The complete mitochondrial genome and phylogeny of Diacronema viridis (Pavlovales, Pavlovophyceae).

The complete mitochondrial genome of the pavlovophycean microalga Diacronema viridis CCMP 620 was sequenced and characterized. The circular mitogenome is a total 29,282 bp in length with 39.2% GC content and contains 47 genes, including 20 protein-coding, three rRNA, and 24 tRNA genes. The gene synteny of D. viridis and D. lutheri has been highly conserved; however, the gene content (absence of introns and ORFs) and repeat regions (3.7 kbp) of D. viridis contributed to significant difference of mitogenomes within the Diacronema.

Complete mitochondrial genome of Polyopes lancifolius and comparison with related species in Halymeniales (Rhodophyta).

Polyopes lancifolius is a species of Halymeniales, the fifth species-rich order within Rhodophyta. Using next-generation sequencing techniques, we recovered the complete mitochondrial genome of P. lancifolius, i.e. total 26,142 bp in length with 31% GC contents. A total of 49 functional genes were annotated, including 24 protein-coding, 23 transfer RNA, and 2 ribosomal RNA genes. The gene content and synteny have been highly congruent to those of the other halymenialean species, such as Grateloupia taiwanensis, G. filicina, and Grateloupia angusta. Interestingly, the cox1 intron and intronic Open Reading Frame (ORF) are absent in P. lancifolius, that are existed in the other three halymenialean species.

Multigene Phylogeny, Morphological Observation and Re-examination of the Literature Lead to the Description of the Phaeosacciophyceae Classis Nova and Four New Species of the Heterokontophyta SI Clade.

The relationships among the Aurearenophyceae, Phaeothamniophyceae, Phaeophyceae and Xanthophyceae lineages of the Heterokontophyta SI clade are not well known. By adding previously unexamined taxa related to these classes in a five gene phylogeny (SSU rRNA, atpB, psaA, psaB, rbcL), we recovered an assemblage of taxa previously unrecognized. We propose the class Phaeosacciophyceae class. nov., that includes Phaeosaccion collinsii, Phaeosaccion multiseriatum sp. nov., Phaeosaccion okellyi sp. nov., Antarctosaccion applanatum, Tetrasporopsis fuscescens, Tetrasporopsis moei sp. nov., and Psammochrysis cassiotisii gen. & sp. nov. We re-examine the literature for Chrysomeris, Nematochrysis, Chrysowaernella and the invalid name "Giraudyopsis" and conclude some taxa in previous studies are misidentified or misnamed, i.e. Chrysomeris and Chrysowaernella, respectively. We also show that Nematochrysis sessilis var. vectensis and Nematochrysis hieroglyphica may belong in the recently described class Chrysoparadoxophyceae. The phylogenetic relationships of Phaeobotrys solitaria and Pleurochloridella botrydiopsis are not clearly resolved, but they branch near the Xanthophyceae. Here we describe a new class Phaeosacciophyceae, a new order Phaeosacciales, a new family Tetrasporopsidaceae, a new genus Psammochrysis and four new species.

Correction to: Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta).

An amendment to this paper has been published and can be accessed via the original article.

Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta).

BACKGROUND: The Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the molecular evolution of their mitochondrial genomes (mitogenomes). RESULTS: To fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes exhibit the following three features: (i) reduction in genome size and gene inventory, (ii) evolution of unique protein properties including charge, hydropathy, stability, amino acid composition, and protein size, and (iii) distinctive GC-content and skewness of nucleotides. Based on GC-skew-associated characteristics, we postulate that unidirectional DNA replication may have resulted in the rapid evolution of G-type mitogenomes. CONCLUSIONS: The high divergence of G-type mitogenomes was likely driven by natural selection in the multiple extreme environments that Galdieria species inhabit combined with their highly flexible heterotrophic metabolism. We speculate that the interplay between mitogenome divergence and adaptation may help explain the dominance of Galdieria species in diverse extreme habitats.

Further investigations on the phaeothamniophyceae using a multigene phylogeny, with descriptions of five new species.

We examined 12 strains representing eight species classified in the algal class Phaeothamniophyceae (Heterokontophyta). Based upon a five-gene molecular phylogeny (nuclear-encoded SSU rRNA and plastid-encoded psaA, psbA, psbC, and rbcL) and light microscopic observations, we describe five new species: Phaeoschizochlamys santosii sp. nov., Phaeoschizochlamys siveri sp. nov., Phaeothamnion wetherbeei sp. nov., Stichogloea dopii sp. nov. and Stichogloea fawleyi sp. nov. The Phaeothamniophyceae, as delimited here, form a natural group that is sister to the Aurearenophyceae. Molecular phylogenetic analyses proved more reliable than morphological characters for distinguishing species. Evolutionary trends with the SI clade of the heterokont algae are discussed.

Daily variation in the prokaryotic community during a spring bloom in shelf waters of the East China Sea.

To understand prokaryotic responses during a spring bloom in offshore shelf waters, prokaryotic parameters were measured daily at a station located in the middle of the East China Sea over a six-week period from March 25 to May 19. The site experienced a phytoplankton bloom in late April, triggering changes in prokaryotic abundance and production after a lag of approximately one week. Before the bloom, changes in prokaryotic composition were small. Both during the bloom and in the post-bloom period, successive changes among bacterial groups were apparent. A SAR11 group became more dominant during the bloom period, and diverse groups belonging to the Flavobacteriia occurred dominantly during both the bloom and post-bloom periods. However, bacterial community changes at the species level during the bloom and post-bloom periods occurred rapidly in a time scale of a few days. Especially, NS5, NS4 and Formosa bacteria belonging to Flavobacteriia and bacteria belonging to Halieaceae and Arenicellaceae families of Gammaproteobacteria showed a successive pattern with large short-term variation during the period. The changes in prokaryotic composition were found to be related to phytoplankton biomass and composition, as well as seawater temperature and variations in nutrients.

Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta.

Red algae (Rhodophyta) underwent two phases of large-scale genome reduction during their early evolution. The red seaweeds did not attain genome sizes or gene inventories typical of other multicellular eukaryotes. We generated a high-quality 92.1 Mb draft genome assembly from the red seaweed Gracilariopsis chorda, including methylation and small (s)RNA data. We analyzed these and other Archaeplastida genomes to address three questions: 1) What is the role of repeats and transposable elements (TEs) in explaining Rhodophyta genome size variation, 2) what is the history of genome duplication and gene family expansion/reduction in these taxa, and 3) is there evidence for TE suppression in red algae? We find that the number of predicted genes in red algae is relatively small (4,803-13,125 genes), particularly when compared with land plants, with no evidence of polyploidization. Genome size variation is primarily explained by TE expansion with the red seaweeds having the largest genomes. Long terminal repeat elements and DNA repeats are the major contributors to genome size growth. About 8.3% of the G. chorda genome undergoes cytosine methylation among gene bodies, promoters, and TEs, and 71.5% of TEs contain methylated-DNA with 57% of these regions associated with sRNAs. These latter results suggest a role for TE-associated sRNAs in RNA-dependent DNA methylation to facilitate silencing. We postulate that the evolution of genome size in red algae is the result of the combined action of TE spread and the concomitant emergence of its epigenetic suppression, together with other important factors such as changes in population size.

Diversity of the Photosynthetic Paulinella Species, with the Description of Paulinella micropora sp. nov. and the Chromatophore Genome Sequence for strain KR01.

The thecate filose amoeba Paulinella chromatophora is a good model organism for understanding plastid organellogenesis because its chromatophore was newly derived from an alpha-cyanobacterium. Paulinella chromatophora was the only known photosynthetic Paulinella species until recent studies that suggested a species level of diversity. Here, we described a new photosynthetic species P. micropora sp. nov. based on morphological and molecular evidence from a newly established strain KR01. The chromatophore genome of P. micropora KR01 was fully determined; the genome was 976,991bp in length, the GC content was 39.9%, and 908 genes were annotated. A pairwise comparison of chromatophore genome sequences between strains KR01 and FK01, representing two different natural populations of P. micropora, showed a 99.85% similarity. Differences between the two strains included single nucleotide polymorphisms (SNPs) in CDSs, which resulted in 357 synonymous and 280 nonsynonymous changes, along with 245 SNPs in non-coding regions. Indels (37) and microinversions (14) were also detected. Species diversity for photosynthetic Paulinella was surveyed using samples collected from around the world. We compared our new species to two photosynthetic species, P. chromatophora and P. longichromatophora. Phylogenetic analyses using four gene markers revealed three distinct lineages of photosynthetic Paulinella species including P. micropora sp. nov.

Complete mitochondrial genome of Skeletonema marinoi (Mediophyceae, Bacillariophyta), a clonal chain forming diatom in the west coast of Korea.

The complete mitochondrial DNA of common planktonic diatom, Skeletonema marinoi JK029 was sequenced and characterized. The circular mitogenome contains 62 genes in 38 515 bp (29.7% GC), including 35 protein-coding, 2 rRNA, and 25 tRNA genes. Total 80% of protein-coding genes have usual ATG start codon and 20% have alternative start codons. The GC content of tRNA genes (39.8%) is relatively higher than those of the rRNA (32.9%) and CDS (29.3%). There are four cases of gene overlapping between neighboring genes, i.e., rrs-trnM, rps2-rps4, nad1-tatC, and rps11-trnY. Newly determined mitogenome of S. marinoi was compared with available seven diatoms and eight stramenopiles by using the maximum-likelihood analysis. The 34-CDS concatenated data (8528 amino acids) support the monophyly of Bacillariophyta. However, mitogenome data showed different higher class-levels clustering with previous study. These results suggested that additional mitogenome data will provide useful information for mitochondrial genome diversity and evolution of the diatoms and stramenopiles.

Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes.

The integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta.

Divergence time estimates and the evolution of major lineages in the florideophyte red algae.

The Florideophyceae is the most abundant and taxonomically diverse class of red algae (Rhodophyta). However, many aspects of the systematics and divergence times of the group remain unresolved. Using a seven-gene concatenated dataset (nuclear EF2, LSU and SSU rRNAs, mitochondrial cox1, and plastid rbcL, psaA and psbA genes), we generated a robust phylogeny of red algae to provide an evolutionary timeline for florideophyte diversification. Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 943 (817-1,049) million years ago (Ma). The major divergences in this class involved the emergence of Hildenbrandiophycidae [ca. 781 (681-879) Ma], Nemaliophycidae [ca. 661 (597-736) Ma], Corallinophycidae [ca. 579 (543-617) Ma], and the split of Ahnfeltiophycidae and Rhodymeniophycidae [ca. 508 (442-580) Ma]. Within these clades, extant diversity reflects largely Phanerozoic diversification. Divergences within Florideophyceae were accompanied by evolutionary changes in the carposporophyte stage, leading to a successful strategy for maximizing spore production from each fertilization event. Our research provides robust estimates for the divergence times of major lineages within the Florideophyceae. This timeline was used to interpret the emergence of key morphological innovations that characterize these multicellular red algae.

Repeat region absent in mitochondrial genome of tube-dwelling diatom Berkeleya fennica (Naviculales, Bacillariophyceae).

The complete mitochondrial DNA of tube-dwelling diatom, Berkeleya fennica was sequenced and characterized. The circular mitogenome contains 63 genes in 35,509 bp (29.7% GC), including 36 protein-coding, 25 tRNA, 2 rRNA genes. Most of the protein-coding (27) genes have usual ATG start codon, except 9 genes such as ATA for rps8; ATC for rps14; ATT for rps12 and orf51; GTG for nad5; TTA for cox3, nad4 and orf147; and TTG for cob. The nad11 and rrs are the only interrupted genes in the mitogenome. Gene content and synteny of B. fennica are very similar to Phaeodactylum tricoruntum (NC_016739). Absence of repeat region in B. fennica resulted in mitogenome size difference to P. tricoruntum. A new mitogenome will provide useful information for mitochondrial genome diversity and evolution of the diatoms.

Complete mitochondrial genome of Upogebia yokoyai (Decapoda, Crustacea) from Jejudo, Korea.

The complete mitochondrial DNA of an ecologically important crustacean mud shrimp, Upogebia yokoyai (Decapoda, Crustacea) was sequenced. We used next generation sequencing strategy for total genomic DNA and organelle genome pipeline for mitogenome assembly. A newly determined mitogenome was 16,063 bp in total length with 28% of GC content. Thirty-seven genes were identified including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. We found ten case of overlapping between neighboring genes. Based on genome comparison, the mitogenome of U. yokoyai shows general crustacean gene content and identical synteny to the sister species, such as U. major and U. pusilla. Our results will provide useful information for mitochondrial genome diversity and evolution of the Crustacea.

Complete mitochondrial genome of biraphid benthic diatom, Navicula ramosissima (Naviculales, Bacillariophyceae).

The complete mitochondrial DNA of biraphid benthic diatom, Navicula ramosissima TA439 was sequenced and characterized. The circular mitogenome contains 67 genes in 48,652 bp (31.1% GC), including 41 protein-coding, 24 transfer RNA (tRNA) and 2 rRNA genes. Twenty-four protein-coding sequences (CDS, 59%) have start with ATG codon and 17 CDS start with alternatives such as ATA (5), ATT (6), TTA (5) and TTG (1). The GC content of tRNA genes (42.1%) is relatively higher than those of the rRNA (35.2%) and CDS (30.5%). Three genes are consisted of multiple exons and introns, i.e. cox1 (three exons, two introns), rps11 (two exons, one intron), rrl (four exons, three introns). Phylogeny of diatoms based on mitogenome data (34 CDS, 8530 amino acids combined) supports the monophyly of Naviculales, including N. ramosissima (Naviculaceae), Berkeleya fennica (Berkeleyaceae), Fistulifera solaris (Stauroneidaceae) and Phaeodactylum tricornutum (Phaeodactylaceae). Mitogenome data may be useful for phylogenetic study of the diatoms and stramenopiles.

Highly Conserved Mitochondrial Genomes among Multicellular Red Algae of the Florideophyceae.

Two red algal classes, the Florideophyceae (approximately 7,100 spp.) and Bangiophyceae (approximately 193 spp.), comprise 98% of red algal diversity in marine and freshwater habitats. These two classes form well-supported monophyletic groups in most phylogenetic analyses. Nonetheless, the interordinal relationships remain largely unresolved, in particular in the largest subclass Rhodymeniophycidae that includes 70% of all species. To elucidate red algal phylogenetic relationships and study organelle evolution, we determined the sequence of 11 mitochondrial genomes (mtDNA) from 5 florideophycean subclasses. These mtDNAs were combined with existing data, resulting in a database of 25 florideophytes and 12 bangiophytes (including cyanidiophycean species). A concatenated alignment of mt proteins was used to resolve ordinal relationships in the Rhodymeniophycidae. Red algal mtDNA genome comparisons showed 47 instances of gene rearrangement including 12 that distinguish Bangiophyceae from Hildenbrandiophycidae, and 5 that distinguish Hildenbrandiophycidae from Nemaliophycidae. These organelle data support a rapid radiation and surprisingly high conservation of mtDNA gene syntheny among the morphologically divergent multicellular lineages of Rhodymeniophycidae. In contrast, we find extensive mitochondrial gene rearrangements when comparing Bangiophyceae and Florideophyceae and multiple examples of gene loss among the different red algal lineages.

Extracellular Vesicles of the Hyperthermophilic Archaeon "Thermococcus onnurineus" NA1T.

Extracellular vesicles (EVs) produced by a sulfur-reducing, hyperthermophilic archaeon, "Thermococcus onnurineus" NA1(T), were purified and characterized. A maximum of four EV bands, showing buoyant densities between 1.1899 and 1.2828 g cm(-3), were observed after CsCl ultracentrifugation. The two major EV bands, B (buoyant density at 25°C [ρ(25)] = 1.2434 g cm(-3)) and C (ρ(25) = 1.2648 g cm(-3)), were separately purified and counted using a qNano particle analyzer. These EVs, showing different buoyant densities, were identically spherical in shape, and their sizes varied from 80 to 210 nm in diameter, with 120- and 190-nm sizes predominant. The average size of DNA packaged into EVs was about 14 kb. The DNA of the EVs in band C was sequenced and assembled. Mapping of the T. onnurineus NA1(T) EV (ToEV) DNA sequences onto the reference genome of the parent archaeon revealed that most genes of T. onnurineus NA1(T) were packaged into EVs, except for an ∼9.4-kb region from TON_0536 to TON_0544. The absence of this specific region of the genome in the EVs was confirmed from band B of the same culture and from bands B and C purified from a different batch culture. The presence of the 3'-terminal sequence and the absence of the 5'-terminal sequence of TON_0536 were repeatedly confirmed. On the basis of these results, we hypothesize that the unpackaged part of the T. onnurineus NA1(T) genome might be related to the process that delivers DNA into ToEVs and/or the mechanism generating the ToEVs themselves.

Evidence of ancient genome reduction in red algae (Rhodophyta).

Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl-phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle.

Complete mitochondrial genome of a rhodolith, Sporolithon durum (Sporolithales, Rhodophyta).

We present the first mitochondrial genome of the nongeniculate coralline red alga, Sporolithon durum (Sporolithales). The genome consists of 45 genes, including 24 protein-coding, 2 rRNA and 19 tRNA genes in a circular molecule of 26,202 bp with overall 28.4% GC content.

Complete mitochondrial genome of Pacific abalone (Haliotis discus hannai) from Korea.

We have sequenced and characterized the complete mitochondrial DNA of an economically and ecologically important Pacific abalone, Haliotis discus hannai (Haliotidae, Gastropoda). The mitogenome of the Pacific abalone is 16,886 nt total length with a 39.6% G+C composition. Thirty-seven genes were identified including 13 protein-coding, 2 rRNA and 22 tRNA genes. We compared the mitogenome of the Pacific abalone to a putative relative species, H. rubra.