Molecular Phylogeny and Evolution of Parabasalia with Improved Taxon Sampling and New Protein Markers of Actin and Elongation Factor-1A
Total Page：16
File Type：pdf, Size：1020Kb
Molecular Phylogeny and Evolution of Parabasalia with Improved Taxon Sampling and New Protein Markers of Actin and Elongation Factor-1a Satoko Noda1,2*, Cle´a Mantini3, Dionigia Meloni3,4, Jun-Ichi Inoue1, Osamu Kitade5, Eric Viscogliosi3, Moriya Ohkuma1* 1 Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama, Japan, 2 Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Yamanashi, Japan, 3 Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France, and Inserm U1019, CNRS UMR 8204, and University Lille – Nord de France, Lille, France, 4 Department of Biomedical Sciences, Division of Experimental and Clinical Microbiology, University of Sassari, Sassari, Italy, 5 Natural History Laboratory, College of Science, Ibaraki University, Mito, Ibaraki, Japan Abstract Background: Inferring the evolutionary history of phylogenetically isolated, deep-branching groups of taxa—in particular determining the root—is often extraordinarily difficult because their close relatives are unavailable as suitable outgroups. One of these taxonomic groups is the phylum Parabasalia, which comprises morphologically diverse species of flagellated protists of ecological, medical, and evolutionary significance. Indeed, previous molecular phylogenetic analyses of members of this phylum have yielded conflicting and possibly erroneous inferences. Furthermore, many species of Parabasalia are symbionts in the gut of termites and cockroaches or parasites and therefore formidably difficult to cultivate, rendering available data insufficient. Increasing the numbers of examined taxa and informative characters (e.g., genes) is likely to produce more reliable inferences. Principal Findings: Actin and elongation factor-1a genes were identified newly from 22 species of termite-gut symbionts through careful manipulations and seven cultured species, which covered major lineages of Parabasalia. Their protein sequences were concatenated and analyzed with sequences of previously and newly identified glyceraldehyde-3-phosphate dehydrogenase and the small-subunit rRNA gene. This concatenated dataset provided more robust phylogenetic relationships among major groups of Parabasalia and a more plausible new root position than those previously reported. Conclusions/Significance: We conclude that increasing the number of sampled taxa as well as the addition of new sequences greatly improves the accuracy and robustness of the phylogenetic inference. A morphologically simple cell is likely the ancient form in Parabasalia as opposed to a cell with elaborate flagellar and cytoskeletal structures, which was defined as most basal in previous inferences. Nevertheless, the evolution of Parabasalia is complex owing to several independent multiplication and simplification events in these structures. Therefore, systematics based solely on morphology does not reflect the evolutionary history of parabasalids. Citation: Noda S, Mantini C, Meloni D, Inoue J-I, Kitade O, et al. (2012) Molecular Phylogeny and Evolution of Parabasalia with Improved Taxon Sampling and New Protein Markers of Actin and Elongation Factor-1a. PLoS ONE 7(1): e29938. doi:10.1371/journal.pone.0029938 Editor: John W. Stiller, East Carolina University, United States of America Received August 16, 2011; Accepted December 8, 2011; Published January 9, 2012 Copyright: ß 2012 Noda et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was partially supported by a grant from the Biomass Engineering Program from RIKEN, Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS) (Nos. 19780067 to SN, and 19380055 and 20658024 to MO, respectively), and a grant from the French Ministe`re de l’Education Nationale, de la Recherche et de la Technologie to CM, and by the Centre National de la Recherche Scientifique, the Institut National de la Sante´ et de la Recherche Me´dicale, the Institut Pasteur of Lille, the University Lille–Nord de France. EV was the recipient of the JSPS Invitation Fellowship Program for Research in Japan FY2010 and the JSPS BRIDGE Fellowship Program FY2011. CM was the recipient of the JSPS Predoctoral-Postdoctoral Fellowship for Foreign Researchers FY2009. DM was supported by grants from the ERASMUS Program and Regione Automa della Sardegna. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] (SN); [email protected] (MO) Introduction far [1,3]. Most parabasalids inhabit the digestive tract of animal hosts as commensals, parasites, or symbionts. In particular, The phylum Parabasalia, or commonly parabasalids, comprises symbiotic parabasalids found in the gut of termites and wood- a monophyletic but complex assemblage of diverse species of eating cockroaches play a central role in the digestion of cellulose flagellated protists typified by the presence of a characteristic [4]. This symbiotic relationship is considered a key element in the parabasal apparatus (Golgi complex associated with striated evolution of social behavior in the hosts [5] and has ecological fibers), closed mitosis with an external spindle (cryptopleuromi- significance for the decomposition of plant litter in terrestrial tosis), and anaerobic energy-generating organelles called hydro- ecosystems [6]. Several parabasalids are also of considerable genosomes [1,2]. Based on morphological characters, more than medical and veterinary importance as pathogens—i.e., Trichomonas 80 genera and 400 parabasalid species have been described thus vaginalis and Tritrichomonas foetus [7,8]. PLoS ONE | www.plosone.org 1 January 2012 | Volume 7 | Issue 1 | e29938 Phylogeny and Evolution of Parabasalia In addition to the functional host interactions of parabasalids, In phylogenetic analyses based on SSU rRNA gene or their biodiversity, conspicuous morphology, unique anaerobic concatenated data of protein sequences, Trichonymphea, the biochemistry, and potentially crucial position in various schemes of most morphologically complex group of parabasalids, frequently eukaryotic evolution have long fascinated researchers. Indeed, occurs as the most basal lineage of Parabasalia [31–33,35,54,55]. Parabasalia is included in the supergroup Excavata and in Support for this rooting often has been poor, however, and the Metamonada with Fornicata (e.g., Giardia) and Preaxostyla (e.g., differences among several alternative positions in parabasalid Monocercomonoides and Trimastix) [9]. The monophyly of Excavata, lineages have been insignificant [20,33,35,55]. This uncertainty although supported morphologically [9,10], is debated still has been explained by the absence of any close outgroup species to intensely, but multigene analyses interestingly suggest that Parabasalia [20]. The parabasalid lineage usually branches out Excavata stems from a very deep branching event within the deeply in eukaryote phylogenies, and the branch leading to history of eukaryotes [11–13]. Parabasalia is very long. Such a long branch may attract the fast- Molecular phylogenetic studies based on small-subunit (SSU) evolving Trichonymphea, causing artificial rooting. Furthermore, rRNA gene sequences have focused mainly on cultured represen- the gene encoding GAPDH, like many other glycolytic enzymes, tatives of parabasalids [14–27]. In contrast, molecular studies of of Parabasalia has been derived from a bacterium via lateral gene the parabasalids found in the gut of termites have been impeded transfer (LGT) [51,62–64], which disturbs root inference in because these organisms live in complex microbial communities comparisons to other eukaryotes. and are very difficult to culture [28,29]. SSU rRNA gene Approaches using the sequence data of multiple genes increase sequences from parabasalid symbionts, however, have been the number of informative characters for phylogenetic inference. identified subsequently by culture-independent studies [30–50] In parallel, increasing the number of sampling taxa (or species) is (see also Table 1 for reference in each parabasalid species). also important. Assembling datasets rich in both genes and taxa is Because of a high level of sequence divergence of the SSU rRNA likely to produce more accurate and robust results, although gene across parabasalid lineages, a lack of resolution and possible controversy exists about which strategy (increasing the number of tree-construction artifacts have occurred, even though a large genes or taxa) contributes most to the accurate inference [65–67]. number of taxa have been investigated [26,39,43,46]. To overcome In general, recent genome sequencing efforts have increased the this drawback, multiple protein-encoding genes such as glyceralde- number of genes for some species, but the genome analyses of hyde-3-phosphate dehydrogenase (GAPDH), enolase, and tubulins either cultured microbial species or yet-uncultivated species are have been examined [51–57]. In these phylogenetic reconstructions, still poor. In terms of taxon sampling, data availability is also however, taxon sampling was limited, and some conflicting results restricted, particularly for yet-uncultivated species. The goal of this for relationships