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We sequenced the M. honghuensis genome with a PacBio RSII, yielding 136 coverage and a 16-kilobase (kb) average read length (Additional file 1: Table S1). The final long-read data contained 2,030,357 sequences with a mean length of 10.4 kb (Additional file 1: Table S2). The genome size was estimated by k-mer analysis using Jellyfish software (Additional file 2: Fig. S1) to be 206 megabases (Mb). The FALCON-assembled genome contained 1118 contigs (161 Mb, N50 1.3 Mb; Table 1). M. honghuensis has a relatively larger myxozoan genome (Additional file 1: Table S3). The assembly showed high integrity and quality, with >98.5% of Illumina genome survey reads mapped to the PacBio assembly (Additional file 1: Table S4), and successful reconstruction of the nuclear rRNAs. Core Eukaryotic Genes Mapping Approach (CEGMA)  identified only 42.7% of CEGs; a low percentage also seen in another myxozoan  and possibly due to fast-evolutionary rates rendering even common eukaryotic genes difficult to recognize.
To identify factors that contribute to the relatively large genome of M. honghuensis, we analyzed the transposable element (TE) content and whole-genome duplications (WGDs) in M. honghuensis and compared it with other cnidarians [29, 30]. The M. honghuensis genome contained 36.1% (55.5 Mb) repetitive sequences, most of which are TEs (23.7% of the total genome; Table 2 and Additional file 1: Table S7). Long terminal repeats (LTRs, 9.2%) and terminal inverted repeats (TIRs, 11.9%) are the major contributors of retrotransposons (11.1%) and DNA transposons (12.6%) respectively (Fig. 1a). We calculated the relative age of transposable element copies using Kimura distance analyses and comparisons with other cnidarians, and revealed that M. honghuensis has had at least two transposon bursts (Fig. 1b).
To identify potential WGD events in M. honghuensis, we determined the number of syntenic gene pairs in five myxozoans and two free-living cnidarian genomes (Additional file 1: Table S8). We found few syntenic blocks and syntenic gene pairs in the M. honghuensis genome, suggesting that it has not undergone WGD. We then calculated fourfold synonymous third-codon transversion (4DTv) values (a neutral genetic distance used to estimate the relative timing of evolutionary events ) for paralogous gene pairs in the free-living Acropora digitifera, and myxozoans M. honghuensis, Thelohanellus kitauei, and Myxobolus squamalis. We observed no sharp peaks in the 4DTv plots of the myxozoans, which supported a hypothesis that WGD has not occurred in these species (Fig. 2).
We detected the expansion of genes related to recognition, rapid proliferation, and migration. C-type lectins (CLEC), which recognize complex carbohydrates on cells and tissues , are significantly expanded in the M. honghuensis genome (Additional file 1: Table S13), as are gene families related to meiotic cell cycle processes and meiotic nuclear division (Additional file 1: Table S16; Additional file 2: Fig. S9). KEGG analysis revealed M. honghuensis is enriched in lineage-specific regulators of the actin cytoskeleton (Additional file 1: Table S17), which is involved with cell migration and adhesion . In addition, gene families involved in tumor metastasis and hyperplasia, such as tenascin and extracellular matrix (ECM)-receptor interaction, are significantly expanded (Additional file 1: Table S13), which is in line with the enrichment of M. honghuensis lineage-specific genes of cancer pathways (Additional file 1: Table S17). A previous study indicated that the metastasis of cancer cells is partly analogous to the expansion mechanism of protozoan parasites . Since miniaturization has enabled myxozoans to converge on patterns of host exploitation similar to those of protists , we suggest that this tumor-related gene expansion, together with enhanced meiotic and actin cytoskeleton activity, played an important role in the migration and rapid proliferation of M. honghuensis in host tissues.
Endoparasites live in a nutrition-restricted environment within the host and thus may have unique energy metabolism strategies . We showed that the lineage-specific genes of M. honghuensis were enriched in GO terms associated with single-organism and cellular catabolic processes (Additional file 2: Fig. S4). By calculating Ka/Ks ratios, we detected positive selection in genes related to enzymatic catalysis in carbohydrate metabolism (Additional file 1: Table S15). Compared to other cnidarians, we observed marked expansion of gene families involved in fatty acid biosynthesis, elongation, and degradation, (Additional file 1: Table S13), but contraction of low-density lipoprotein receptors (LDLRs) (genes, which reduce cholesterol  Additional file 1: Table S14). Reduction of LDLRs might promote accumulation of cholesterol, which could improve success of M. honghuensis within its hosts, as has been shown for other parasites including amoeba and flagellates [46, 47].
We observed expansion of gene families related to the cellular processes of nutrient uptake and waste excretion, such as the ATP-binding cassette (ABC)-2 family transporter protein (involved in extra- and intracellular transmembrane nutrition and the extrusion of noxious substances ) and the major facilitator superfamily (MFS) facilitates the movement of small solutes across cell membranes and is responsible for drug metabolism and metabolite transport in other parasites [49, 50]) (Additional file 1: Table S13). Endocytosis pathways were also expanded (Additional file 1: Table S13). We observed genes linked with probable enhancement of intra- and intercellular communications in the M. honghuensis genome; e.g., the glycosphingolipid biosynthesis pathway, which mediates and modulates intercellular coordination  (Additional file 1: Table S18). Also, we found significant expansion of genes encoding Notch ligands Delta and Serrate and the pathway involved with gap junction, which play key roles in intercellular communication [52, 53] (Additional file 1: Table S13). Relative to other cnidarians, M. honghuensis has more genes of the focal adhesion pathway, which regulates communication between the cell and the surrounding extracellular matrix  (Additional file 1: Table S13).
The diverse life cycle development and body forms of cnidarians are regulated in part by homeobox genes, and the Wnt and Hedgehog signaling pathways, which determine body polarity, tissue identity, and polyp-to-jellyfish transition [64, 65]. In M. honghuensis, we detected 43/83 Wnt signaling pathway genes, including 9 key genes (Fig. 5) that could control neuronal development, left-right axis establishment, and mesoderm segmentation. Ten genes in the Wnt pathway are expanded (Additional file 1: Table S13), including LRP5 and beta-TrCP, which trigger beta-catenin signaling and mediate ubiquitination, respectively . Two genes that stabilize beta-catenin and regulate many cellular processes, PS1 and csnk2b , are contracted (Additional file 1: Table S14). We detected 21/52 components of the Hedgehog pathway, including growth arrest-specific 1 (Fig. 5). More Wnt and Hedgehog signaling pathway genes were found in the M. honghuensis genome (43/83 = 51.8%, 21/52 = 40.4%) than in the other myxozoans K. iwatai (22/72 = 30.6%, 4/19 = 21.1%) and M. cerebralis (23/72 = 31.9%, 5/19 = 26.3%). We found 7/24 of ANTP class Homeobox genes in M. honghuensis (1 Hox-like and 6 NK-like), compared to 18-24/24 in free-living Cnidaria (Additional file 1: Table S19).
The genome size of M. honghuensis is 206 Mb, with a smaller final assembly size of 161 Mb likely due to abundant repetitive sequences. These estimates place M. honghuensis as having a slightly larger genome than closely related T. kitauei (188.5 Mb) , ninefold larger than the smallest (K. iwatai, 22.5 Mb) . The M. honghuensis genome is equivalent in size to some free-living cnidarians, including Nemopilema nomurai (213 Mb)  and S. malayensis (185 Mb) (Additional file 1: Table S3) , despite having a body size at the micron scale, compared with vastly larger N. nomurai (up to 2 m in diameter)  and S. malayensis (up to 13.5 cm in diameter) . Concomitant with its larger genome size, M. honghuensis has 2.8 times the number of protein-coding genes than the distantly related myxozoan K. iwatai (5533 genes, 22.5 Mb) , but is comparable to that of the more closely related T. kitauei (16,638 genes, 188.5 Mb)  (Additional file 2: Fig. S17), and similar to free-living cnidarians Hydra vulgaris (16,839 genes, 1,005 Mb) , and Nematostella vectensis (18,000 genes, 450 Mb)  (Additional file 1: Table S3). The M. honghuensis genome is less compact (mean intron size 507 bp) compared with myxozoans K. iwatai (82 bp), T. kitauei (240 bp), and the non-myxozoan Sanderia malayensis (381bp; Additional file 1: Table S3). M. honghuensis has a mean exon size of 132 bp, compared with 102 bp in K. iwatai, 235 bp in T. kitauei, 218 bp in H. vulgaris, and 208 bp in N. vectensis (Additional file 1: Table S3).
Host invasion by a myxozoan involves molecular and physical evasion of immune responses. We found genes coding for C-type lectins (CLEC) were expanded in M. honghuensis, and thus may be an important tool for mediating immunological recognition within its hosts, much as other parasites release CLEC homologous to key host receptors to possibly interfere with immune response or effector function . Myxozoans require motile stages both to avoid host immune responses  and to reach target tissues. In Ceratonova shasta and Ceratomyxa puntazzi, actin has an important role in stage motility [83, 84], and our finding that here M. honghuensis is enriched in lineage-specific regulators of the actin cytoskeleton (Additional file 1: Table S17), suggests that actin may be important for success of diverse myxozoan taxa. 041b061a72