The relationship between ribosomal repeat length and genome size in Vicia

The organization of the ribosomal RNA genes was examined in several species of Vicia in an attempt to determine whether a relationship exists between genome size and ribosomal repeat length. Species within this genus exhibit a sevenfold variation in haploid DNA content. Our data suggest that species with an intermediate genome size maintain one predominant Eco RI class of ribosomal repeat of about 9 kilobases (kb). In contrast, the smallest and largest genomes of Vicia possess one major and several minor classes. The possible relationship between repeat classes among species is discussed. We examined the species with the smallest (V. villosa) and largest (V. faba) genomes in closer detail by R-loop analysis of a satellite DNA from Hoechst 33258 dye-CsCl gradients. Heterogeneity was found in the length of the ribosomal repeat for both species, but no appreciable difference was observed in the distribution of these lengths, which averaged 11–12 kb. This heterogeneity is associated with the nontranscribed spacer region. Intervening sequences were not found in either the 25S or 18S coding regions of the ribosomal repeat of either of these two plants. A putative ribosomal RNA precursor of 7 kb was identified for both species.     

Characterization of the ribosomal DNA units in two related Prunus species (P. Cerasifera and P. Spinosa)

Summary The genetic relationships between two Prunus species, involved in rootstock breeding, were examined at the level of the ribosomal RNA genes. Twenty clones of P. cerasifera, a diploid species, and 12 clones of P. spinosa, a tetraploid wild species, were studied. The use of three heterologous ribosomal DNA probes covering different regions of the ribosomal tandem repeats enabled us to construct restriction maps for EcoRI and BamHI. We identified two unit types (unit I and unit II) in P. cerasifera. In P. spinosa, P. cerasifera units were present in addition to a third ribosomal unit type (unit III). These results appeared to confirm previous cytological studies (Salesses 1973) indicating that one of the genomes in P.spinosa has homology with the one from P. cerasifera.     

Divergence and species discrimination in freshwater bryozoans (Bryozoa: Phylactolaemata)

We explored the suitability of nuclear and mitochondrial ribosomal markers [small subunit nuclear ribosomal RNA gene, large subunit nuclear ribosomal RNA gene, and a region spanning partial small mitochondrial ribosomal RNA subunit, four transfer RNA genes, and partial large mitochondrial ribosomal RNA subunit (referred to as rrnS‐rrnL)] for resolving patterns of diversification of 27 freshwater bryozoan species (class: Phylactolaemata) and evaluated the utility of statoblast ultrastructural features and molecular phylogenies for species discrimination in the Fredericellidae and Plumatellidae. Molecular data identified Plumatella fruticosa as distinct from the rest of the plumatellids, rendering the latter polyphyletic. rrnS‐rrnL was the most suitable marker for species discrimination and identified two undescribed species of Plumatella and at least two undescribed species of Fredericella. Lack of wide dispersal by fredericellid statoblasts may underlie the observed propensity for cryptic speciation and phylogeographical structure in Fredericella. Conversely, the strong dispersal potential of plumatellid statoblasts may mediate efficient gene flow between distant populations and explain the relatively low intraspecific divergence and lack of evidence for cryptic speciation. We show that species identification based on external features of statoblasts can be problematic in both genera, including for a putatively highly invasive, biofouling species, Plumatella vaihiriae, thereby highlighting the utility of rrnS‐rrnL sequences for species barcoding. © 2013 The Linnean Society of London     

Comparison of the nuclear ribosomal units of five Chlamydomonas species

The organization of the nuclear ribosomal units of five different species of Chlamydomonas has been examined by hybridization of their nuclear DNA fragments produced by several restriction endonucleases with a radioactively labelled probe consisting of the two cloned BamHI ribosomal fragments of C. reinhardii. The results indicate that a) the ribosomal units of these five species are structurally related, b) changes in the non transcribed spacer occur in C. eugametos and in C. globosa, c) the rDNA unit of C. intermedia contains either an enlarged internal transcribed spacer or a ribosomal intervening sequence, d) the rDNA units of C. reinhardii and C. callosa are indistinguishable.     

Chromosomal patterns of major and 5S ribosomal DNA in six icefish species (Perciformes,Notothenioidei, Channichthyidae)

Comparative chromosomal mapping of major and 5S ribosomal genes in six species of the family Channichthyidae, namely Champsocephalus gunnari, Channichthys rhinoceratus, Chionodraco hamatus, Cryodraco atkinsoni, Pagetopsis macropterus and Neopagetopsis ionah, was performed by fluorescence in-situ hybridization, and using 28S and 5S ribosomal gene (rDNA) sequences as probes. Clusters of major and 5S ribosomal genes co-localize and likely compose the entire arm of a single pair of submetacentric chromosomes in all the species. In one species, P. macropterus, a second pair of chromosomes bears an additional common locus for both the two families of ribosomal genes. In all species, except N. ionah, additional copies of 5S rDNA sequences are also present on two other chromosome pairs, including the Y-chromosome in the males of Chionodraco hamatus. The pattern of ribosomal DNAs contributes to species-specific characterization in this fish family, and to our general knowledge and understanding of the chromosomal organization and evolution of the icefish genome.     

利用基因组学和MALDI-TOF MS技术鉴定放线菌纲细菌的核糖体蛋白质标志物

【目的】基质辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)法基于微生物的特征蛋白指纹图谱鉴定菌种,本研究利用基因组学和MALDI-TOFMS技术鉴定放线菌纲细菌的核糖体蛋白质标志物。【方法】从MALDI-TOF MS图谱数据库选取放线菌纲代表菌种,在基因组数据库检索目标菌种,获取目标菌株或其参比菌株的核糖体蛋白质序列,计算获得分子质量理论值,用于注释目标菌株MALDI-TOFMS指纹图谱中的核糖体蛋白质信号。【结果】从8目,24科,53属,114种,142株放线菌的MALDI-TOFMS图谱中总共注释出31种核糖体蛋白质。各菌株的指纹图谱中核糖体蛋白质信号数量差异显著。各种核糖体蛋白质信号的注释次数差异显著。总共15种核糖体蛋白质在超过半数图谱中得到注释,注释次数最高的是核糖体大亚基蛋白质L36。【结论】本研究找到了放线菌纲细菌MALDI-TOF MS图谱中常见的15种核糖体蛋白质信号,可为通过识别核糖体蛋白质的质谱特征峰鉴定放线菌的方法建立提供依据。     

Phylogeny and Genetic/Morphological Variation of Strombidinopsis minima‐like Species (Ciliophora: Choreotrichia)

Six isolates of mineral‐enveloped Strombidinopsis minima‐like species were collected from the coastal waters across several regions in Korea. Morphological observations and molecular analyses were performed. The ribosomal DNA sequences (including small subunit ribosomal DNA, internal transcriber spacer 1‐5.8S ribosomal DNA‐internal transcriber spacer 2; and part of large subunit ribosomal DNA) of these six isolates were compared. Their morphological characteristics were also compared with those of S. minima populations reported. The marked genetic differences (with a similarity range of 96.85–98.48%) in SSU rDNA among these S. minima‐like entities suggest the existence of multiple species. This finding is also supported by morphological variations detected in this study and reported in the literature (e.g. 15–32 collar membranelles in different populations). In addition, S. minima‐like species are clustered with S. batos and S. sinicum, and therefore, our SSU rDNA results support previous results suggesting that the genus Strombidinopsis is not monophyletic in origin. Further collection of morphological and molecular data may facilitate the determination of a new genus carrying mineral‐enveloped Strombidinopsis species.     

Karyotypes of basal lineages in notothenioid fishes: the genus Bovichtus

Using comparative cytogenetic techniques, we characterized the chromosomes of fishes from the family Bovichtidae, the basal lineage of the largely Antarctic suborder Notothenioidei. We focused on three Sub-Antarctic species of the genus Bovichtus that differ greatly in their circumpolar distributions: B. diacanthus (Tristan da Cunha Island Group), B. variegatus (New Zealand) and B. angustifrons (Tasmania). Chromosomes were analyzed both by conventional karyotyping and by cytogenetic mapping of ribosomal genes using fluorescence in situ hybridization. The three species displayed a strongly conserved karyotype consisting entirely of telocentric chromosomes (diploid number = 48; Fundamental Number = 48), in agreement with our previously published hypothesis that the bovichtid karyotype is the basal state for notothenioid fishes. The chromosomal distribution of ribosomal genes differed from those of most notothenioid species studied to date, with the 45S and 5S genes separated on two different chromosome pairs. Separation of two classes of ribosomal genes is the most widespread condition in teleosts, including the bovichtids. Most notothenioid lineages on the other hand exhibit a derived consolidation of these genes.     

A new genus of athecate interstitial dinoflagellates, Togula gen. nov., previously encompassed within Amphidinium sensu lato: Inferred from light and electron microscopy and phylogenetic analyses of partial large subunit ribosomal DNA sequences

The recent emendation of Amphidinium (Dinophyc‐eae), which now only consists of species with minute left‐deflected epicone, has left more than 100 species without a clear generic affiliation. In the present study, a strain identified as one of the species with a divergent epicone type, Amphidinium britannicum (Herdman) Lebour, and six strains resembling A. britannicum but smaller in size were examined by light, scanning and transmission electron microscopy and by sequence analyses of nuclear‐encoded partial large subunit ribosomal DNA to establish their phylog‐eny. Amphidinium britannicum was not closely related to other genera included in the molecular phylogenetic analyses, but formed a highly supported clade in Bayesian analysis together with the six small‐sized strains. The six strains also formed a highly supported clade, consisting of two closely related, albeit distinct, clades. Light and scanning electron microscopy did not reveal significant differences between the vegetative motile cells; however, cells about to undergo mitosis developed longitudinal grooves on the hypocone in one of the clades but not in the other. Both clades differed substantially from A. britannicum in partial large subunit ribosomal DNA as well as in size and shape. Based on morphological similarity and partial large subunit ribosomal DNA evidence, we erect the new genus, Togula gen. nov. with the emended type species Togula britannica (Herdman) comb. nov. Based on differences in division pattern and partial large subunit ribosomal DNA gene divergence we further describe the species Togula compacta (Herdman) comb. nov. and Togula jolla sp. nov.     

Novel class of rDNA repeat units in somatic hybrids between Nicotiana and Atropa

Summary Behavior of ribosomal RNA genes in the process of somatic hybridization was analyzed using hybrids Nicotiana tabacum + Atropa belladonna. Blothybridization of parental species DNAs to ³²P-rDNA specific probes revealed two classes of ribosomal repeats in both tobacco and nightshade; their length was 11.2 kb, 10.4 kb (tobacco) and 9.4 kb, 10.2 kb (night-shade). For analysis of hybrids, labelled ³²P rDNA specific probes were hybridized to DNA of parental species and somatic hybrids digested with restriction endonucleases EcoR1, EcoRV and BamH1. A new class of ribosomal DNA repeat, absent in parental species, was found in hybrid line NtAb-1. Possible mechanisms of appearence of a new rDNA class in the process of somatic cell fusion are discussed.     

Molecular-cytogenetic studies of ribosomal genes and heterochromatin reveal conserved genome organization among 11 Quercus species

Genomes of 11 Quercus species were characterized using cytogenetic (Giemsa C-banding, fluorochrome banding), molecular-cytogenetic (fluorescence in situ hybridization, FISH, to ribosomal genes) and molecular (dot-blot for ribosomal gene-copy number assessment) techniques. Ribosomal genes are the first DNA sequences to be physically mapped in oaks, and the copy number of the 18S-5.8S-26 S rRNA genes is estimated for the first time. Oak karyotypes were analysed on the basis of DAPI banding and FISH patterns; five marker chromosomes were found. In addition, chromosomal organization of ribosomal genes with respect to AT- and GC-differentiated heterochromatin was studied. Fluorochrome staining produced very similar CMA/DAPI banding patterns, and the position and number of ribosomal loci were identical for all the species studied. The 18S-5.8S-26 S rRNA genes in oak complements were represented by a major locus at the subterminal secondary constriction (SC) of the only subtelocentric chromosome pair and a minor locus at paracentromeric SC of one metacentric pair. The only 5 S rDNA locus was revealed at the paracentromeric region of the second largest metacentric pair. A striking karyotypic similarity, shown by both fluorochrome banding and FISH patterns, implies close genome relationships among oak species no matter their geographic origin (European or American) or their ecophysiology (deciduous or evergreens). Dot-blot analysis gave preliminary evidence for different copy numbers of 18S-5.8S-26 S rRNA genes in diploid genomes of Q. cerris, Q. ilex, Q. petraea, Q. pubescens and Q. robur (2700, 1300, 2200, 4000 and 2200 copies, respectively) that was correlated with the size polymorphism of the major locus. Received: 26 February 1999 / Accepted: 16 March 1999     

Characteristics and utility of nuclear-encoded large-subunit ribosomal gene sequences in phylogenetic studies of red algae

Primer sequences are described for amplifying and sequencing a large fragment (approximately 2500 b.p.) of the nuclear-encoded large-subunit ribosomal RNA gene (LSU) from red algae. In comparison to RuBisCo large-subunit gene (rbcL) and nuclear-encoded small-subunit ribosomal RNA gene (SSU) sequence data, LSU sequence data was intermediate in the number of phylogenetically informative positions and sequence divergence. Parsimony analysis of LSU sequences for 16 Gelidiales species resolved some nodes unresolved in rbcL and SSU parsimony trees. An analysis of LSU sequences from 13 species of red algae classified in 11 orders suggests that this gene may be useful in studies of higher-level relationships of red algae.     

Molecular phylogeny of the nematode genus Longidorus (Nematoda: Longidoridae) with description of three new species

The phylum Nematoda includes the genus Longidorus, a remarkable group of invertebrates that are polyphagous root‐ectoparasites of many plants including various agricultural crops and trees. Damage is caused by direct feeding on root cells as well as by transmitting nepoviruses. Species discrimination in Longidorus is complicated by phenotypic plasticity (intraspecific variability and minor interspecific differences) leading to potential misidentification. We conducted nematode surveys in cultivated and natural environments in southern Spain that detected 11 species of Longidorus. We developed a comparative study amongst these related species by considering morphological and morphometric features together with molecular data from nuclear ribosomal RNA genes [D2‐D3 expansion segments of large ribosomal subunit (28S), internal transcribed spacer 1 (ITS1), and partial small ribosomal subunit (18S)]. The results of our molecular and phylogenetic analyses confirmed the morphological hypotheses and allowed the delimitation and discrimination of three new species of the genus, described herein as Longidorus baeticus sp. nov. , Longidorus oleae sp. nov. , and Longidorus andalusicus sp. nov. , and eight known species (Longidorus alvegus, Longidorus crataegi, Longidorus fasciatus, Longidorus intermedius, Longidorus iuglandis, Longidorus magnus, Longidorus rubi, and Longidorus vineacola). Phylogenetic analyses of Longidorus spp. based on the three molecular markers resulted in a general consensus of these species grouping, as lineages were maintained for the majority of species (i.e. species with a conoid‐rounded lip region, amphidial fovea asymmetrically bilobed, female tail bluntly rounded), but not in some others (i.e. positions of L. crataegi, L. intermedius, and L. rubi were quite variable). To date, this is the most complete phylogenetic analysis for Longidorus and Paralongidorus species, with the highest number of species included. No correspondence between phylogenetic trees and morphological characters was found for ribosomal markers, with the exception of amphidial shape. Thus, polyphasic identification, based on integration of molecular analysis with morphology, is a tool beyond doubt in Longidorus identification. © 2013 The Linnean Society of London     

Phylogenetic analysis of Glomeromycota by partial LSU rDNA sequences

We analyzed the large subunit ribosomal RNA (rRNA) gene [LSU ribosomal DNA (rDNA)] as a phylogenetic marker for arbuscular mycorrhizal (AM) fungal taxonomy. Partial LSU rDNA sequences were obtained from ten AM fungal isolates, comprising seven species, with two new primers designed for Glomeromycota LSU rDNA. The sequences, together with 58 sequences available from the databases, represented 31 AM fungal species. Neighbor joining and parsimony analyses were performed with the aim of evaluating the potential of the LSU rDNA for phylogenetic resolution. The resulting trees indicated that Archaeosporaceae are a basal group in Glomeromycota, Acaulosporaceae and Gigasporaceae belong to the same clade, while Glomeraceae are polyphyletic. The results support data obtained with the small subunit (SSU) rRNA gene, demonstrating that the LSU rRNA gene is a useful molecular marker for clarifying taxonomic and phylogenetic relationships in Glomeromycota.     

Evolution of mushroom mitochondrial DNA:Suillus and related genera

Summary Mapping studies were performed with 18 cloned probes on mitochondrial DNA (mtDNA) from 15 species ofSuillus and four species from three related genera of fleshy pore mushrooms (Boletaceae). WithinSuillus, mtDNAs vary in size from 36 to 121 kb, differ in gene order by only one major rearrangement, and have diverged in nucleotide sequence within the large subunit ribosomal RNA gene region by up to 2.9%. Three additional gene orders exist in related genera. Two of the three can be transformed into the predominantSuillus order by either one or two rearrangements. The fourth requires two to three rearrangements to be converted to any of the others. The minimum estimates of nucleotide divergence within the large subunit ribosomal RNA gene region vary from 8.3% to 11% in comparisons betweenSuillus and these related species. Trees based on restriction-site and size differences within the mitochondrial ribosomal RNA genes were consistent with the hypothesized sequence of genome rearrangements and provide suggestive evidence for a major expansion of the mitochondrial genome withinSuillus. Structural and sequence changes in mtDNA provided information about phylogenetic relationships within the Boletaceae.     

Cyst‐motile stage relationship and molecular phylogeny of a new freshwater dinoflagellate Gymnodinium plasticum from Plastic Lake,Canada

The dinophyceaen genus Gymnodinium was established with the freshwater species G. fuscum as type. According to Thessen et al. (2012), there are 268 species, with the majority marine species. In recently published molecular phylogenies based on ribosomal DNA sequences, Gymnodinium is polyphyletic. Here, a new freshwater Gymnodinium species, G. plasticum, is described from Plastic Lake, Ontario, Canada. Two strains were established by incubating single cysts, and their morphology was examined with light microscopy and scanning electron microscopy. The cyst had a rounded epicyst and hypocyst with a wide cingulum and smooth surface. Vegetative cells were characterized by an elongated nucleus running vertically and a deep sulcal intrusion. The apical structure complex was horseshoe‐shaped and consisted of two pronounced ridges with a deep internal groove, encircling 80% of the apex. Small subunit ribosomal DNA (SSU rDNA), large subunit ribosomal DNA (LSU rDNA) and internal transcribed spacer (ITS) sequences were obtained from cultured strains. Molecular phylogeny based on concatenated SSU, LSU and ITS sequences supports the monophyly of the Gymnodiniales sensu stricto clade but our results suggest that many Gymnodinium species might need reclassification. Gymnodinium plasticum is closest to Dissodinium pseudolunula in our phylogeny but distant from the type species G. fuscum, as are the other gymnodiniacean taxa.     

Characterization of yeast ribosomal DNA fragments generated by EcoR1 restriction endonuclease

Summary The action of Escherichia coli restriction endonuclease R1 (EcoR1) on DNA isolated from Saccharomyces cerevisiae (strain MAR-33) generates three predominent homogenously sized DNA fragments (species of 1.8, 2.2 and 2.5 kilo nucleotide base pairs (KB). Many DNA species of molecular weight greater than 2 million daltons can be recognized upon incomplete EcoR1 digestion of yeast DNA. Four additional DNA species ranging from 0.3–0.9 KB can be identified as the second major class of EcoR1-yeast DNA products.Hybridization with radioactive ribosomal RNA (rRNA) and competition with nonradioactive rRNA show that of the three predominent EcoR1-yeast DNA species, the 2.5 KB species hybridizes only with the 25S rRNA while the lighter 1.8 KB species hybridizes with the 18S rRNA. The intermediate DNA species of 2.2 KB hybridizes to a small extent with the 25S rRNA and could be a result of the presence of the 2.5 KB DNA species. The mass proportions and hybridization values of these 3 DNA species account for about 60% of the total ribosomal DNA (rDNA).The 5EcoR1-yeast DNA species of less than 0.9 KB (4 major and 1 minor species) hybridize to varying degrees with the 2 rRNA and can be grouped in two classes. In one class there are 3 DNA species that hybridize exclusively with the 18S rRNA. In the second class there are 2 DNA species that besides hybridizing predominently with the 25S rRNA also hybridize with the 18S rRNA. The 7 EcoR1-yeast DNA species (excluding the 2.2 KB DNA species) that hybridize with the two rRNA account for nearly a 5 million dalton DNA segment, which is very close to the anticipated gene size of rRNA precursor molecule. If the 2.2 KB DNA species is a part of the rDNA that is not transcribed or 5 sRNA then the cistron encoding the rRNA in S. cerevisiae has at least 8 EcoR1 recognition sites resulting in 8 DNA fragments upon digestion with the EcoR1. Consideration is given to the relationship of the rRNA species generated by EcoR1 digestion and the chromosomes containing ribosomal cistrons.     

Chromosome Localization of 5S and 45S Ribosomal DNA in the Genomes of Linum L. Species of the Section Linum (Syn. Protolinum and Adenolinum)

Fluorescence in situ hybridization (FISH) was for the first time used to study the chromosomal location of the 45S (18S–5.8S–26S) and 5S ribosomal genes in the genomes of five flax species of the section Linum (syn. Protolinum and Adenolinum). In L. usitatissimum L. (2n = 30), L. angustifolium Huds. (2n = 30), and L. bienne Mill. (2n = 30), a major hybridization site of 45S rDNA was observed in the pericentric region of a large metacentric chromosome. A polymorphic minor locus of 45S rDNA was found on one of the small chromosomes. Sites of 5S rDNA were colocalized with those of 45S rDNA, but direct correlation between signal intensities from the 45S and 5S rDNA sites was observed only in some cases. Other 5S rDNA sites mapped to two chromosomes in these flax species. In L. grandiflorum Desf. (2n = 16) and L. austriacum L. (2n = 18), large regions of 45S and 5S rDNA were similarly located on a pair of homologous satellite-bearing chromosomes. An additional large polymorphic site of 45S and 5S rDNA was found in the proximal region of one arm of a small chromosome in the L. usitatissimum, L. angustifolium, and L. bienne karyotypes. The other arm of this chromosome contained a large 5S rDNA cluster. A similar location of the ribosomal genes in the pericentric region of the pair of satellite-bearing metacentrics confirmed the close relationships of the species examined. The difference in chromosomal location of the ribosomal genes between flax species with 2n = 30 and those with 2n = 16 or 18 testified to their assignment to different sections. The use of ribosomal genes as chromosome markers was assumed to be of importance for comparative genomic studies in cultivated flax, a valuable crop species of Russia, and in its wild relatives.     

Molecular and chromosomal analysis of ribosomal cistrons in two cartilaginous fish, <Emphasis Type="Italic">Taeniura lymma</Emphasis> and <Emphasis Type="Italic">Raja montagui</Emphasis> (Chondrichthyes,Batoidea)

We used silver nitrate staining, CMA₃ and FISH to study the chromosomal localization of both the major ribosomal genes and the nucleolar organizer regions as well as that of the minor ribosomal genes (5S rDNA) in two species of Batoidea, Taeniura lymma (Dasyatidae) and Raja montagui (Rajidae). In both species, all the metaphases examined showed the presence of multiple NOR-bearing sites, while the gene for 5S rRNA proved to be localized on two chromosome pairs. Furthermore, one of the two 5S rDNA sites in T. lymma was shown to be co-localized with the major ribosomal cluster. The presence of multiple nucleolar organizer regions in the two species might be interpreted as being the result of intraspecific polymorphisms, or as a phenomenon of the amplified transposition of mobile elements of the genome. We also determined the nucleotide sequence of the 5S rRNA gene, consisting of 564 bp in R. montagui and 612 bp in T. lymma. We also found TATA-like and (TGC)_n trinucleotides, (CA)_n dinucleotides and (GTGA)_n tetranucleotides, which probably influence gene regulation.     

Symbiont diversity in scleractinian corals from tropical reefs and subtropical non-reef communities in Taiwan

We examined zooxanthellae diversity in scleractinian corals from southern Taiwan and the Penghu Archipelago, a tropical coral reef and a subtropical non-reefal community, respectively. Zooxanthellae diversity was investigated in 52 species of scleractinian corals from 26 genera and 13 families, using restriction fragment length polymorphism (RFLP), and phylogenetic analyses of the nuclear small-subunit ribosomal DNA (nssrDNA) and large-subunit ribosomal DNA (nlsrDNA). RFLP and phylogenetic analyses of nuclear-encoded ribosomal RNA genes showed that Symbiodinium clade C was the dominant zooxanthellae in scleractinian corals in the seas around Taiwan; Symbiodinium clade D was also found in some species. Both Symbiodinium clade C and D were found in colonies of seven species of scleractinian corals. Symbiodinium clade D was associated with corals that inhabit either shallow water or the reef edge in deep water, supporting the hypothesis that Symbiodinium clade D is a relatively stress-tolerant zooxanthellae found in marginal habitats.Communicated by Biological Editor H.R. Lasker