Gene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition.

The paper nautilus or greater argonaut, Argonauta argo, is a species of octopods which is characterized by its pelagic lifestyle and by the presence of a protective spiral-shaped shell-like eggcase in females. To reveal the genomic background of how the species adapted to the pelagic lifestyle and acquired its shell-like eggcase, we sequenced the draft genome of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters, and some gene clusters that could probably be related to the pelagic lifestyle, such as reflectin, tyrosinase, and opsin. The gene models also revealed several homologous genes related to calcified shell formation in Conchiferan mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the shell-less octopus, as well as Nautilus, which has a true outer shell. Therefore, the draft genome sequence of Arg. argo presented here has helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes to form an important, converging extended phenotypic structure such as the shell and the shell-like eggcase. Additionally, it allows us to explore the evolution of from benthic to pelagic lifestyles in cephalopods and octopods.

Partial redescriptions of three holothurians with hook papillae (Apodida: Chiridotidae): Taeniogyrus japonicus (Marenzeller, 1882), T. dendyi (Mortensen, 1925), Scoliorhapis theelii (Heding, 1928).

New specimens of Taeniogyrus japonicus (Marenzeller) were collected from Iwami coast and Sado island of the Sea of Japan. According to detailed observations of external and internal organs, we transferred T. japonicus, T. dendyi (Mortensen), and Scoliorhapis theelii (Heding) to the newly revived genus Scoliodota, with a large retractor organ and hook papillae as major diagnostic characters. We also concluded that Scoliorhapis dianthus Solis-marin et al. is a synonym of T. japonicus. Our molecular phylogeny and genetic distance analysis showed that specimens from Iwami and specimens from Sado of T. japonicus form a monophyletic clade, indicating that they are most likely the same species despite their morphological variation. The phylogenetic analysis also indicated that T. japonicus forms a sister group relationship with Taeniogyrus verruculosus Yamana Tanaka and Scoliorhapis sesokoensis Yamana Tanaka, suggesting that Taeniogyrus is not monophyletic. Taken together, these results brought new insights to sea cucumber diversity in Japanese waters.

Molecular phylogeny of Nipponacmea (Patellogastropoda, Lottiidae) from Japan: a re-evaluation of species taxonomy and morphological diagnosis.

The patellogastropod limpet genus Nipponacmea is widely distributed in Japan and adjacent East Asia. Species identification within Nipponacmea is challenging due to the high variation in shell morphology. In this study, we examined the taxonomy of this genus represented by nine nominal species from 43 localities (including type localities). Results of the molecular phylogenetic analysis revealed that: (1) N.gloriosa, the sole species in this genus inhabiting the subtidal zone, represents the most basal independent branch; (2) the remaining species are divided into two large clades with lower- and higher-apex shell profiles; and (3) the high-apex morphology was derived from the low-apex type. The terminal clades defined using the molecular data were consistent with nine morphospecies and had 100% bootstrap values, strongly supporting the conventional taxonomy of Nipponacmea. Although morphological similarities do not always reflect phylogeny, the set of morphological characters used in the current taxonomy were proven to be adequate for diagnosis. In conclusion, this study provided solid evidence to uphold the monophyly of known species of Nipponacmea in Japan and demonstrated the usefulness of morphological characters for species diagnosis.

A new species of dendrochirotid holothuroid from deep water of southern Japan, with the erection of a new genus, Satsumaocnus (Echinodermata: Holothuroidea: Dendrochirotida: Cucumariidae: Colochirinae).

A new dendrochirotid sea cucumber, Satsumaocnus kaiyomarui gen. nov., sp. nov. from deep water of southern Japan is herein described. The new species displays the following unique characters : a cylindrical, soft body; mouth surrounded by five oral valves; 10 equal, dendritic tentacles arranged in a single circle, each composed of two tufts; a low, stout, compact, calcareous ring without posterior prolongations; body wall ossicles comprising an external layer of small, x-framed hourglass-shaped cups originally described as "double-faced x-framed cup ossicles" in a previous study reported by Yamana et al. (2019), and an inner layer of scarce dendriform/branched rods, sometimes taking the shape of delicate plate-like deposits. Although the general (external and internal) morphological characters of the new species correspond well with the characters of species within the cucumariid subfamily Colochirinae Panning, 1949, our material lacks any buttons or elaborate plate-like ossicles which characterize all extant genera within this subfamily. We, therefore, describe our material as a new species S. kaiyomarui sp. nov. within the new genus Satsumaocnus. The predominant body wall deposits of the new species strongly resemble the hourglass type ossicles of some species of the psolid genus Lissothuria (Verrill, 1867), but differ in their possession of a supporting x-shaped frame. In addition, it is noteworthy that these hourglass deposits also resemble the table ossicles of some holothuriids and stichopodids, when viewed from the side, especially the small tables of some Labidodemas and/or Stichopus species, while the dendriform rods resemble those of Thelenota.

Hydrophilic Shell Matrix Proteins of Nautilus pompilius and the Identification of a Core Set of Conchiferan Domains.

Despite being a member of the shelled mollusks (Conchiferans), most members of extant cephalopods have lost their external biomineralized shells, except for the basally diverging Nautilids. Here, we report the result of our study to identify major Shell Matrix Proteins and their domains in the Nautilid Nautilus pompilius, in order to gain a general insight into the evolution of Conchiferan Shell Matrix Proteins. In order to do so, we performed a multiomics study on the shell of N. pompilius, by conducting transcriptomics of its mantle tissue and proteomics of its shell matrix. Analyses of obtained data identified 61 distinct shell-specific sequences. Of the successfully annotated 27 sequences, protein domains were predicted in 19. Comparative analysis of Nautilus sequences with four Conchiferans for which Shell Matrix Protein data were available (the pacific oyster, the pearl oyster, the limpet and the Euhadra snail) revealed that three proteins and six protein domains were conserved in all Conchiferans. Interestingly, when the terrestrial Euhadra snail was excluded, another five proteins and six protein domains were found to be shared among the four marine Conchiferans. Phylogenetic analyses indicated that most of these proteins and domains were probably present in the ancestral Conchiferan, but employed in shell formation later and independently in most clades. Even though further studies utilizing deeper sequencing techniques to obtain genome and full-length sequences, and functional analyses, must be carried out in the future, our results here provide important pieces of information for the elucidation of the evolution of Conchiferan shells at the molecular level.

Mesozoic origin and 'out-of-India' radiation of ricefishes (Adrianichthyidae).

The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast-East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward 'out-of-India' after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast-East Asia. A review of geographic distributions of 'out-of-India' taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.

Complete mitochondrial genome of the Pacific limpet Cellana nigrolineata (Gastropoda: Patellogastropoda) determined by shotgun sequencing using the Illumina NGS platform.

The Pacific limpet Cellana nigrolineata is one of the most commonly found limpets in the intertidal shores of Japan. Here, we report the full mitogenome sequence of an individual specimen of the species, which was collected from the intertidal rocky beach in the Nada beach of Gobo City, Wakayama, Japan (33.8316 N, 135.1751 E), in 2018. The sequence was determined by the shotgun sequencing method using the NGS Illumina MiSeq platform. The genomic structure of C. nigrolineata is the same as the previously reported congener, C. radiata, which shows a representative Nacellidae and metazoan mitogenomic structures. The mitogenome has all of its 37 genes included in its 16,153 bp, with one control region located between the tRNA-Cys and tRNA-Gly genes. In order to clarify the phylogenetic position of C. nigrolineata in Gastropoda, a data set including the mitogenomes of 10 patellogastropods, 10 non-patellogastropod gastropods, and four outgroups were used in maximum likelihood inferences. Although with some exceptions, the resulting phylogeny supported the monophylies of traditionally accepted gastropod subclasses, and thus confirms the position of C. nigrolineata in Patellogastropoda.

The first complete mitochondrial genome of the Northern Pacific deep-sea goniasterid sea star Ceramaster japonicus (Sladen, 1889) determined using NGS-based shotgun sequencing.

The full mitogenome of an ethanol-preserved museum specimen of Ceramaster japonicus was determined using the NGS Illumina MiSeq platform. The specimen was collected from Tosa Bay, Japan, facing the Pacific Ocean (33.0781 N 134.0601 E), at 700 m depth in 2011. The mitogenome shows a typical metazoan genomic structure, with all of the 37 genes included in its 16,370 base-long mitogenome. We conducted phylogenetic analyses using a data set including 18 publicly available asteroids rooted against five ophiuroids as outgroups. The result confirms the position of C. japonicus in the order Valvatida. The complete mitogenome of C. japonicus reported here is the first reported for the family Goniasteridae Forbes, 1841.

The full mitochondrial genome sequence of the greater argonaut Argonauta argo (Cephalopoda, Argonautoidea) and its phylogenetic position in Octopodiformes.

The greater argonaut Argonauta argo is a species of the paper nautilus (Argonautidae), which is a family in Octopoda. In this paper, we report its full mitogenome sequence, which was obtained from a specimen collected in the Japan Seas near Oki Island, Shimane Prefecture, in Japan. The sequence was determined using the NGS Illumina HiSeq platform. With its 37 genes, the mitogenome shows a typical metazoan and Octopoda genomic structure, and similar to the mitogenome of the previously reported congener, A. hians. To confirm A. argo phylogenetic position in Octopoda, we conducted maximum likelihood phylogenetic analysis, using a data set including publicly available 17 Octopodiformes, five Decapodiformes, three Nautiloids and two outgroup Conchiferans. The result confirmed the affinity of Argonautidae to Tremoctopus, and the sister group position of this clade against the rest of incirrate Octopods. The mitogenome and phylogeny of A. argo reported here will be useful for future studies involving this enigmatic species, including on the reacquisition of external calcified shell structures in mollusks.

Full-Genome Sequence of Bacillus safensis Strain IDN1, Isolated from Commercially Available Natto in Indonesia.

We isolated a strain of Bacillus safensis, which we called IDN1, from natto sold in Indonesia. In order to gain insights into its genomic structure and understand its biology, we used the Oxford Nanopore MinION platform followed by PCR to verify the ends and determine its full circular genome sequence.

Review and analysis of current responses to COVID-19 in Indonesia: Period of January to March 2020.

The world is under pressure from the novel COVID-19 pandemic. Indonesia is the fourth most populous country in the world and predicted to be affected significantly over a longer time period. Our paper aims to provide detailed reporting and analyses of the present rapid responses to COVID-19, between January and March 2020, in Indonesia. We particularly highlight responses taken by the governments, non-government organisations and the community. We outline gaps and limitations in the responses, based on our rapid analysis of media contents, from government speeches and reports, social and mass media platforms. We present five recommendations toward more rapid, effective, and comprehensive responses.

A new microsporidium Percutemincola moriokae gen. nov., sp. nov. from Oscheius tipulae: A novel model of microsporidia-nematode associations.

Here, we describe a new microsporidium Percutemincola moriokae gen. nov., sp. nov., which was discovered in the intestinal and hypodermal cells of a wild strain of the nematode Oscheius tipulae that inhabits in the soil of Morioka, Iwate Prefecture, Japan. The spores of Pe. moriokae had an average size of 1.0 × 3.8 µm and 1.3 × 3.2 µm in the intestine and hypodermis, respectively, and electron microscopy revealed that they exhibited distinguishing features with morphological diversity in the hypodermis. Isolated spores were able to infect a reference strain of O. tipulae (CEW1) through horizontal transmission but not the nematode Caenorhabditis elegans. Upon infection, the spores were first observed in the hypodermis and then in the intestine the following day, suggesting a unique infectious route among nematode-infective microsporidia. Molecular phylogenetic analysis grouped this new species with the recently identified nematode-infective parasites Enteropsectra and Pancytospora forming a monophyletic sister clade to Orthosomella in clade IV, which also includes human pathogens such as Enterocytozoon and Vittaforma. We believe that this newly discovered species and its host could have application as a new model in microsporidia-nematode association studies.

Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas.

Comprising more than 800 extant species, the class Cephalopoda (octopuses, squid, cuttlefish, and nautiluses) is a fascinating group of marine conchiferan mollusks. Recently, the first cephalopod genome (of Octopus bimaculoides) was published, providing a genomic framework, which will enable more detailed investigations of cephalopod characteristics, including developmental, morphological, and behavioural traits. Meanwhile, a robust phylogeny of the members of the subclass Coleoidea (octopuses, squid, cuttlefishes) is crucial for comparative and evolutionary studies aiming to investigate the group's traits and innovations, but such a phylogeny has proven very challenging to obtain. Here, we present the results of phylogenetic inference at the genus level using mitochondrial and nuclear marker sequences available from public databases. Topologies are presented which show support for (1) the monophyly of the two main superorders, Octobrachia and Decabrachia, and (2) some of the interrelationships at the family level. We have mapped morphological characters onto the tree and conducted molecular dating analyses, obtaining congruent results with previous estimates of divergence in major lineages. Our study also identifies unresolved phylogenetic relationships within the cephalopod phylogeny and insufficient taxonomic sampling among squids excluding the Loliginidae in the Decabrachia and within the Order Cirromorphida in the Octobrachia. Genomic and transcriptomic resources should enable resolution of these issues in the relatively near future. We provide our alignment as an open access resource, to allow other researchers to reconstruct phylogenetic trees upon this work in the future.

Complete mitochondrial genome and the phylogenetic position of the Lake Eyre hardyhead (Craterocephalus eyresii), a freshwater atherinid fish endemic to Lake Eyre Basin, South Australia.

The Lake Eyre hardyhead (Craterocephalus eyresii) is an endemic freshwater fish living in the Lake Eyre basin in South Australia. Here, I report the full mitogenome description and the phylogenetic position of this species based on the mitogenome phylogenetics. The mitogenome is 16,602 bp-long with the standard 37 genes all included, with a genomic structure typical of a vertebrate mitogenome. A maximum likelihood phylogenetic analysis to confirm this species position was conducted, using a data set including publicly available 28 atherinomorphs, nine percomorphs, and two outgroups. The result confirms C. eyresii position's in Atherinoidei. The complete mitogenome data of C. eyresii reported here would be useful for further genetics, phylogeography, and phylogenetics studies involving this species.

Complete mitochondrial genome of the smallmouth hardyhead (Atherinosoma microstoma) and its phylogenetic position among the Atheriniform fishes.

In this paper, I report the full mitochondrial genome sequence of the smallmouth hardyhead (Atherinosoma microstoma), an endemic marine fish from the shallow coastal waters of southeastern Australia. The mitogenome is 16,573 bp-long with the standard 37 genes all included, with a genomic structure typical of a vertebrate mitogenome. In order to confirm the phylogenetic position of this species, phylogenetic trees were inferred using a data set including publicly available 28 atherinomorph, nine percomorph, and two outgroup mitogenome sequences. The complete mitogenome data of A. microstoma reported here will be useful for further genetics, phylogeography, and phylogenetics studies involving this species.

An in-silico genomic survey to annotate genes coding for early development-relevant signaling molecules in the pearl oyster, Pinctada fucata.

The pearl oyster Pinctada fucata has great potential as a model system for lophotrochozoan developmental biology research. Pinctada fucata is an important commercial resource, and a significant body of primary research on this species has emphasized its basic aquaculture biology such as larval biology and growth, aquaculture, pearl formation and quality improvement, shell formation, and biomineralization. Recently, a draft genome sequence of this species was published, and many experimental resources are currently being developed, such as bioinformatics tools, embryo and larva manipulation methods, gene knockdown technique, etc. In this paper, we report the results from our genomic survey pertaining to gene families that encode developmental signaling ligands (Fgf, Hedgehog, PDGF/VEGF, TGFß, and Wnt families). We found most of the representative genes of major signaling pathways involved in axial patterning, as well as copies of the signaling molecule paralogs. Phylogenetic character mapping was used to infer a possible evolutionary scenario of the signaling molecules in the protostomes, and to reconstruct possible copy numbers of signaling molecule-coding genes for the ancestral protostome. Our reconstruction suggests that P. fucata retains the ancestral protostome gene complement, providing further justifications for the use of this taxon as a model organism for developmental genomics research.

Left-right asymmetric expression of dpp in the mantle of gastropods correlates with asymmetric shell coiling.

BACKGROUND: Various shapes of gastropod shells have evolved ever since the Cambrian. Although theoretical analyses of morphogenesis exist, the molecular basis of shell development remains unclear. We compared expression patterns of the decapentaplegic (dpp) gene in the shell gland and mantle tissues at various developmental stages between coiled-shell and non-coiled-shell gastropods. RESULTS: We analyzed the expression patterns of dpp for the two limpets Patella vulgata and Nipponacmea fuscoviridis, and for the dextral wild-type and sinistral mutant lineage of the pond snail Lymnaea stagnalis. The limpets had symmetric expression patterns of dpp throughout ontogeny, whereas in the pond snail, the results indicated asymmetric and mirror image patterns between the dextral and sinistral lineages. CONCLUSION: We hypothesize that Dpp induces mantle expansion, and the presence of a left/right asymmetric gradient of the Dpp protein causes the formation of a coiled shell. Our results provide a molecular explanation for shell, coiling including new insights into expression patterns in post-embryonic development, which should aid in understanding how various shell shapes are formed and have evolved in the gastropods.

A comparative study of the shell matrix protein aspein in pterioid bivalves.

Aspein is one of the unusually acidic shell matrix proteins originally identified from the pearl oyster Pinctada fucata. Aspein is thought to play important roles in the shell formation, especially in calcite precipitation in the prismatic layer. In this study, we identified Aspein homologs from three closely related pterioid species: Pinctada maxima, Isognomon perna, and Pteria penguin. Our immunoassays showed that they are present in the calcitic prismatic layer but not in the aragonitic nacreous layer of the shells. Sequence comparison showed that the Ser-Glu-Pro and the Asp-Ala repeat motifs are conserved among these Aspein homologs, indicating that they are functionally important. All Aspein homologs examined share the Asp-rich D-domain, suggesting that this domain might have a very important function in calcium carbonate formation. However, sequence analyses showed a significantly high level of variation in the arrangement of Asp in the D-domain even among very closely related species. This observation suggests that specific arrangements of Asp are not required for the functions of the D-domain.

Essential role of Dkk3 for head formation by inhibiting Wnt/ß-catenin and Nodal/Vg1 signaling pathways in the basal chordate amphioxus.

To dissect the molecular mechanism of head specification in the basal chordate amphioxus, we investigated the function of Dkk3, a secreted protein in the Dickkopf family, which is expressed anteriorly in early embryos. Amphioxus Dkk3 has three domains characteristic of Dkk3 proteins-an N-terminal serine rich domain and two C-terminal cysteine-rich domains (CRDs). In addition, amphioxus Dkk3 has a TGFß-receptor 2 domain, which is not present in Dkk3 proteins of other species. As vertebrate Dkk3 proteins have been reported to regulate either Nodal signaling or Wnt/ß-catenin signaling but not both in the same species, we tested the effects of Dkk3 on signaling by these two pathways in amphioxus embryos. Loss of function experiments with an anti-sense morpholino oligonucleotide (MO) against amphioxus Dkk3 resulted in larvae with truncated heads and concomitant loss of expression of anterior gene markers. The resemblance of the headless phenotype to that from upregulation of Wnt/ß-catenin signaling with BIO, a GSK3ß inhibitor, suggested that Dkk3 might inhibit Wnt/ß-catenin signaling. In addition, the Dkk3 MO rescued dorsal structures in amphioxus embryos treated with SB505124, an inhibitor of Nodal signaling, indicating that amphioxus Dkk3 can also inhibit Nodal signaling. In vitro assays in Xenopus animal caps showed that Nodal inhibition is largely due to domains other than the TGFß domain. We conclude that amphioxus Dkk3 regulates head formation by modulating both Wnt/ß-catenin and Nodal signaling, and that these functions may have been partitioned among various vertebrate lineages during evolution of Dkk3 proteins.

Tail regression induced by elevated retinoic acid signaling in amphioxus larvae occurs by tissue remodeling, not cell death.

The vitamin A derived morphogen retinoic acid (RA) is known to function in the regulation of tissue proliferation and differentiation. Here, we show that exogenous RA applied to late larvae of the invertebrate chordate amphioxus can reverse some differentiated states. Although treatment with the RA antagonist BMS009 has no obvious effect on late larvae of amphioxus, administration of excess RA alters the morphology of the posterior end of the body. The anus closes over, and gut contents accumulate in the hindgut. In addition, the larval tail fin regresses, although little apoptosis takes place. This fin normally consists of columnar epidermal cells, each characterized by a ciliary rootlet running all the way from an apical centriole to the base of the cell and likely contributing substantial cytoskeletal support. After a few days of RA treatment, the rootlet becomes disrupted, and the cell shape changes from columnar to cuboidal. Transmission electron microscopy (TEM) shows fragments of the rootlet in the basal cytoplasm of the cuboidal cell. A major component of the ciliary rootlet in amphioxus is the protein Rootletin, which is encoded by a single AmphiRootletin gene. This gene is highly expressed in the tail epithelial cells of control larvae, but becomes downregulated after about a day of RA treatment, and the breakup of the ciliary rootlet soon follows. The effect of excess RA on these epidermal cells of the larval tail in amphioxus is unlike posterior regression in developing zebrafish, where elevated RA signaling alters connective tissues of mesodermal origin. In contrast, however, the RA-induced closure of the amphioxus anus has parallels in the RA-induced caudal regression syndrome of mammals.