Molecular phylogeny of symbiotic dinoflagellates inferred from partial chloroplast large subunit (23S)-rDNA sequences

Santos, Scott R.; Taylor, Derek J.; Kinzie, Robert A.; Hidaka, Michio; Sakai, Kazuhiko; Coffroth, Mary Alice

doi:10.1016/s1055-7903(02)00010-6

Cited by 220 publications

(198 citation statements)

References 48 publications

Supporting

Mentioning

187

Contrasting

Unclassified

Order By: Relevance

“…Recently, whole genome sequences of an Acropora coral (Shinzato et al, 2011) and Symbiodinium (Shoguchi et al, 2013;Lin et al, 2015;Aranda et al, 2016) have been published, and nextgeneration sequencing (NGS) technologies have been used to investigate coral reef biodiversity (Shinzato et al, 2014b(Shinzato et al, , 2015Combosch and Vollmer, 2015;Bongaerts et al, 2017). In the genus Symbiodinium, each clade contains multiple genetic types, and identification has been performed using ribosomal, mitochondrial, plastid, and nuclear DNA markers (Rowan and Powers, 1991;Wilcox, 1998;Lajeunesse, 2001;Santos et al, 2002;Takabayashi et al, 2004). Recently internal-transcribed spacer 2 (ITS-2) regions have been widely used as genetic markers (Lajeunesse, 2001(Lajeunesse, , 2002(Lajeunesse, , 2005Pochon et al, 2007;Stat et al, 2011) and databases of Symbiodinium DNA sequences, such as SYM-BLAST (https://www.auburn.edu/~santosr/symblast.htm), SymbioGBR (Tonk et al, 2013), and GeoSymbio (Franklin et al, 2012), are currently available.…”

Section: Introductionmentioning

confidence: 99%

Using Seawater to Document Coral-Zoothanthella Diversity: A New Approach to Coral Reef Monitoring Using Environmental DNA

et al. 2018

View full text Add to dashboard Cite

Frequent, high-density coral monitoring is essential to understand coral reef ecosystems. For this purpose, we developed a novel method for simultaneous monitoring of Acropora corals and their symbiont, Symbiodinium, from environmental DNA (eDNA) in seawater using next generation sequencing technology (NGS). We performed a tank experiment with running seawater using 19 Acropora species. Complete mitochondrial genomes of all the Acropora species were assembled to create a database and major types of their Symbiodinium symbionts were identified. Then eDNA was isolated by filtering inlet and outlet seawater from the tanks. Acropora and Symbiodinium DNA were amplified by PCR and sequenced. We detected all of the tested Acropora types from eDNA samples. Proportions and numbers of DNA sequences were both positively correlated with masses of corals in the tanks. In this trial, we detected DNA sequences from as little as 0.04 kg of Acropora colony, suggesting that existence of at least one adult Acropora colony (∼30 cm diameter = 1 kg) per m 2 at depths <10 m could be detected using eDNA in the field. In addition, we detected major types of Symbiodinium within host corals from seawater, suggesting that it should be possible to detect major coral symbiont types if Acropora corals exist nearby, and possible free-living state Symbiodinium cells from eDNA in seawater. eDNA abundance of Symbiodinium types did not correlate well with frequencies of major Symbiodinium types in the corals, suggesting that quantification of Symbiodinium is difficult at this stage. Although this is the initial attempt to detect coral and Symbiodinium simultaneously from eDNA in seawater, this method may allow us to perform high-frequency, high-density coral reef monitoring of both corals and their symbionts in the near future.

show abstract

Section: Introductionmentioning

confidence: 99%

Using Seawater to Document Coral-Zoothanthella Diversity: A New Approach to Coral Reef Monitoring Using Environmental DNA

et al. 2018

View full text Add to dashboard Cite

show abstract

“…A symbiotic lineage of single-cell dinoflagellate protists is divided into clades (A-I) and numerous phylogenetically distinct types (Santos et al, 2002;Pochon et al, 2004). Out of the nine clades, Symbiodinium clades A, B, C and D are commonly associated with corals and other metazoans (Pochon and Gates, 2010).…”

Section: Introductionmentioning

confidence: 99%

Unfolding the secrets of coral–algal symbiosis

et al. 2014

View full text Add to dashboard Cite

Dinoflagellates from the genus Symbiodinium form a mutualistic symbiotic relationship with reefbuilding corals. Here we applied massively parallel Illumina sequencing to assess genetic similarity and diversity among four phylogenetically diverse dinoflagellate clades (A, B, C and D) that are commonly associated with corals. We obtained more than 30 000 predicted genes for each Symbiodinium clade, with a majority of the aligned transcripts corresponding to sequence data sets of symbiotic dinoflagellates and o2% of sequences having bacterial or other foreign origin. We report 1053 genes, orthologous among four Symbiodinium clades, that share a high level of sequence identity to known proteins from the SwissProt (SP) database. Approximately 80% of the transcripts aligning to the 1053 SP genes were unique to Symbiodinium species and did not align to other dinoflagellates and unrelated eukaryotic transcriptomes/genomes. Six pathways were common to all four Symbiodinium clades including the phosphatidylinositol signaling system and inositol phosphate metabolism pathways. The list of Symbiodinium transcripts common to all four clades included conserved genes such as heat shock proteins (Hsp70 and Hsp90), calmodulin, actin and tubulin, several ribosomal, photosynthetic and cytochrome genes and chloroplast-based hemecontaining cytochrome P450, involved in the biosynthesis of xanthophylls. Antioxidant genes, which are important in stress responses, were also preserved, as were a number of calcium-dependent and calcium/calmodulin-dependent protein kinases that may play a role in the establishment of symbiosis. Our findings disclose new knowledge about the genetic uniqueness of symbiotic dinoflagellates and provide a list of homologous genes important for the foundation of coral-algal symbiosis.

show abstract

“…LaJeunesse, 2001; Trench, 1997], even though the genus includes numerous strains separated by large genetic distances (Rowan, 1998;LaJeunesse, 2001; RodriguezLanetty, 2003;Baker, 2003). The genus is currently divided into seven highly divergent clades, designated A-G based on nuclear and plastid rDNA sequences (Rowan & Powers, 1992;Carlos et al, 1999;Baillie et al, 2000;LaJeunesse, 2001;Pochon et al, 2001;Santos et al, 2002Santos et al, , 2003 RodriguezLanetty, 2003;Baker, 2003). Clade C is dominant in corals of the Great Barrier Reef, and studies based on rDNA sequence analysis have found considerable diversity occurs within this clade (Carter, 2000;Loh et al, 2001;van Oppen et al, 2001;LaJeunesse et al, 2003;Rodriguez-Lanetty, 2003).…”

Section: Introductionmentioning

confidence: 99%

Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium

Moore

2003

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

View full text Add to dashboard Cite

The chloroplast genes of dinoflagellates are distributed among small, circular dsDNA molecules termed minicircles. In this paper, we describe the structure of the non-coding region of the psbA minicircle from Symbiodinium. DNA sequence was obtained from five Symbiodinium strains obtained from four different coral host species (Goniopora tenuidens, Heliofungia actiniformis, Leptastrea purpurea and Pocillopora damicornis), which had previously been determined to be closely related using LSU rDNA region D1/D2 sequence analysis. Eight distinct sequence blocks, consisting of four conserved cores interspersed with two metastable regions and flanked by two variable regions, occurred at similar positions in all strains. Inverted repeats (IRs) occurred in tandem or 'twin' formation within two of the four cores. The metastable regions also consisted of twin IRs and had modular behaviour, being either fully present or completely absent in the different strains. These twin IRs are similar in sequence to double-hairpin elements (DHEs) found in the mitochondrial genomes of some fungi, and may be mobile elements or may serve a functional role in recombination or replication. Within the central unit (consisting of the cores plus the metastable regions), all IRs contained perfect sequence inverses, implying they are highly evolved. IRs were also present outside the central unit but these were imperfect and possessed by individual strains only. A central adenine-rich sequence most closely resembled one in the centre of the non-coding part of Amphidinium operculatum minicircles, and is a potential origin of replication. Sequence polymorphism was extremely high in the variable regions, suggesting that these regions may be useful for distinguishing strains that cannot be differentiated using molecular markers currently available for Symbiodinium. INTRODUCTIONUnigenic DNA minicircles of 2-3 kbp that encode plastid gene functions have been found in a number of different peridinin-containing dinoflagellates, including species of Heterocapsa (Zhang et al., 1999(Zhang et al., , 2002, Amphidinium operculatum (Barbrook & Howe, 2000;Barbrook et al., 2001), Amphidinium carterae (Hiller, 2001) and Protoceratium reticulatum (Zhang et al., 2002). The non-coding regions of the minicircles are highly divergent across dinoflagellate genera, except that short stretches of a single nucleotide are frequent. A common format across dinoflagellate genera and species is that the non-coding regions contain conserved core regions, usually of between two and four in number, separated by variable regions (Zhang et al., 2002;Howe et al., 2003). In a given species, two or more cores are often identical to each other, seemingly duplicated or triplicated within the same minicircle, such as the two 9G regions of Heterocapsa triquetra (Zhang et al., 1999(Zhang et al., , 2002, and the three 5G regions of Heterocapsa pygmeae (Zhang et al., 2002).It has been shown that conserved core regions are shared between all the minicircles present in one culture of Abbreviat...

show abstract

Molecular phylogeny of symbiotic dinoflagellates inferred from partial chloroplast large subunit (23S)-rDNA sequences

Cited by 220 publications

References 48 publications

Using Seawater to Document Coral-Zoothanthella Diversity: A New Approach to Coral Reef Monitoring Using Environmental DNA

Using Seawater to Document Coral-Zoothanthella Diversity: A New Approach to Coral Reef Monitoring Using Environmental DNA

Unfolding the secrets of coral–algal symbiosis

Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium

Contact Info

Product

Resources

About