particular when comparing BUSCO scores (94% compared to 11%) [ 32 ]. Therefore, we anticipate that the scaffolded giant kelp genome presented here will be the universal reference for future giant kelp genomic projects.…”
Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.
“…This includes a recently published, highly fragmented genome that merely encompass 11 completed stramenopile BUSCO genes, as well as a limited set of gene models that underwent reciprocal blast against Ectocarpus siliculosus and encompassed 78 complete BUSCO genes (Fig. 2 ) [ 32 , 33 ]. Fig.…”
Section: Resultsmentioning
confidence: 99%
“…This giant kelp reference genome compares favorably to the three published major brown macroalgae genomes, Ectocarpus siliculosus , Saccharina japonica , and Undaria pinnatifida , with similar N50 values (genome contiguity) and BUSCO scores (genome completeness) [ 25 – 27 , 43 ]. Additionally, our study presents a comprehensive analysis of whole genome linkage disequilibrium, nucleotide diversity and Tajima’s D. Compared to previous giant kelp genomes, the giant kelp assembly presented here vastly improves on genome contiguity and completeness, in particular when comparing BUSCO scores (94% compared to 11%) [ 32 ]. Therefore, we anticipate that the scaffolded giant kelp genome presented here will be the universal reference for future giant kelp genomic projects.…”
Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.
“…Brown algae, which consists of approximately 2000 species and are categorized into 16 orders, are a prominent group of multicellular organisms that can be found extensively in marine environments [13]. There are only a few brown algae genomes that have been sequenced, including Ectocarpus siliculosus [14], Saccharina japonica [15], Nemacystus decipiens [16], Cladosiphon okamuranus [17], Tribonema minus [18], Macrocystis pyrifera [19], Sargassum fusiforme [20], and Undaria pinnatifida [21,22]. These genome sequences were collected in June 2022.…”
Sargassum horneri, a prevalent species of brown algae found along the coast of the northwest Pacific Ocean, holds significant importance as a valuable source of bioactive compounds. However, its rapid growth can lead to the formation of a destructive “golden tide”, causing severe damage to the local economy and coastal ecosystems. In this study, we carried out de novo whole-genome sequencing of S. horneri using next-generation sequencing to unravel the genetic information of this alga. By utilizing a reference-guided de novo assembly pipeline with a closely related species, we successfully established a final assembled genome with a total length of 385 Mb. Repetitive sequences made up approximately 30.6% of this genome. Among the identified putative genes, around 87.03% showed homology with entries in the NCBI non-redundant protein database, with Ectocarpus siliculosus being the most closely related species for approximately one-third of these genes. One gene encoding an alkaline phosphatase family protein was found to exhibit positive selection, which could give a clue for the formation of S. horneri golden tides. Additionally, we characterized putative genes involved in fucoidan biosynthesis metabolism, a significant pathway in S. horneri. This study represents the first genome-wide characterization of a S. horneri species, providing crucial insights for future investigations, such as ecological genomic analyses.
Alginate oligosaccharides (AOs), derived from alginate degradation, exhibit diverse biological activities and hold significant promise in various fields. The enzymatic preparation of AOs relies on alginate lyases, which offers distinct advantages. In contrast to the conventional use of sodium alginate derived from brown algae as the substrate for the enzymatic preparation of AOs, AO preparation directly from brown algae is more appealing due to its time and energy efficiency. Thus, the identification of potent alginate lyases and cost-effective brown algae substrates is crucial for optimizing AO production. Herein, we identified and characterized an alginate lyase, AlyP18, capable of efficiently decomposing algae, from a marine bacterium Pseudoalteromonas agarivorans A3 based on secretome analysis. AlyP18 is a mesothermal, endo-type and bifunctional alginate lyase with high enzymatic activity. Two brown algae substrates, Laminaria japonica roots and Macrocystis pyrifera, were used for the AO preparation by AlyP18. Upon optimization of AlyP18 hydrolysis parameters, the substrate degradation efficiency and AO production reached 53% and ~32% for L. japonica roots, respectively, and 77% and ~46.5% for M. pyrifera. The generated AOs primarily consisted of dimers to pentamers, with trimers and tetramers being dominant. This study provides an efficient alginate lyase and alternative brown algal feedstock for the bioconversion of high-value AOs from brown algae.
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