Dicyemid Mesozoans: A Unique Parasitic Lifestyle and a Reduced Genome

GBE Dicyemid Mesozoans: A Unique Parasitic Lifestyle and a Reduced Genome Tsai-Ming Lu1,4,*, Miyuki Kanda2, Hidetaka Furuya3, and Noriyuki Satoh1,* 1 Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Japan 2 DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Japan Department of Biology, Graduate School of Science, Osaka University, Japan 4 Present address: Sars International Centre for Marine Molecular Biology, University of Bergen, Norway *Corresponding authors: E-mails: ; . 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 transcriptome 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 Dicyemids, together with orthonectids, were previously called “mesozoans,” an animal group of intermediate complexity between unicellular protozoans and multicellular metazoans (Stunkard 1954; Lapan and Morowitz 1972; Furuya and Tsuneki 2003; Brusca et al. 2016). Adults consist of only 30 cells (fig. 1A), and are parasitic in renal sacs of cephalopods. Their simplified bodies consist of three regions: a collate, a central axial cell, and ciliated epidermal cells (fig. 1A). The collate region (the most anterior eight cells) is used to attach to the surface of octopus renal tissues. The central axial cell is surrounded by an outer layer of ciliated epidermal cells that are used mainly for reproduction, where vermiform or infusoriform embryos develop. Ciliated epidermal cells absorb nutrients directly from host urine via endocytosis (Ridley 1968; Furuya and Tsuneki 2003). Dicyemids lack a digestive tract, coelom, circulatory system, and other differentiated tissues (fig. 1A). This is probably the most extreme case of secondary reduction of body plan complexity in spiralian parasites. In contrast to the simple body plan, the life cycle of dicyemids is characterized by two reproductive modes (asexual and sexual) and there are larva and adult stages in each mode (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 3 GBE Dicyemid Mesozoans IN THE RENAL SAC A nematogen B rhombogen PP MP C Ecdysozoa Orthonectida AX DV AN IN Dicyemida E Platyhelminthes AN AG Gastrotricha DI AX Mollusca Annelida vermiform embryo infusoriform 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 (fig. 1A). Then, inside the central axial cell of the nematogen, the agamete (axoblast) develops into asexual reproductive vermiform embryos (Furuya et al. 2003) (fig. 1A). While embryos mature, the vermiform larvae escape from the axial cell of the nematogen and develop to new nematogens that attach to renal tissue of the same host, which increases the population density. Once the population density inside a host reaches a certain threshold or if nematogens receive certain chemical cues from the environment, nematogens transform into sexually reproductive adults, called rhombogens (fig. 1A) (Lapan and Morowitz 1972). Inside the central axial cell of a rhombogen, the hermaphroditic gonad (infusorigen) generates sperm and eggs. Released gametes fertilize and develop into mature, free-swimming infusoriform larvae (fig. 1A) (Furuya et al. 1992), which have to sense and locate new hosts in the open sea. The phylogenetic position of this enigmatic group remained controversial for a long time (Giribet 2008; Edgecombe et al. 2011). Due to an extremely high rate of molecular changes in mesozoans, molecular phylogenetic approaches did not always produce reasonable conclusions (Katayama et al. 1995; Pawlowski et al. 1996; Petrov et al. 2010; Suzuki et al. 2010). A recent molecular phylogenetic analysis with sequence information for 348 nuclear genes showed that dicyemids have close affinities to orthonectids (fig. 1B) (Lu et al. 2017), although these have recently been categorized as two independent taxa (Stunkard 1954; Mikhailov et al. 2016). The Mesozoa has affinity for the Rouphozoa (Platyhelminths and Gastrotricha), rather than for mollusks and annelids (fig. 1B) (Lu et al. 2017). The possession of a “spiralian peptide” by dicyemids also supports the position that dicyemids ar (...truncated)