Dicyemid Mesozoans: a Unique Parasitic Lifestyle and a Reduced Genome
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GBE Dicyemid Mesozoans: A Unique Parasitic Lifestyle and a Reduced Genome Tsai-Ming Lu1,4,*, Miyuki Kanda2, Hidetaka Furuya3,andNoriyukiSatoh1,* 1Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Japan 2DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Japan 3Department of Biology, Graduate School of Science, Osaka University, Japan 4Present address: Sars International Centre for Marine Molecular Biology, University of Bergen, Norway *Corresponding authors: E-mails: [email protected]; [email protected]. Accepted: July 16, 2019 Data deposition: This genome project has been registered at NCBI under BioProject accession PRJNA496385. Sequencing reads of the genome and transcriptomes have been deposited at the NCBI Sequence Read Archive (SRR8079359, SRR8079349-52, SRR8079348, SRR8079591, SRR8061618, SRR8061630-3). Genome and transcriptome assemblies have been deposited at DDBJ/ENA/GenBank (RDEW00000000) and NCBI Transcriptome Shotgun Assembly Sequence Database (GHAB00000000), respectively. A genome browser is available at https:// marinegenomics.oist.jp. Abstract Dicyemids, previously called “mesozoans” (intermediates between unicellular protozoans and multicellular metazoans), are an enigmatic animal group. They have a highly simplified adult body, comprising only 30 cells, and they have a unique parasitic lifestyle. Recently, dicyemids were shown to be spiralians, with affinities to the Platyhelminthes. In order to understand molecular mechanisms involved in evolution of this odd animal, we sequenced the genome of Dicyema japonicum and a reference tran- scriptome assembly using mixed-stage samples. The D. japonicum genome features a high proportion of repetitive sequences that account for 49% of the genome. The dicyemid genome is reduced to 67.5 Mb with 5,012 protein-coding genes. Only four Hox genes exist in the genome, with no clustering. Gene distribution in KEGG pathways shows that D. japonicum has fewer genes in most pathways. Instead of eliminating entire critical metabolic pathways, parasitic lineages likely simplify pathways by eliminating pathway-specific genes, while genes with fundamental functions may be retained in multiple pathways. In principle, parasites can stand to lose genes that are unnecessary, in order to conserve energy. However, whether retained genes in incomplete pathways serve intermediate functions and how parasites overcome the physiological needs served by lost genes, remain to be investigated in future studies. Key words: mesozoan, dicyemids, unique parasite, genome, reduction. Introduction are used mainly for reproduction, where vermiform or infu- Dicyemids, together with orthonectids, were previously called soriform embryos develop. Ciliated epidermal cells absorb “mesozoans,” an animal group of intermediate complexity nutrients directly from host urine via endocytosis (Ridley between unicellular protozoans and multicellular metazoans 1968; Furuya and Tsuneki 2003). Dicyemids lack a digestive (Stunkard 1954; Lapan and Morowitz 1972; Furuya and tract, coelom, circulatory system, and other differentiated Tsuneki 2003; Brusca et al. 2016). Adults consist of only tissues (fig. 1A). This is probably the most extreme case of 30 cells (fig. 1A), and are parasitic in renal sacs of cephalo- secondary reduction of body plan complexity in spiralian pods. Their simplified bodies consist of three regions: a collate, parasites. a central axial cell, and ciliated epidermal cells (fig. 1A). The In contrast to the simple body plan, the life cycle of dicye- collate region (the most anterior eight cells) is used to attach mids is characterized by two reproductive modes (asexual and to the surface of octopus renal tissues. The central axial cell is sexual) and there are larva and adult stages in each mode surrounded by an outer layer of ciliated epidermal cells that (fig. 1A). After infecting an octopus host, the germinal cell ß The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2232 Genome Biol. Evol. 11(8):2232–2243. doi:10.1093/gbe/evz157 Advance Access publication July 26, 2019 Dicyemid Mesozoans GBE A IN THE RENAL SAC B nematogen rhombogen Ecdysozoa PP C MP Orthonectida AX IN Dicyemida DV E Platyhelminthes AN AN Gastrotricha AG DI AX Mollusca Spiralia Annelida vermiform infusoriform embryo embryo IN THE SEA FIG.1.—The mesozoan, Dicyema japonicum, with a unique life cycle. (A) Life cycle of dicyemids. See the text for details. AG, agamete; AN, axial cell nucleus; AX, axial cell; C, calotte; DI, developing infusoriform embryo; DV, developing vermiform embryo; E, epidermal cell; IN, infusorigen; MP, metapolar cell; PP, propolar cell; Adapted and modified from Furuya and Tsuneki 2003.(B) Dicyemida is a member of Spiralia. develops into an asexual reproductive adult nematogen have recently been categorized as two independent taxa (fig. 1A). Then, inside the central axial cell of the nematogen, (Stunkard 1954; Mikhailov et al. 2016). The Mesozoa has the agamete (axoblast) develops into asexual reproductive affinity for the Rouphozoa (Platyhelminths and vermiform embryos (Furuya et al. 2003)(fig. 1A). While em- Gastrotricha), rather than for mollusks and annelids bryos mature, the vermiform larvae escape from the axial cell (fig. 1B)(Lu et al. 2017). The possession of a “spiralian of the nematogen and develop to new nematogens that at- peptide” by dicyemids also supports the position that tach to renal tissue of the same host, which increases the dicyemids are morphologically simplified spiralians population density. Once the population density inside a (Kobayashi et al. 1999; Lu et al. 2017). host reaches a certain threshold or if nematogens receive cer- Parasitism is more common in animals than previously tain chemical cues from the environment, nematogens trans- noted and has been reported in 15 of the 35 generally rec- form into sexually reproductive adults, called rhombogens ognized animal phyla (Weinstein and Kuris 2016). Parasitism is (fig. 1A)(Lapan and Morowitz 1972). Inside the central axial likely to have evolved independently >200 times (Wang et al. cell of a rhombogen, the hermaphroditic gonad (infusorigen) 2011). Each parasitism event reflects the interaction of a given generates sperm and eggs. Released gametes fertilize and host–parasite pair, and adaptations to a parasitic lifestyle vary develop into mature, free-swimming infusoriform larvae case by case. Parasites usually exhibit convergence, such as (fig. 1A)(Furuya et al. 1992),whichhavetosenseandlocate simplified morphology and complex lifecycles, reflecting se- new hosts in the open sea. lective pressures common to parasitism. Molecular conver- The phylogenetic position of this enigmatic group gence has also been reported across parasitic lineages, for remained controversial for a long time (Giribet 2008; example, in relation to gene expansions associated with par- Edgecombe et al. 2011). Due to an extremely high rate of asite surface modifications to avoid triggering host immune molecular changes in mesozoans, molecular phylogenetic systems (Wang et al. 2011). In addition, many unique adap- approaches did not always produce reasonable conclu- tations have been observed at the genomic level that enable sions (Katayama et al. 1995; Pawlowski et al. 1996; flatworm parasites to exploit specific niches (Zarowiecki and Petrov et al. 2010; Suzuki et al. 2010). A recent molecular Berriman 2015). Thus, to understand evolution of parasitism, phylogenetic analysis with sequence information for 348 it is necessary to examine genomic innovations that make it nuclear genes showed that dicyemids have close affinities possible. Comparative studies between parasites and closely to orthonectids (fig. 1B)(Lu et al. 2017), although these related nonparasitic species could provide an opportunity to Genome Biol. Evol. 11(8):2232–2243 doi:10.1093/gbe/evz157 Advance Access publication July 26, 2019 2233 Lu et al. GBE test long-standing hypotheses of genome reduction and The Contamination-Removing Assembly Pipeline molecular changes for adaptation to a parasitic lifestyle Eight runs of MiSeq sequencing generated 207 million read (Jackson 2015). pairs of paired-end library (supplementary table S1, As mentioned earlier, dicyemids are microscopic endopar- Supplementary Material online). The quality-trimming process asites inhabiting renal sacs of cephalopods. Although more employed Trimmomatic (v0.33) (Bolger et al. 2014)witha than one dicyemid species can inhabit an individual host quality threshold of 20 and a minimum length of 50 bases (Furuya et al. 2003), dicyemids tend to be highly host- (SLIDINGWINDOW: 4: 20, LEADING: 20, TRAILING: 20, specific (Catalano 2013). Histological studies suggest that MINLEN: 50). In addition, the sequencing of four mate-pair dicyemids employ endocytosis to absorb nutrients from host libraries generated 76.3 million read pairs (supplementary ta- urine via epithelial cell membranes (Ridley 1969). However, ble S1, Supplementary Material online). NextClip (Leggett there are many questions regarding the enigmatic lifestyle of et al. 2014) was used to categorize mate-pair reads by check- dicyemids, especially, what genomic adaptations enable ing