Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae.

Sargassum hemiphyllum var. chinense, a prevalent seaweed along the Chinese coast, has economic and ecological significance. However, systematic positions within Sargassum and among the three orders of Phaeophyceae, Fucales, Ectocarpales, and Laminariales are in debate. Here, we reported the organellar genomes of S. hemiphyllum var. chinense (34,686-bp mitogenome with 65 genes and 124,323 bp plastome with 173 genes) and the investigation of comparative genomics and systematics of 37 mitogenomes and 22 plastomes of Fucales (including S. hemiphyllum var. chinense), Ectocarpales, and Laminariales in Phaeophyceae. Whole genome collinearity analysis showed gene number, type, and arrangement were consistent in organellar genomes of Sargassum with 360 SNP loci identified as S. hemiphyllum var. chinense and two genes (rps7 and cox2) identified as intrageneric classifications of Sargassum. Comparative genomics of the three orders of Phaeophyceae exhibited the same content and different types (petL was only found in plastomes of the order Fucales and Ectocarpales) and arrangements (most plastomes were rearranged, but trnA and trnD in the mitogenome represented different orders) in genes. We quantified the frequency of RNA-editing (canonical C-to-U) in both organellar genomes; the proportion of edited sites corresponded to 0.02% of the plastome and 0.23% of the mitogenome (in reference to the total genome) of S. hemiphyllum var. chinense. The repetition ratio of Fucales was relatively low, with scattered and tandem repeats (nine tandem repeats of 14-24 bp) dominating, while most protein-coding genes underwent negative selection (Ka/Ks < 1). Collectively, these findings provide valuable insights to guide future species identification and evolutionary status of three important Phaeophyceae order species.

Floridean Starch and Floridoside Metabolic Pathways of Neoporphyra haitanensis and Their Regulatory Mechanism under Continuous Darkness.

Floridean starch and floridoside are the main storage carbohydrates of red algae. However, their complete metabolic pathways and the origin, function, and regulatory mechanism of their pathway genes have not been fully elucidated. In this study, we identified their metabolic pathway genes and analyzed the changes in related gene expression and metabolite content in Neoporphyra haitanensis under continuous dark conditions. Our results showed that genes from different sources, including eukaryotic hosts, cyanobacteria, and bacteria, were combined to construct floridean starch and floridoside metabolic pathways in N. haitanensis. Moreover, compared with those in the control, under continuous dark conditions, floridean starch biosynthesis genes and some degradation genes were significantly upregulated with no significant change in floridean starch content, whereas floridoside degradation genes were significantly upregulated with a significant decrease in floridoside content. This implies that floridean starch content is maintained but floridoside is consumed in N. haitanensis under dark conditions. This study elucidates the "floridean starch-floridoside" metabolic network and its gene origins in N. haitanensis for the first time.

Gametophyte phase of commercial kelps, the potential food supplements for essential fatty acids and n-3 polyunsaturated fatty acids.

For heteromorphic algae with alternating generations, the thallus and gametophyte phases are different morphologies in free-living life history. The thalli are popular used as traditional vegetables and herbal drugs, whereas the gametophyte phases are little involved. To better understand the functional lipids in the gametophyte phase of three commercial kelps, Saccharina japonica, Undaria pinnatifida, and Costaria costata, the contents of total lipids (TLs), fatty acid (FA) profiles, and transcriptomic analysis were performed. For the studied kelps, the TL contents in gametophyte phase were always almost twice more than those in the thallus, and the kelp species, their life stage, and the gender were critical factors affecting lipid accumulation. The gametophyte phases of U. pinnatifida and C. costata were rich in essential FA C18:2 n - 6 and C18:3 n - 3. The S. japonica gametophyte phase contained abundant C20:5 n - 3 and C18:4 n - 3, possessed an ideal ratio of n - 6/n - 3 polyunsaturated fatty acid below 1.0, and was supported by the transcriptome data which showed that the key sjD12/15 (n - 3) gene of gametophyte partially upregulated than sporophyte. The results suggested that S. japonica gametophyte phase was the worthiest of further development and utilization as a functional food. PRACTICAL APPLICATION: It is the first report on the fatty acid characteristics of three gametophyte phases of Saccharina japonica, Undaria pinnatifida, and Costaria costata and find that the S. japonica was worthy of further development and utilization as a functional food owing to its satisfactory fatty acid composition.

The Complete Plastid Genomes of Seven Sargassaceae Species and Their Phylogenetic Analysis.

Sargassum is one of the most important genera of the family Sargassaceae in brown algae and is used to produce carrageenan, mannitol, iodine, and other economic substances. Here, seven complete plastid genomes of Sargassum ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei, and S. henslowianum were assembled using next-generation sequencing. The sizes of the seven circular genomes ranged from 124,258 to 124,563 bp, with two inverted regions and the same set of plastid genes, including 139 protein-coding genes (PCGs), 28 transfer (t)RNAs, and 6 ribosomal (r)RNAs. Compared with the other five available plastid genomes of Fucales, 136 PCGs were conserved, with two common ones shared with Coccophora langsdorfii, and one with S. fusiforme and S. horneri. The co-linear analysis identified two inversions of trnC(gca) and trnN(gtt) in ten Sargassum species, against S. horneri and C. langsdorfii. The phylogenetic analysis based on the plastid genomes of 55 brown algae (Phaeophyceae) showed four clades, whose ancient ancestor lived around 201.42 million years ago (Mya), and the internal evolutionary branches in Fucales started to be formed 92.52 Mya, while Sargassum species were divided into two subclades 14.33 Mya. Our novel plastid genomes provided evidence for the speciation of brown algae and plastid genomic evolution events.

The complete mitochondrial genome and phylogenetic analysis of Neorhodomela munita.

Neorhodomela munita (Perestenko) Masuda 1982 is distributed in the coastal areas of Shandong and Liaoning in China, and also in Japan. In this study, the complete nucleotide sequence of the circular mitochondrial DNA of the red alga Neorhodomela munita has been determined. The complete mitochondrial DNA sequence of Neorhodomela munita was 25,318 bp in length with an overall GC content of 25.1% and encoded 23 protein-coding genes, two ribosomal RNAs and 24 transfer RNAs. Phylogenetic tree showed that Neorhodomela munita clustered together with Choreocolax polysiphoniae. The phylogenetic analysis may provide a better understanding of the evolution of the Rhodophyta species.

The complete plastid genome and phylogenetic analysis of Codium fragile.

Codium fragile, a nutrient-rich green algae that is both edible and medicinal, it is called a 'rat tail' because of its unique shape, it can reach up to a metre in length and has the functions of clearing heat and detoxifying, detumescence and water, and repelling insects. The plastid genome sequence of C. fragile is 83,422 bp. A total of 105 genes were determined, including 77 protein-encoding genes, 3 rRNA genes, and 25 tRNA genes. Phylogenetic analysis showed that C. fragile clustered together into a single branch with C. simulans and Codium sp. 'arenicola' as sister branches. The plastid genome analysis will help the understanding of Chlorophyta evolution.

The complete chloroplast genome of Sargassum fusiforme.

The complete chloroplast genome sequence of Sargassum fusiforme is presented here. Circular mapping revealed that the complete chloroplast DNA sequence of S. fusiforme was 124,298 bp in length and had an overall AT content of 69.57%, including 137 protein-coding genes, 2 open reading frames, 28 transfer RNA genes, and 6 ribosomal RNA genes. The phylogenetic tree based on Bayesian shows that all kinds of Phaeophyceae were clustered into two monophyletic groups.

The complete mitochondrial genome of brown algae: Sargassum fusiforme (Harvey) Setchell.

We describe the complete mitochondrial genome sequence of Sargassum fusiforme. This mitogenome is a circular molecule of 34,695 bp in length and had an overall GC content of 37.54%%. Gene annotation showed that 35 protein-coding genes, 2 open reading frames, 25 transfer RNA genes, and 3 ribosomal RNA genes. The phylogenetic tree based on Bayesian shows that S. fusiforme belongs to genus Sargassum, support current taxonomic systems.

OGDA: a comprehensive organelle genome database for algae.

Algae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provide an organelle genome platform for algae, we have developed a user-friendly database named Organelle Genome Database for Algae (OGDA, http://ogda.ytu.edu.cn/). OGDA contains organelle genome data either retrieved from several public databases or sequenced in our laboratory (Laboratory of Genetics and Breeding of Marine Organism [MOGBL]), which are continuously updated. The first release of OGDA contains 1055 plastid genomes and 755 mitochondrial genomes. Additionally, a variety of applications have been integrated into this platform to analyze the structural characteristics, collinearity and phylogeny of organellar genomes for algae. This database represents a useful tool for users, enabling the rapid retrieval and analysis of information related to organellar genomes for biological discovery.

The complete plastid genome and phylogenetic analysis of Gracilaria textorii.

The complete plastid genome of Gracilaria textorii, a marine red macroalga, was determined and analyzed. The plastid genome sequence of G. textorii is 179,609 bp. It contains 237 genes, including 203 protein-encoding genes, 30 tRNA genes, 3 rRNA genes, 1 ribonuclease gene, and 1 intron inserted into the trnM gene. Phylogenetic analysis showed that G. textorii clustered together with Gracilaria salicornia, which helps the better understanding of Gracilaria evolution process.

The complete mitogenome of Gracilaria chouae and its phylogenetic analysis.

Gracilaria chouae, a marine red macroalgae, is a rich source of active substances and is listed as biological and health food material with high economic value. The mitogenome sequence of G. chouae is 25,829 bp. A total of 50 genes were determined, including 24 protein-encoding genes, two rRNA genes, 23 tRNA genes, and one unidentified open reading frame (ORF). Phylogenetic analysis showed that G. chouae clustered together with Gracilariopsis chorda, Gracilariopsis lemanaeformis, Gracilariopsis andersonii, Gracilariophila oryzoides, and Gracilariopsis heteroclada. The mitogenome analysis will help the understanding of Gracilaria evolution.

The complete mitogenome of Caulerpa lentillifera and its phylogenetic analysis.

Caulerpa lentillifera is a marine nutrient-rich edible green algae, with its external shape similar to 'sea grape', it has functions of purifying blood, anti-oxidation, anti-cancer, and anti-tumor. The mitogenome sequence of C. lentillifera is 209,894 bp long. A total of 67 genes were determined, including 17 protein-encoding genes, 3 rRNA genes, 27 tRNA genes, and 20 unidentified open reading frame (ORF). Phylogenetic analysis showed that C. lentillifera clustered together into a single branch. The mitogenome analysis will help the understanding of Ulvophyceae evolution.

The complete chloroplast genome of Sargassum horneri and its phylogenetic analysis.

Complete chloroplast genome of Sargassum horneri was obtained in this work. Circular mapping revealed that the complete chloroplast DNA sequences of S. horneri was 124,075 bp in length and had an overall AT content of 69.41%, including 139 protein-coding genes, 28 transfer RNA genes, and 6 ribosomal RNA genes. The phylogenetic tree shows that S. horneri and Sargassum confusum constituted a sister clade along with Fucus vesiculosus.

The complete plastid genome and phylogenetic analysis of Gracilaria edulis.

Gracilaria edulis, a marine red macroalgae, is a rich source of sulfated polysaccharides, carbohydrate, vitamins, and minerals, and showed multiple bioactivities such as antibacterial, antitumour, and cholinesterase inhibitory activity. The plastid genome sequence of G. edulis is 179,410 bp. A total of 235 genes were determined, including 201 protein-encoding genes, 30 tRNA genes, 3 rRNA genes, 1 ribonuclease gene, and 1 intron inserted into the trnM gene. Phylogenetic analysis showed that G. edulis clustered together with Gracilaria salicornia, Gracilaria tenuistipitata var. liui and Gracilaria chilensis. The plastid genome analysis will help in the understanding of Gracilaria evolution.

The complete plastid genome and phylogenetic analysis of Gracilaria spinulosa.

Gracilaria spinulosa is an economical species of marine red algae. The length of its plastid genome sequence is 179,082 bp; a total of 236 genes were determined, including 203 protein-encoding genes, 3 rRNA genes, 29 tRNA genes, 1 ribonuclease gene, and 1 intron inserted into the trnM gene. The gene content and structure of Gracilariaceae species were relatively well conserved. Phylogenetic analysis showed that G. spinulosa had a closer relationship with Gracilaria salicornia in Gracilaria. The complete plastid genome sequence provided will help the understanding of Gracilaria evolution.

The complete chloroplast genome of Enhalus acodoides and its phylogenetic analysis.

Complete chloroplast genome of Enhalus acodoides was obtained in this work. Circular mapping revealed that the complete chloroplast sequences of E. acodoides was 176,748 bp in length and had an overall GC content of 38.3%, encoded 132 genes which contained 86 protein-coding genes (PCGs), 38 transfer RNA genes (tRNA) and 8 ribosomal RNA genes (rRNA). The phylogenetic tree shows that E. acodoides had a closer relationship with Thalassia hemprichii in Hydrocharitaceae and its analysis will help better understand the evolution of Alismatales species.