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Sproles AE, Kirk NL, Kitchen SA, Oakley CA, Grossman AR, Weis VM, Davy SK. Phylogenetic characterization of transporter proteins in the cnidarian-dinoflagellate symbiosis. Mol Phylogenet Evol 2017; 120:307-320. [PMID: 29233707 DOI: 10.1016/j.ympev.2017.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 10/22/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Metabolic exchange between cnidarians and their symbiotic dinoflagellates is central to maintaining their mutualistic relationship. Sugars are translocated to the host, while ammonium and nitrate are utilized by the dinoflagellates (Symbiodinium spp.). We investigated membrane protein sequences of each partner to identify potential transporter proteins that move sugars into cnidarian cells and nitrogen products into Symbiodinium cells. We examined the facilitated glucose transporters (GLUT), sodium/glucose cotransporters (SGLT), and aquaporin (AQP) channels in the cnidarian host as mechanisms for sugar uptake, and the ammonium and high-affinity nitrate transporters (AMT and NRT2, respectively) in the algal symbiont as mechanisms for nitrogen uptake. Homologous protein sequences were used for phylogenetic analysis and tertiary structure deductions. In cnidarians, we identified putative glucose transporters of the GLUT family and glycerol transporting AQP proteins, as well as sodium monocarboxylate transporters and sodium myo-inositol cotransporters homologous to SGLT proteins. We hypothesize that cnidarians use GLUT proteins as the primary mechanism for glucose uptake, while glycerol moves into cells by passive diffusion. We also identified putative AMT proteins in several Symbiodinium clades and putative NRT2 proteins only in a single clade. We further observed an upregulation of expressed putative AMT proteins in Symbiodinium, which may have emerged as an adaptation to conditions experienced inside the host cell. This study is the first to identify transporter sequences from a diversity of cnidarian species and Symbiodinium clades, which will be useful for future experimental analyses of the host-symbiont proteome and the nutritional exchange of Symbiodinium cells in hospite.
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Affiliation(s)
- Ashley E Sproles
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Nathan L Kirk
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Sheila A Kitchen
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Clinton A Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand.
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Rosic N, Ling EYS, Chan CKK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O. Unfolding the secrets of coral-algal symbiosis. ISME JOURNAL 2015; 9:844-56. [PMID: 25343511 DOI: 10.1038/ismej.2014.182] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 08/05/2014] [Accepted: 08/25/2014] [Indexed: 11/09/2022]
Abstract
Dinoflagellates from the genus Symbiodinium form a mutualistic symbiotic relationship with reef-building 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 <2% 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 heme-containing 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.
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Affiliation(s)
- Nedeljka Rosic
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Edmund Yew Siang Ling
- University of Queensland Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Chon-Kit Kenneth Chan
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Hong Ching Lee
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Paulina Kaniewska
- 1] School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia [2] Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - David Edwards
- 1] School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia [2] School of Plant Biology, University of Western Australia, Perth, Western Australia, Australia [3] Australian Centre for Plant Functional Genomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Sophie Dove
- 1] School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia [2] ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland, Australia
| | - Ove Hoegh-Guldberg
- 1] School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia [2] ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland, Australia [3] Global Change Institute and ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland, Australia
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Rehm P, Meusemann K, Borner J, Misof B, Burmester T. Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing. Mol Phylogenet Evol 2014; 77:25-33. [PMID: 24732681 DOI: 10.1016/j.ympev.2014.04.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/31/2014] [Accepted: 04/03/2014] [Indexed: 02/02/2023]
Abstract
Myriapods had been considered closely allied to hexapods (insects and relatives). However, analyses of molecular sequence data have consistently placed Myriapoda either as a sister group of Pancrustacea, comprising crustaceans and hexapods, and thereby supporting the monophyly of Mandibulata, or retrieved Myriapoda as a sister group of Chelicerata (spiders, ticks, mites and allies). In addition, the relationships among the four myriapod groups (Pauropoda, Symphyla, Diplopoda, Chilopoda) are unclear. To resolve the phylogeny of myriapods and their relationship to other main arthropod groups, we collected transcriptome data from the symphylan Symphylella vulgaris, the centipedes Lithobius forficatus and Scolopendra dehaani, and the millipedes Polyxenus lagurus, Glomeris pustulata and Polydesmus angustus by 454 sequencing. We concatenated a multiple sequence alignment that contained 1550 orthologous single copy genes (1,109,847 amino acid positions) from 55 euarthropod and 14 outgroup taxa. The final selected alignment included 181 genes and 37,425 amino acid positions from 55 taxa, with eight myriapods and 33 other euarthropods. Bayesian analyses robustly recovered monophyletic Mandibulata, Pancrustacea and Myriapoda. Most analyses support a sister group relationship of Symphyla in respect to a clade comprising Chilopoda and Diplopoda. Inclusion of additional sequence data from nine myriapod species resulted in an alignment with poor data density, but broader taxon average. With this dataset we inferred Diplopoda+Pauropoda as closest relatives (i.e., Dignatha) and recovered monophyletic Helminthomorpha. Molecular clock calculations suggest an early Cambrian emergence of Myriapoda ∼513 million years ago and a late Cambrian divergence of myriapod classes. This implies a marine origin of the myriapods and independent terrestrialization events during myriapod evolution.
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Affiliation(s)
- Peter Rehm
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany
| | - Karen Meusemann
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, D-53113 Bonn, Germany; CSIRO Ecosystem Sciences, Australian National Insect Collection, Clunies Ross Street, Acton, ACT 2601, Australia
| | - Janus Borner
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, D-53113 Bonn, Germany
| | - Thorsten Burmester
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany.
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Kocot KM, Citarella MR, Moroz LL, Halanych KM. PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics. Evol Bioinform Online 2013; 9:429-35. [PMID: 24250218 PMCID: PMC3825643 DOI: 10.4137/ebo.s12813] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner/.
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Affiliation(s)
- Kevin M Kocot
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, USA
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Aranda M, DeSalvo MK, Bayer T, Medina M, Voolstra CR. Evolutionary insights into scleractinian corals using comparative genomic hybridizations. BMC Genomics 2012; 13:501. [PMID: 22994626 PMCID: PMC3469353 DOI: 10.1186/1471-2164-13-501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/11/2012] [Indexed: 12/04/2022] Open
Abstract
Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization). Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies.
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Affiliation(s)
- Manuel Aranda
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Moroz LL. Phylogenomics meets neuroscience: how many times might complex brains have evolved? ACTA BIOLOGICA HUNGARICA 2012; 63 Suppl 2:3-19. [PMID: 22776469 DOI: 10.1556/abiol.63.2012.suppl.2.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The origin of complex centralized brains is one of the major evolutionary transitions in the history of animals. Monophyly (i.e. presence of a centralized nervous system in urbilateria) vs polyphyly (i.e. multiple origins by parallel centralization of nervous systems within several lineages) are two historically conflicting scenarios to explain such transitions. However, recent phylogenomic and cladistic analysis suggests that complex brains may have independently evolved at least 9 times within different animal lineages. Indeed, even within the phylum Mollusca cephalization might have occurred at least 5 times. Emerging molecular data further suggest that at the genomic level such transitions might have been achieved by changes in expression of just a few transcriptional factors - not surprising since such events might happen multiple times over 700 million years of animal evolution. Both cladistic and genomic analyses also imply that neurons themselves evolved more than once. Ancestral polarized secretory cells were likely involved in coordination of ciliated locomotion in early animals, and these cells can be considered as evolutionary precursors of neurons within different lineages. Under this scenario, the origins of neurons can be linked to adaptations to stress/injury factors in the form of integrated regeneration-type cellular response with secretory signaling peptides as early neurotransmitters. To further reconstruct the parallel evolution of nervous systems genomic approaches are essential to probe enigmatic neurons of basal metazoans, selected lophotrochozoans (e.g. phoronids, brachiopods) and deuterostomes.
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Affiliation(s)
- L L Moroz
- The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd. St. Augustine Florida 32080, USA.
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Ebersberger I, de Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, von Haeseler A. A consistent phylogenetic backbone for the fungi. Mol Biol Evol 2011; 29:1319-34. [PMID: 22114356 PMCID: PMC3339314 DOI: 10.1093/molbev/msr285] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.
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Affiliation(s)
- Ingo Ebersberger
- Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Vienna, Austria.
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Voolstra CR, Sunagawa S, Matz MV, Bayer T, Aranda M, Buschiazzo E, DeSalvo MK, Lindquist E, Szmant AM, Coffroth MA, Medina M. Rapid evolution of coral proteins responsible for interaction with the environment. PLoS One 2011; 6:e20392. [PMID: 21633702 PMCID: PMC3102110 DOI: 10.1371/journal.pone.0020392] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/02/2011] [Indexed: 12/14/2022] Open
Abstract
Background Corals worldwide are in decline due to climate change effects (e.g., rising seawater temperatures), pollution, and exploitation. The ability of corals to cope with these stressors in the long run depends on the evolvability of the underlying genetic networks and proteins, which remain largely unknown. A genome-wide scan for positively selected genes between related coral species can help to narrow down the search space considerably. Methodology/Principal Findings We screened a set of 2,604 putative orthologs from EST-based sequence datasets of the coral species Acropora millepora and Acropora palmata to determine the fraction and identity of proteins that may experience adaptive evolution. 7% of the orthologs show elevated rates of evolution. Taxonomically-restricted (i.e. lineage-specific) genes show a positive selection signature more frequently than genes that are found across many animal phyla. The class of proteins that displayed elevated evolutionary rates was significantly enriched for proteins involved in immunity and defense, reproduction, and sensory perception. We also found elevated rates of evolution in several other functional groups such as management of membrane vesicles, transmembrane transport of ions and organic molecules, cell adhesion, and oxidative stress response. Proteins in these processes might be related to the endosymbiotic relationship corals maintain with dinoflagellates in the genus Symbiodinium. Conclusion/Relevance This study provides a birds-eye view of the processes potentially underlying coral adaptation, which will serve as a foundation for future work to elucidate the rates, patterns, and mechanisms of corals' evolutionary response to global climate change.
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Affiliation(s)
- Christian R. Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- * E-mail: (CRV); (MM)
| | | | - Mikhail V. Matz
- Section of Integrative Biology, School of Biological Sciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Till Bayer
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manuel Aranda
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Emmanuel Buschiazzo
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Michael K. DeSalvo
- Department of Anesthesia, UCSF School of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Erika Lindquist
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Alina M. Szmant
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, United States of America
| | - Mary Alice Coffroth
- Graduate Program in Evolution, Ecology and Behavior and Department of Geology, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Mónica Medina
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
- * E-mail: (CRV); (MM)
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Campbell V, Lapointe FJ. Retrieving a mitogenomic mammal tree using composite taxa. Mol Phylogenet Evol 2011; 58:149-56. [DOI: 10.1016/j.ympev.2010.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 10/17/2010] [Accepted: 11/19/2010] [Indexed: 10/18/2022]
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Campbell V, Lapointe FJ. The Use and Validity of Composite Taxa in Phylogenetic Analysis. Syst Biol 2009; 58:560-72. [DOI: 10.1093/sysbio/syp056] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Véronique Campbell
- Département de sciences biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, Québec H3C 3J7, Canada
| | - François-Joseph Lapointe
- Département de sciences biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, Québec H3C 3J7, Canada
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Abstract
Since the discovery of the marine worm Xenoturbella bocki in 1915 by Sixten Bock and its first published description by Einar Westblad (Westblad,1949, Arkiv Zoologi 1:3-29), Xenoturbella was generally allied to the turbellarian flatworms, perhaps most closely to acoelomorphs. In 1997, however, analyses of ribosomal DNA (Norén and Jondelius, 1997, Nature 390:31-32) and developing oocytes (Israelsson, 1997, Nature 390:32) [and, subsequently, embryos (Israelsson, 1999, Proc R Soc Lond B 266:835-841)] recovered from Xenoturbella specimens led to the surprising conclusion that it was in fact a highly degenerate bivalve mollusc. Bourlat et al. showed in 2003 that this result was due to contamination from bivalves in its diet (Bourlat et al.,2003, Nature 424:925-928). Our analyses showed Xenoturbella is a deuterostome, related to the Ambulacraria (echinoderms and hemichordates). Subsequent work has shown that Xenoturbellida is a separate lineage from the Ambulacraria and therefore constitutes the fourth deuterostome phylum (Bourlat et al.,2006, Nature 444:85-88). I consider this phylogenetic position in the light of what is known of its genetics, morphology, and ontogeny. I examine what this phylogenetic position for Xenoturbella can tell us about its own evolution and what light this might shine on the common ancestor of the deuterostomes and hence on the origins of the chordates.
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Affiliation(s)
- Maximilian J Telford
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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Voolstra CR, Sunagawa S, Schwarz JA, Coffroth MA, Yellowlees D, Leggat W, Medina M. Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2008; 4:67-74. [PMID: 20403741 DOI: 10.1016/j.cbd.2008.11.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 11/13/2008] [Accepted: 11/16/2008] [Indexed: 10/21/2022]
Abstract
Dinoflagellates are ubiquitous marine and freshwater protists. The endosymbiotic relationship between dinoflagellates of the genus Symbiodinium (also known as zooxanthellae) and corals forms the basis of coral reefs. We constructed and analyzed a cDNA library from a cultured Symbiodinium species clade A (CassKB8). The majority of annotated ESTs from the Symbiodinium sp. CassKB8 library cover metabolic genes. Most of those belong to either carbohydrate or energy metabolism. In addition, components of extracellular signal transduction pathways and genes that play a role in cell-cell communication were identified. In a subsequent analysis, we determined all orthologous cDNA sequences between this library (1,484 unique sequences) and a library from a Symbiodinium species clade C (C3) (3,336 unique sequences) that was isolated directly from its symbiotic host. A set of 115 orthologs were identified between Symbiodinium sp. CassKB8 and Symbiodinium sp. C3. These orthologs were subdivided into three groups that show different characteristics and functions: conserved across eukaryotes (CE), dinoflagellate-specific (DS) and Symbiodinium-specific (SS). Orthologs conserved across eukaryotes are mainly comprised of housekeeping genes, photosynthesis-related transcripts and metabolic proteins, whereas the function for most of the dinoflagellate-specific orthologs remains unknown. A dN/dS analysis identified the highest ratio in a Symbiodinium-specific ortholog and evidence for positive selection in a dinoflagellate-specific gene. Evolution of genes and pathways in different dinoflagellates seems to be affected by different lifestyles, and a symbiotic lifestyle may affect population structure and strength of selection. This study is the first evolutionary comparative analysis of orthologs from two coral dinoflagellate symbionts.
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Affiliation(s)
- Christian R Voolstra
- School of Natural Sciences, University of California, Merced, P.O. Box 2039, Merced, CA 95344, USA
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Horvath JE, Weisrock DW, Embry SL, Fiorentino I, Balhoff JP, Kappeler P, Wray GA, Willard HF, Yoder AD. Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs. Genes Dev 2008; 18:489-99. [PMID: 18245770 PMCID: PMC2259113 DOI: 10.1101/gr.7265208] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 12/19/2007] [Indexed: 12/29/2022]
Abstract
Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships poorly supported or entirely unresolved. We used genomic resources to develop 11 novel markers from nine chromosomes, representing approximately 9 kb of nuclear sequence data. In combination with previously published nuclear and mitochondrial loci, this yields a data set of more than 16 kb and adds approximately 275 kb of DNA sequence to current databases. Our phylogenetic analyses confirm hypotheses of lemuriform monophyly and provide robust resolution of the phylogenetic relationships among the five lemuriform families. We verify that the genus Daubentonia is the sister lineage to all other lemurs. The Cheirogaleidae and Lepilemuridae are sister taxa and together form the sister lineage to the Indriidae; this clade is the sister lineage to the Lemuridae. Divergence time estimates indicate that lemurs are an ancient group, with their initial diversification occurring around the Cretaceous-Tertiary boundary. Given the power of this data set to resolve branches in a notoriously problematic area of primate phylogeny, we anticipate that our phylogenomic toolkit will be of value to other studies of primate phylogeny and diversification. Moreover, the methods applied will be broadly applicable to other taxonomic groups where phylogenetic relationships have been notoriously difficult to resolve.
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Affiliation(s)
- Julie E Horvath
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA.
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