- Comparative genomics of four strains of the edible brown alga, Cladosiphon. - Background: The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is one of the most important edible seaweeds, and it is cultivated for market primarily in Okinawa, Japan. - We previously reported a draft genome of the S-strain. - To facilitate studies of seaweed biology for future aquaculture, we here decoded and analyzed genomes of the other three strains (K, O, and C).. - Results: Here we improved the genome of the S-strain (ver. - 2, 130 Mbp, 12,999 genes), and decoded the K-strain (135 Mbp, 12,511 genes), the O-strain (140 Mbp, 12,548 genes), and the C-strain (143 Mbp, 12,182 genes). - Molecular phylogenies, using mitochondrial and nuclear genes, showed that the S-strain diverged first, followed by the K- strain, and most recently the C- and O-strains. - Comparisons of genome architecture among the four strains document the frequent occurrence of inversions. - Conclusions: Our study compares the genomes of four strains of C. - majority of edible brown algae (the class Phaeophyceae) include members of the order Laminariales, Saccharina japonica (“kombu” in Japanese) and Undaria pinnatifida (“wakame. - Full list of author information is available at the end of the article. - okamuranus com- menced in the 1980s and the predominant strain is the S-strain (‘Shikenjo-kabu’, registered as Inou-no-Megumi in Japanese). - The S-strain exhibits comparatively long lateral branches, and the body is not tough or fibrous.. - Although nucleic acid extraction from algae is compli- cated because of the abundance of polysaccharides in cell walls and in the extracellular matrix, we decoded a draft genome of the S-strain in 2016 [4]. - During the past 35 years, three other strains have been cultivated, including the K-strain, originally from the Katsuren coast, the O- strain from the Onna coast, and the C-strain from the Chinen coast (Fig. - The K- strain comprises thicker, tougher lateral branches (Fig. - The O-strain is composed of smaller, denser lateral branches (Fig. - 1a), and the C-strain is intermediate in size, with thinner lateral branches (Fig. - Genetic characterization of the strains is essential for future aqua- culture. - To help support this industry, we decoded draft genomes of the S- (ver. - Genome constituents of four strains. - The S-strain genome assembly. - 1 a Four strains (S, K, O and C) of Cladosiphon okamuranus have distinctive morphologies. - b Locations from which the four strains were isolated since 2008 in Okinawa, Japan. - Repetitive se- quences comprised 11.2% of the genome (Table 1).. - Using Illumina platforms, we sequenced and assem- bled draft genomes of the K-, O-, and C-strains (Supple- mentary Table S1), which are summarized in Table 1 and Supplementary Figure S2. - Scaffold N50s of the four genomes ranged from kb (Table 1). - The GC content of the four strains was identical, amounting to 54% of the DNA sequences (Table 1). - The genome size of the K-strain was 135 Mbp, with an estimated 12,511 protein-coding genes. - That of the O-strain was 140 Mbp with an estimated 12,548 genes, and that of the C-strain was 143 Mbp with 12,182 estimated genes (Table 1).. - CEGMA [9] completeness and partial scores were 86 and 94% (Table 1), indicating that genome assemblies of the four strains were adequate for comparative analyses of their genomic and gene constituents.. - Repetitive sequences were estimated to constitute and 12.6% of the S-, K-, O-, and C-strain ge- nomes, respectively. - Simple repeats and unclassified re- peats accounted for 2.2–2.5% and 4.7–5.6% of the genome sequences, respectively. - Molecular phylogeny of the four strains. - Although the four strains each show unique morphology, the origins of these differences and phylo- genetic relationships of the strains are unclear. - The S- strain diverged first, followed by the K-strain, and finally the C- and O-strains. - The branch length or divergence time between the S-strain. - Four strains of Cladosiphon okamuranus are classified as the order Chordariales. - and the K/C/O-strains is longer than that between the K-strain and the C/O-strains. - This suggests that the S-strain is the likely ancestor of the four strains, and that the K-strain probably blanched out first from the K/C/O-strains ancestor. - Conservation of genome architecture among the four strains. - 3b-f) suggested that the four strains of C. - On the other hand, a weaker linear correlation was evident in se- quence comparisons between the S-strain and N. - okamuranus belongs to the family Chor- dariaceae of the order Chordariales, whereas N. - decipiens pertains to the family Spermatochnaceae in the same order. - Table 2 Classified repeat sequences in the three Cladosiphon okamuranus strain genome Percentage in the assembly. - Inversions appear to have occurred during diversifica- tion of the four strains, especially between the O- and C-strains (Fig. - Synteny analysis of the four strain genomes. - Next we examined synteny of genes in the four C . - Analyses using i-ADHoRe [12] iden- tified 550 genomic regions showing shared synteny among the four genomes (Fig. - #276 of the S-strain manifests a syntenic region compris- ing six genes (gene IDs, g8865, g8866, g8867, g8868, g8869 and g8870) (Fig. - In this synteny, g8865 was present only in the S-strain, suggesting a gene loss in the ancestor of the K/O/C strains after their divergence from the S-strain. - This provides support for the phylo- genetic gap between the S-strain and K/O/C-strains, dis- cussed earlier.. - Scaffold #228 of the S-strain offers a second example comprising 13 genes (gene IDs, g8477, g8476, g8475. - 2 Phylogenetic relationships of the four strains of Cladosiphon okamuranus . - All genes occur in exactly the same order in corresponding scaffolds K-#485 and O-#136, although two differences were evident in the C- strain. - One is an inversion of g17337, corresponding to g8473 of the S-strain, moving beyond g17336 and next to 17,339 (Fig. - This result provides further support for the supposition that the C-strain genome was uniquely modified after its divergence.. - The genome project documented approximately 12,500 genes in genomes of the four strains of Cladosiphon ([4], the present study), 15,156 genes in the Nemacystus gen- ome [5] and 17,418 genes in the Ectocarpus genome [6]. - 187 families unique to the S-strain, 210 to the K-strain, 225 to the O-strain, and 155 to the C-strain (Fig. - There were many patterns depending on how families were shared by combinations of the six genomes (Fig. - For example, different numbers of gene fam- ilies were shared among different combinations of strains: 123 (S/O/K), 60 (S/K/C), 59 (S/O), 59 (S/K), 55 (S/C), 53 (O/K), 42 (S/O/C), 34 (O/K/C), 26 (K/C), and 18 (O/C), providing more information about diversifica- tion of the four strains.. - We further compared gene families in the four Clado- siphon strains using OrthoFinder [13]. - The four strains shared 9544 gene families (Fig. - 5c), but the S-, K-, O-, and C-strains include and 262 unique families each, constituting and 2.2% of the orthologous genes in those strains, respectively. - These gene families may be involved in the evident morpho- logical diversification of the four strains, and may also support different physiology as well, although that re- mains to be explored.. - In general, the four strains dis- played similar GO annotation profiles. - Four strains of C. - In such circumstances, it is desirable to understand genetic properties and the evolutionary trajectories of the strains. - To this end, we decoded the 130 ~ 143 Mbp nuclear genomes of the four C. - The S-strain genome was first assembled in a previous study [4], but was improved in this study, and the K-, O- and C-strain genomes were assembled for the first time in this study. - Molecular phylogeny using mitochondrial and nuclear DNA sequences allowed us to infer the evolutionary tra- jectories of the four strains (Fig. - The S-strain di- verged first, then the K-strain, and finally the O- and C- strains. - In addition, all nodes had 100% bootstrap support, indicat- ing that this represents the most probable history of the four strains. - 4 Two examples of synteny blocks among genomes of the four strains. - One gene inversion and one gene deletion are evident in the C-strain. - the mitochondrial tree than in the nuclear tree. - This suggests an occurrence of introgression of mitochondrial genome from Nemacystus to the S-strain or common ancestor of C. - Together with results of molecular phylogeny, we speculate that the morphology of the Cladosiphon okamuranus ancestor was likely close to that of the extant S-strain, with comparatively long lateral branches and a soft body, because the closely-related Nemacystus decipiens exhibits morphology similar to that of the S-strain. - From this ancestor, the K-strain became a middle-sized sporophyte with thicker and tougher lateral branches, and the O-strain diverged further with smaller and more dense lateral branches.. - The C-strain is intermediate in size with thinner lat- eral branches (Fig. - Instead, each of the four genomes has likely undergone its own modification.. - The most interesting finding was that the four strains contain unique gene families that equate to 2. - a Numbers of gene family in the six genomes. - c Venn diagram showing the numbers of gene families shared among the four Cladosiphon okamuranus strains. - This might sug- gest that the genetic distances among the four strains of Cladosiphon might reach the grade, in which the four strains are distinguished as “related species or subspecies.” Although we conducted BLAST searches of these genes, most of them showed no sequence similarity to any genes in the NCBI database. - It is likely that these gene families are involved in development of the dis- tinctive morphology of the four Cladosiphon strains, although details of molecular mechanisms remain to be explored. - Comparative gen- omics of the deciphered genomes show the expansion of genes that may be required for their survival [19]. - okamuranus strains with distinctively different morphologies revealed that they possess unique gene families, and phylogenetic analysis indicated that the S-strain is closest to the ancestral strain. - oka- muranus were produced in fiscal year 2017, representing more than 90% of the entire Japanese harvest. - Originally, four strains of Cladosiphon okamuranus were isolated from four local fisheries (Fig. - The S-strain came from Iheya in 2008, the O-strain from Onna in 2008, the K-strain from Katsuren in 2009, and the C- strain was collected in Chinen in 2012 (Fig. - Subsequent scaffolding of the Newbler or Platanus output was performed using. - Paired-end genomic DNA reads that were not used in each of the strain-genome assembly processes were collected with kneaddata v0.6.1 (https://bitbucket.org/. - Cladosiphon okamuranus . - A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of ‘ mozuku ’ biology. - Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain:. - Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. - Dissection of the Octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. - The sequence and de novo assembly of the giant panda genome
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