Characterization of a high‐growth‐rate mutant strain of Pyropia yezoensis using physiology measurement and transcriptome analysis

A mutant strain of Pyropia yezoensis, strain E, was isolated from the free‐living conchocelis of a pure strain (NA) treated with ethyl methane sulfonate. The incremental quantities of young strain E blades were higher than those of NA after 14 d of cultivation, indicating that young blades of mutant strain E released more archeospores. The mean length and weight of large E blades were both over three times greater than those of NA after 4 weeks of cultivation. The photosynthetic parameters (Fv/Fm, Y[I], Y[II], and O₂ evolution rate) and pigment contents (including phycoerythrin and phycocyanin) of strain E blades were higher than those of NA (P < 0.05). The cellular respiratory rate of strain E blades was lower than that of NA (P < 0.05). In order to investigate the causes of changes in strain E blades, total RNA in strain E and NA blades were sequenced using the Illumina Hiseq platform. Compared with NA, 1,549 unigenes were selected in strain E including 657 up‐regulated and 892 down‐regulated genes. According to the physiology measurement and differentially expressed genes analysis, cell respiration in strain E might decrease, whereas anabolic‐like photosynthesis and protein biosynthesis might increase compared with NA. This means substance accumulation might be greater than decomposition in strain E. This might explain why strain E blades showed improved growth compared with NA. In addition, several genes related to stress resistance were up‐regulated in strain E indicating that strain E might have a higher stress resistance. The sequencing dataset may be conducive to Pyropia yezoensis molecular breeding research.     

Nuclear division of the vegetative cells, conchosporangial cells and conchospores of Porphyra yezoensis (Bangiales, Rhodophyta)

To confirm the position and timing of meiosis in Porphyra yezoensis Ueda, the nuclear division of vegetative cells, conchosporangial cells and conchospores was observed. An improved staining method using modified carbol fuchsin was introduced to stain the chromosomes of Porphyra. Pit‐connections between conchosporangial cells also stained well with this method. Leptotene, zygotene, pachytene, diplotene, diakinesis, metaphase, anaphase and telophase were observed in the conchosporangial cells. During the germination of conchospores, no characteristics of meiosis I were found. No difference between the nuclear division of vegetative cells and that of conchospores was observed, and 2–3 days were needed for the first cell division both in vegetative cells and conchospores. Therefore, the cell division that occurs during conchospore germination is not meiosis I. Our results indicate that the prophase of meiosis I begins during the formation of conchosporangial branches, and metaphase I, anaphase I and telophase I take place during the maturation of conchosporangial branches. Then the three‐bivalent nucleate sporangia complete cell division to form two individual conchospores, each with one three‐univalent nucleus. The conchospores released from the sporangia are at meiotic interphase. Meiosis II occurs at the first nuclear division during conchospore germination, which is a possible explanation for the observation of mosaic thalli in mutant germlings of P. yezoensis. The mosaic thalli might also arise from gene conversion/post meiotic segregation events, comparable to those in Sordaria fimicola (Roberge ex Desm.) Ces. & De Not. and Neurospora crassa Shear & B.O. Dodge.     

CHIMERAS WITH MOSAIC PATTERN IN ARCHEOSPORE GERMLINGS OF PYROPIA YEZOENSIS UEDA (BANGIALES,RHODOPHYTA)1

In the marine crop Pyropia yezoensis (Ueda) M. S. Hwang et H. G. Choi, it is known that conchospores from heterozygous conchocelis develop into sectored gametophytic blades (chimeras), but archeospores asexually released from haploid blades do not usually grow into chimeric blades. In this study, chimeras with mosaic pattern consisting of the green and wildtype colors were developed from archeospores that were released from a blade piece containing a cell cluster of green color induced by heavy‐ion beam irradiation. To make clear whether these archeospores were produced from the green‐colored cells or the wildtype‐colored cells, cell clusters of the green mutant, wildtype, and mosaic pattern were cut out from the grown chimera, and archeospores were released from each of the three blade pieces. Archeospores from the green‐mutant blade piece and from the wildtype blade piece developed into only green‐mutant blades and wildtype blades, respectively. In contrast, archeospores from the blade piece with mosaic pattern developed into green‐mutant blades, wildtype blades, and chimeric blades with mosaic pattern of the two colors, although the frequency of the chimeras was low. Because each gametophytic cell possesses a single plastid, it is difficult to explain the occurrence of the new chimeras as a mutation of the plastid DNA. Thus, the new chimeras are considered to be due to transposable elements in Pyropia.     

The characterization of color mutations in Bangiaceae (Bangiales, Rhodophyta)

The color mutations in Bangiaceae were investigated by treating the blades, conchocelis and conchospores phase of Bangia sp., Porphyra yezoensis, and P. haitanensis sampled in China with mutagen N-methyl-N′-nitro-N-nitrosoguanidine (MNNG). A high percentage of mutation in different expression characteristics in all three phases were shown within optimum mutagen concentrations. Among mutagenized blades, mutations occurred on single cells, which is a direct outcome of mutation of haploid cells. The mutation of mutagenized conchocelis resulted in a two-step process: low-level expression in conchocelis phase, and high-level expression in progeny, explaining that mutation took place in diploid cells. The mutations of conchospores were expressed immediately at germination of spores, indicating a change in ploidy. This paper reports the process of meiosis and its effect on frond development, and the relation between color mutations and morphological characteristics expressed by mutations in Bangiaceae.     

Co‐suppression in Pyropia yezoensis (Rhodophyta) Reveals the Role of PyLHCI in Light Harvesting and Generation Switch

The red macroalga Pyropia yezoensis is an economically important seaweed widely cultured in Asian countries and is a model organism for molecular biological and commercial research. This species is unique in that it utilizes both phycobilisomes and transmembrane light‐harvesting proteins as its antenna system. Here, one of the genes of P. yezoensis (PyLHCI) was selected for introduction into its genome to overexpress PyLHCI. However, the co‐suppression phenomenon occurred. This is the first documentation of co‐suppression in algae, in which it exhibits a different mechanism from that in higher plants. The transformant (T1) was demonstrated to have higher phycobilisomes and lower LHC binding pigments, resulting in a redder color, higher sensitivity to salt stress, smaller in size, and slower growth rate than the wildtype (WT). The photosynthetic performances of T1 and WT showed similar characteristics; however, P700 reduction was slower in T1. Most importantly, T1 could release a high percentage of carpospores in young blades to switch generation during its life cycle, which was rarely seen in WT. The co‐suppression of PyLHCI revealed its key roles in light harvesting, stress resistance, and generation alternation (generation switch from gametophytes to sporophytes, and reproduction from asexual to sexual).     

Genetic analysis of artificial pigmentation mutants in Porphyra yezoensis Ueda (Bangiales, Rhodophyta)

Porphyra yezoensis Ueda artificial pigmentation mutants, yel (green), fre (red‐orange) and bop (pink), obtained by treatment with /V‐methyl‐/V′‐nitro‐N‐nitrosoguanidine, were genetically analysed. The mutations associated with color phenotypes are recessive because all of the heterozygous conchocelis resembled the wild type color when they were crossed with the wild type (wt). In the reciprocal crosses of yel × wt, both parental colors and eight types of blades appeared in the F₁ gametophytic blades from the heterozygous conchocelis. Both colors segregated in the sectored F₁ blades in a 1:1 ratio, indicating that the color pheno‐type of yel resulted from a single mutation in the nuclear gene. In the reciprocal crosses of fre × wt, however, four colors and more than 40 types of blades appeared in the F₁ blades from the heterozygous conchocelis, indicating that the color phenotype of fre resulted from two mutations in different genes. In the reciprocal crosses of bop×wt, three colors and 12 types of blades were observed in the F₁ blades from the heterozygous conchocelis. Both parental colors appeared far more frequently than the third new color. These results indicated that the color phenotype of bop resulted from two closely linked mutations in different genes, and the epistasis occurred in the F₁ blades. The mutants, yel, fre and bop, differ from the spontaneous green (C‐O), the red (H‐25) and the violet (V‐O) mutants of P. yezoensis, respectively.     

Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones

Miscanthus × giganteus (Mxg) is an important bioenergy feedstock crop, however, genetic diversity among legacy cultivars may be severely constrained. Only one introduction from Japan to Denmark of this sterile, triploid, vegetatively propagated crop was recorded in the 1930s. We sought to determine if the Mxg cultivars in North America were all synonyms, and if they were derived from the European introduction. We used 64 nuclear and five chloroplast simple sequence repeat (SSR) markers to estimate genetic similarity for 27 Mxg accessions from North America, and compared them with six accessions from Europe, including the species’ type‐specimen. A subset of accessions was also evaluated by restriction‐site associated DNA sequencing (RAD‐seq). In addition, we assessed the potential of new crosses to increase Mxg genetic diversity by comparing eight new triploid Mxg progeny grown from seed, along with samples of the parental species M. sacchariflorus and M. sinensis. Estimates of genotyping error rates were essential for distinguishing between experimental error and true genotypic differences among accessions. Given differences in estimated error rates and costs per marker for SSRs and RAD‐seq, the former is currently more cost‐effective for determining if two accessions are genetically identical. We concluded that all of the Mxg legacy cultivars were derived via vegetative propagation from a single genet. In contrast with the Mxg legacy cultivars, genetic similarity to the type‐specimen of eight new triploid Mxg progeny ranged from 0.46 to 0.56. Though genetic diversity among the Mxg legacy cultivars is critically low, new crosses can provide much‐needed variation to growers.     

INTERSPECIFIC HYBRIDIZATION IN THE HAPLOID BLADE‐FORMING MARINE CROP PORPHYRA (BANGIALES,RHODOPHYTA): OCCURRENCE OF ALLODIPLOIDY IN SURVIVING F1 GAMETOPHYTIC BLADES1

We performed interspecific hybridization in the haploid blade‐forming marine species (nori) of the genus Porphyra, which have a heteromorphic life cycle with a haploid gametophytic blade and a diploid microscopic sporophyte called the “conchocelis phase.” The green mutant HGT‐6 of P. tenera var. tamatsuensis A. Miura was crossed with the wildtype HG‐1 of P. yezoensis f. narawaensis A. Miura; the F₁ heterozygous conchocelis developed normally and released numerous conchospores. However, almost all the conchospore germlings did not survive past the four‐cell stage or thereabouts, and only a few germlings developed into gametophytic blades. These results indicate that hybrid breakdown occurred during the meiosis, while the surviving F₁ gametophytic blades were considered a breakthrough in the interspecific hybridization of Porphyra. Organelle genomes (cpDNA and mtDNA) were found to be maternally inherited in the interspecific hybridization by molecular analyses of the organelle DNA. In particular, molecular analyses of nuclear DNA revealed that the surviving F₁ blades were allodiploids in the haploid gametophytic phase; however, there is a possibility of the occurrence of rapid chromosomal locus elimination and rearrangement in the F₁ conchocelis phase. Our findings are noteworthy to the breeding of cultivated Porphyra and will provide important information for understanding of the speciation of marine plants with high species diversity.     

Speciation in the marine crop Pyropia yezoensis (Bangiales,Rhodophyta)

In the marine red alga Pyropia yezoensis, commonly known in Japan as nori, sympatric occurrence of two cryptic species Pyropia sp. 2 and Pyropia sp. 3 on the same rock in a natural habitat has been confirmed by molecular analysis and detailed morphological observations. To confirm whether Pyropia sp. 2 and Pyropia sp. 3 were reproductively isolated in the sympatric population, 170 blades that had previously been studied using a maternally inherited plastid marker were examined with a nuclear gene marker. The results suggested that Pyropia sp. 2 and Pyropia sp. 3 with identical morphological features were reproductively isolated in the sympatric population and that they were different species based on the biological species concept. Although gametophytic blades of Pyropia were usually assumed to be haploid, 18 of 170 blades possessed both of the two genotypes derived from Pyropia sp. 2 and from Pyropia sp. 3. These results inferred that allodiploid blades were generated from the interspecific hybridization between these two cryptic species. The present findings provide insights for future studies on the speciation mechanism in seaweeds, particularly for genera that contain numerous species.     

Metabolite changes during the life history of Porphyra haitanensis

Plant metabolomics is essentially the comprehensive analysis of complex metabolites of plant extracts. Metabolic fingerprinting is an important part of plant metabolomics research. In this study, metabolic fingerprinting of different stages of the life history of the red alga Porphyra haitanensis was performed. The stages included conchocelis filaments, sporangial branchlets, conchosporangia, discharged conchospores and conchosporangial branchlets after conchospore discharge. Metabolite extracts were analysed with ultra‐performance liquid chromatography coupled with electrospray ionisation quadrupole‐time of flight mass spectrometry. Analyses profiles were subjected to principal components analysis and orthogonal projection to latent structures discriminant analysis using the SIMCA‐P software for biomarker selection and identification. Based on the MS/MS spectra and data from the literature, potential biomarkers, mainly of phosphatidylcholine and lysophosphatidylcholine, were identified. Identification of these biomarkers suggested that plasma membrane phospholipids underwent major changes during the life history of P. haitanensis. The levels of phosphatidylcholine and lysophosphatidylcholine increased in sporangial branchlets and decreased in discharged conchospores. Moreover, levels of sphingaine (d18:0) decreased in sporangial branchlets and increased in discharged conchospores, which indicates that membrane lipids were increasingly synthesised as energy storage in sporangial branchlets, while energy was consumed in sporangial branchlets to discharged conchospores. A metabolomic study of different growth phases of P. haitanensis will enhance our understanding of its physiology and ecology.     

Genetic analysis of the position of meiosis in <Emphasis Type="Italic">Porphyra haitanensis</Emphasis> Chang et Zheng (Bangiales,Rhodophyta)

Crossing experiments were carried out between artificial pigmentation mutants and the wild type in Porphyra haitanensis Chang et Zheng to ascertain where meiosis occurs in its life history by confirming whether the color segregation and the color-sectored blades appear in F₁ gametophytic blades developed from conchospores which are released from heterozygous conchocelis. Two red-type pigmentation mutants (R-10 and SPY-1) were used as the female parent. Their blades are red or red orange in color, thinner than the wild type and weak in elasticity, and have no denticles on their margins. The wild type (W) was used as the male parent; its blades are light brown in color, thick and good in elasticity, and have many marginal denticles. The F₁ gametophytic blades developed from conchospores which were released from heterozygous conchocelis produced in the crosses of R-10(♀)×W(♂) and SPY-1(♀)×W(♂) showed two parental colors (R and W) and two new colors (R', lighter in color than R; W', wild-type-like color and redder than W). Linear segregation of colors occurred in the F₁ blades, forming color-sectored blades with 2–4 sectors. In the color-sectored blades, R and R' sectors were thinner than W and W' sectors, and had weak elasticity and no denticles on their margins, whereas W and W' sectors were thick and had good elasticity and many marginal denticles. Of the F₁ gametophytic blades, 95.2–96.7% were color-sectored and only 3.3–4.8% were unsectored. These results indicate that meiosis of P. haitanensis occurs during the first two cell divisions of a germinating conchospore, and thus it is considered that the initial four cells of a developing conchosporeling constitute a linear genetic tetrad leading to the formation of a color-sectored blade. The new colors of R' and W' were recombinant colors due to the chromosome recombination during the first cell division in meiosis. It is considered that color phenotypes of the two mutants used in this paper were result of two (or more) recessive mutations in different genes, and that they also have mutations concerned with blade thickness and formation of marginal denticles, which are linked with the color mutations.     

ALLOPOLYPLOIDY IN NATURAL AND CULTIVATED POPULATIONS OF PORPHYRA (BANGIALES,RHODOPHYTA)1

To confirm whether allopolyploidy occurs in samples of previously identified Porphyra yezoensis Ueda, P. tenera Kjellm., and P. yezoensis × P. tenera from natural and cultivated populations, we examined these samples by using PCR‐RFLP and microsatellite analyses of multiple nuclear and chloroplast regions [nuclear regions: type II DNA topoisomerase gene (TOP2), actin‐related protein 4 gene (ARP4), internal transcribed spacer (ITS) rDNA and three microsatellite loci; chloroplast region: RUBISCO spacer]. Except for the ITS region, these multiple nuclear markers indicated that the wild strain MT‐1 and the cultivated strain 90‐02 (previously identified as P. yezoensis × P. tenera and cultivated P. tenera, respectively) are heterozygous and possess both genotypes of P. tenera and P. yezoensis in the conchocelis phase. Furthermore, gametophytic blades of two pure lines, HG‐TY1 and HG‐TY2 (F₁ strains of MT‐1 and 90‐02, respectively), were also heterozygous, and six chromosomes per single cell could be observed in each blade of the two pure lines. These results demonstrate that allopolyploidy occurs in Porphyra strains derived from both natural and cultivated populations, even though ITS genotypes of these strains showed homogenization toward one parental ITS.     

CLONING AND QUANTITATIVE ANALYSIS OF THE CARBONIC ANHYDRASE GENE FROM PORPHYRA YEZOENSIS1

Carbonic anhydrase (CA), an enzyme that catalyzes the interconversion of CO₂ and HCO₃^?, has a critical role in inorganic carbon acquisition in many kingdoms, including animals, plants, and bacteria. In this study, the full‐length cDNA of the CA gene from Porphyra yezoensis Ueda (denoted as PyCA) was cloned by using an expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE). The nucleotide sequence of PyCA consists of 1,153 bp, including a 5′ untranslated region (UTR) of 177 bp, a 3′ UTR of 151 bp, and an open reading frame (ORF) of 825 bp that can be translated into a 274‐amino‐acid putative peptide with a molecular mass (M) of 29.8 kDa and putative isoelectric point (pI) of 8.51. The predicted polypeptide has significant homology to the β‐CA from bacteria and unicellular algae, such as Porphyridium purpureum. The mRNA in filamentous thalli, leafy thalli, and conchospores was examined, respectively, by real‐time fluorescent quantitative PCR (qPCR), and the levels of PyCA are different at different stages of the life cycle. The lowest level of mRNA was observed in leafy thalli, and the level in filamentous thalli and in the conchospores was 4‐fold higher and 10‐fold higher, respectively.     

CRYOPRESERVATION OF THE CONCHOCELIS OF PORPHYRA (RHODOPHYTA) BY APPLYING A SIMPLE PREFREEZING SYSTEM1

The conchocelis cells of four strains of Porphyra yezoensis Udea and four other Porphyra species were cryopreserved in liquid nitrogen (LN) using a programmable freezer or a simple prefreezing system, which consisted of a styrofoam box and a deep-freezer at ?40° C. The cells differed in their freezing tolerance but survived maximally when prefrozen to ?40° C in a cryoprotective solution composed of 10% dimethylsulfoxide and 0.5 M sorbitol in 50% seawater. The cryopreservation was successfully performed by applying the simple prefreezing system as well as by a programmable freezer. Conchocelis cells thawed from the LN temperature formed colonies and retained the ability to form conchospores that grew into gametophytic thalli. This technique using a simple prefreezing system will accelerate the spread of Porphyra cryopreservation.     

Research Note: Observations on a terrestrial charophyte in a temperate environment

This study describes the unusual growth forms of Chara (Charales) in a natural terrestrial environment in a temperate region (southern Siberia). Chara vulgaris had a moss‐like habit and grew on wet soil in small compact turfs probably germinated from oospores. The upper branchlets were curved in a hook‐liked manner and convergent above the apex of the thallus. The lowest internode and branchlets of fertile plants were ecorticate, whereas all other parts were normally corticated; the completely ecorticate plants were sterile. The terrestrial growth of charophytes had an irregular appearance but was successfully maintained in culture, providing a potential model of the first steps of land colonization by the ancestors of embryophytes.     

Morphological and AFLP variation of Porphyra yezoensis Ueda form, narawaensis Miura (Bangiales, Rhodophyta)

Detailed morphological observations were made on two strains of cultivated Porphyra: HG‐1 (pure line isolated from Dai‐1) and Noriken‐4 (parental strain of a pure line HG‐4). The two strains were identified as P. yezoensis f. narawaensis based on their macroscopic and microscopic features, such as long linear or oblanceolate blades up to 50 cm in maximum length, division formulae of spermatangia and zygotosporangia, shape of trichogynes and carpogonia, and the second transverse divisional plane formed at the division from c/2 to c/4 in zygotosporangia. Gametophytic blades from two completely homozygous conchocelis strains isolated in this study (HG‐1 and HG‐4) were cultured under the same conditions and compared to confirm whether the differences in their shapes are genetically determined. The shape of blades from both of conchospores and monospores was always more slender in HG‐4 than in HG‐1 at the same blade age, suggesting that the difference in the blade shape between the two pure lines is due to genetic variation. To estimate the level of genetic variation the two pure lines were subjected to amplified fragment length polymorphism fingerprint analysis. A total of 230 bands were detected in HG‐1 and HG‐4 using eight selective primer pairs, and the number of polymorphic bands was only two in HG‐1. These results indicate that the two pure lines certainly show genetic variation, which is, however, at an extremely low level. The importance of pure‐line breeding and the origin of currently cultivated Porphyra are discussed. This is the first report to identify currently cultivated Porphyra strains in Japan based on combined results of detailed morphological observations and molecular analysis.     

MORPHOLOGICAL AND MOLECULAR ANALYSIS OF THE ENDANGERED SPECIES PORPHYRA TENERA (BANGIALES,RHODOPHYTA)1

Porphyra tenera Kjellman, widely cultivated in nori farms before the development of artificial seeding, is currently listed as an endangered species in Japan. To confirm whether a wild‐collected gametophytic blade was P. tenera or the closely related species P. yezoensis Ueda, morphological observations and molecular analyses were made on the pure line HGT‐1 isolated from a wild blade. This pure line was identified as P. tenera based on detailed morphological features. Sequences of the nuclear internal transcribed spacer region 1 and the plastid RUBISCO spacer revealed that P. tenera HGT‐1 was clearly different from P. yezoensis f. narawaensis Miura, the main species cultivated in Japan. PCR‐RFLP analysis of the internal transcribed spacer region was found to be a convenient method for rapid discrimination between P. tenera and cultivated P. yezoensis. The restriction patterns generated by the endonucleases Dra I and Hae III were useful for differentiating between both gametophytic and conchocelis stages of P. tenera HGT‐1 and P. yezoensis f. narawaensis strains. Thus, PCR‐RFLP analysis will serve as a valuable tool for rapid species identification of cultivated Porphyra strains, culture collections of Porphyra strains for breeding material and conservation of biodiversity, and, as codominant cleaved amplified polymorphic sequence markers for interspecific hybridization products between P. tenera and P. yezoensis f. narawaensis. Under the same culture conditions, rate of blade length increase and the blade length‐to‐width ratio were lower in P. tenera HGT‐1 than in P. yezoensis f. narawaensis HG‐4. The HGT‐1 became mature more rapidly than HG‐4 and had thinner blades.     

Cranial morphology and taxonomic resolution of some dolphin taxa (Delphinidae) in Australian waters,with a focus on the genus Tursiops

Phylogenetic relationships in the family Delphinidae have been widely debated. We examined 347 skulls of Tursiops, Stenella, Delphinus, Steno, Lagenodelphis, and Sousa in order to resolve the phylogenetic position of Australian species of Tursiops. Five Tursiops type specimens were included. Cranial morphology was described using 2‐dimensional (2‐D) and 3‐dimensional geometric morphometrics (3‐GM), counts and categorical data. Analyses showed a clear morphological separation of Tursiops, including type specimens, from other genera. The three Stenella species did not cluster together. Stenella attenuata clustered with Delphinus delphis, and Stenella coeruleoalba with Lagenodelphis hosei. Length and width of the skull and rostrum were important discriminators in both methods. For 3‐D data, round vs. angular posterior skull shape distinguished some genera. Taxa that overlapped in the multivariate analyses had different mean tooth counts. Our study challenges genetic studies that identified Tursiops as polyphyletic, with T. aduncus closer to S. attenuata.     

Population genetic data of a model symbiotic cnidarian system reveal remarkable symbiotic specificity and vectored introductions across ocean basins

The Aiptasia–Symbiodinium symbiosis is a promising model for experimental studies of cnidarian–dinoflagellate associations, yet relatively little is known regarding the genetic diversity of either symbiotic partner. To address this, we collected Aiptasia from 16 localities throughout the world and examined the genetic diversity of both anemones and their endosymbionts. Based on newly developed SCAR markers, Aiptasia consisted of two genetically distinct populations: one Aiptasia lineage from Florida and a second network of Aiptasia genotypes found at other localities. These populations did not conform to the distributions of described Aiptasia species, suggesting that taxonomic re‐evaluation is needed in the light of molecular genetics. Associations with Symbiodinium further demonstrated the distinctions among Aiptasia populations. According to 18S RFLP, ITS2‐DGGE and microsatellite flanker region sequencing, Florida anemones engaged in diverse symbioses predominantly with members of Symbiodinium Clades A and B, but also C, whereas anemones from elsewhere harboured only S. minutum within Clade B. Symbiodinium minutum apparently does not form a stable symbiosis with other hosts, which implies a highly specific symbiosis. Fine‐scale differences among S. minutum populations were quantified using six microsatellite loci. Populations of S. minutum had low genotypic diversity and high clonality (R = 0.14). Furthermore, minimal population structure was observed among regions and ocean basins, due to allele and genotype sharing. The lack of genetic structure and low genotypic diversity suggest recent vectoring of Aiptasia and S. minutum across localities. This first ever molecular‐genetic study of a globally distributed cnidarian and its Symbiodinium assemblages reveals host–symbiont specificity and widely distributed populations in an important model system.