Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms.

Echinoderms are an exceptional group of bilaterians that develop pentameral adult symmetry from a bilaterally symmetric larva. However, the genetic basis in evolution and development of this unique transformation remains to be clarified. Here we report newly sequenced genomes, developmental transcriptomes, and proteomes of diverse echinoderms including the green sea urchin (L. variegatus), a sea cucumber (A. japonicus), and with particular emphasis on a sister group of the earliest-diverged echinoderms, the feather star (A. japonica). We learned that the last common ancestor of echinoderms retained a well-organized Hox cluster reminiscent of the hemichordate, and had gene sets involved in endoskeleton development. Further, unlike in other animal groups, the most conserved developmental stages were not at the body plan establishing phase, and genes normally involved in bilaterality appear to function in pentameric axis development. These results enhance our understanding of the divergence of protostomes and deuterostomes almost 500 Mya.

Transcriptome analysis of sea cucumber (Apostichopus japonicus) polian vesicles in response to evisceration.

Polian vesicles are considered as the site of coelomocyte formation, and play crucial roles in the inflammatory reaction in sea cucumber. After evisceration, coelomocytes and internal organs except polian vesicles are excreted. Our previous study found that the total number of coelomocytes was rapidly recovered at 6 h post-evisceration in sea cucumber Apostichopus japonicus, and this regeneration of coelomocytes might be closely related to polian vesicles. To further investigate the related-gene expression pattern of the polian vesicles at 6 h post-evisceration, the transcriptome analysis of polian vesicles was carried out. A total of 2752 differentially expressed genes (DEGs) were identified, including 1,453 up-regulated genes and 1299 down-regulated genes. Gene Ontology (GO) enrichment showed that most of the DEGs were classified under Regulation of transcription, Regulation of RNA metabolic process, Regulation of nucleic acid-templated transcription. Meanwhile, 11 significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified. Among them, Wnt, TGF-ß and Endocytosis pathways are well-related with cell proliferation and differentiation, which may be involved in the regeneration of coelomocytes in A. japonicus after evisceration. In addition, FoxO signaling pathway plays important roles in immunoregulation, in which the expression levels of the DEGs were significantly up-regulated, inferring that polian vesicles could not only participate in the coelomocyte regeneration process, but also undertake a certain immune defense function in A. japonicus after evisceration. These findings will be beneficial for understanding the mechanisms of coelomocyte regeneration and immune defense of A. japonicus after evisceration.

Effects of collagenase type I on the structural features of collagen fibres from sea cucumber (Stichopus japonicus) body wall.

The autolysis of sea cucumber is caused by depolymerisation of collagen fibres and unfolding of fibrils. In order to highlight the role of collagenase in sea cucumber autolysis, collagen fibres from sea cucumber were hydrolysed with collagenase type I. Electron microscopy (EM) results indicated the collagenase caused partial depolymerisation of collagen fibres into fibrils due to the fracture of proteoglycan interfibrillar bridges, as well as uncoiling of collagen fibrils. Chemical analysis and SDS-PAGE both indicated collagenase induced a time-dependent release of glycosaminoglycans (GAGs) and soluble proteins, which further demonstrated the degradation of proteoglycan interfibrillar bridges. Collagenase also degraded collagens by releasing soluble hydroxyproline (Hpy), with the dissolution rate of Hyp reaching 11.11% after 72 h. Fourier transform infrared analysis showed that collagenase caused the reduction of intermolecular interactions and structural order of collagen. Hence, collagenase participated in the autolysis of sea cucumber by deteriorating both macromolecular and monomeric collagens.

De Novo assembly and comparative transcriptome analyses of purple and green morphs of Apostichopus japonicus during body wall pigmentation process.

Pigmentation processes provide a traceable and relevant trait for understanding key issues in evolutionary biology such as adaptation, speciation and the maintenance of balanced polymorphisms. The sea cucumber Apostichopus japonicus, which has nutritive and medical properties, is considered the most valuable commercial species in many parts of Asia. Compared with the green morph, the purple morph is rare and has great appeal to consumers. However, little is currently known about the molecular mechanism of body color formation in A. japonicus, even in echinoderm. Here, we employ illumina sequencing to examine expression patterns of the gene network underlying body wall development in purple and green morphs of A. japonicus. Overall, the number of down-regulated genes in the green morph was significantly more than in the purple morph during the pigmentation stage. We observed dynamic expression patterns of a large number of pigment, regulation and growth genes from the "Melanogenesis", "Melanoma", "Wnt signaling pathway", "Notch signaling pathway", "epithelium development", "epidermal growth factor receptor binding","growth factor activity" and "growth", including contrasting expression patterns of these genes in green and purple morph. This study provides comprehensive lists of differentially expressed genes during body wall development in the green and purple morphs, revealing potential candidate genes that may be involved in regulating body color formation and polymorphism. These data will provide valuable information for future genetic studies on sea cucumbers elucidating the molecular mechanisms underlying pigmentation, and may support the culture of desirable color morphs.

Molecular taxonomy, phylogeny and evolution in the family Stichopodidae (Aspidochirotida: Holothuroidea) based on COI and 16S mitochondrial DNA.

The Stichopodidae comprise a diverse assemblage of holothuroids most of which occur in the Indo-Pacific. Phylogenetic analyses of mitochondrial gene (COI, 16S rRNA) sequence for 111 individuals (7 genera, 17 species) clarified taxonomic uncertainties, species relationships, biogeography and evolution of the family. A monophyly of the genus Stichopus was supported with the exception of Stichopus ellipes. Molecular analyses confirmed genus level taxonomy based on morphology. Most specimens harvested as S. horrens fell in the S. monotuberculatus clade, a morphologically variable assemblage with others from the S. naso clade. Taxonomic clarification of species fished as S. horrens will assist conservation measures. Evolutionary rates based on comparison of sequence from trans-ithmian Isostichopus species estimated that Stichopus and Isostichopus diverged ca. 5.5-10.7Ma (Miocene). More recent splits were estimated to be younger than 1Ma.

Post-autotomy regeneration of respiratory trees in the holothurian Apostichopus japonicus (Holothuroidea, Aspidochirotida).

Specialised respiratory organs, viz. the respiratory trees attached to the dorsal part of the cloaca, are present in most holothurians. These organs evolved within the class Holothuroidea and are absent in other echinoderms. Some holothurian species can regenerate their respiratory trees but others lack this ability. Respiratory trees therefore provide a model for investigating the origin and evolution of repair mechanisms in animals. We conducted a detailed morphological study of the regeneration of respiratory trees after their evisceration in the holothurian Apostichopus japonicus. Regeneration of the respiratory trees occurred rapidly and, on the 15th day after evisceration, their length reached 15-20 mm. Repair involved cells of the coelomic and luminal epithelia of the cloaca. Peritoneocytes and myoepithelial cells behaved differently during regeneration: the peritoneocytes kept their intercellular junctions and migrated as a united layer, whereas groups of myoepithelial cells disaggregated and migrated as individual cells. Although myoepithelial cells did not divide during regeneration, the peritoneocytes proliferated actively. The contractile system of the respiratory trees was assumed to develop during regeneration by the migration of myoepithelial cells from the coelomic epithelium of the cloaca. The luminal epithelium of the respiratory trees formed as a result of dedifferentiation, migration and transformation of cells of the cloaca lining. The mode of regeneration of holothurian respiratory trees is discussed.

Phenotypic plasticity of gut structure and function during periods of inactivity in Apostichopus japonicus.

Apostichopus japonicus is a common sea cucumber that undergoes seasonal inactivity phases and ceases feeding during the summer months. We used this sea cucumber species as a model in which to examine phenotypic plasticity of the digestive tract in response to food deprivation. We measured the body mass, gross gut morphology and digestive enzyme activities of A. japonicus before, during, and after the period of inactivity to examine the effects of food deprivation on the gut structure and function of this animal. Individuals were sampled semi-monthly from June to November (10 sampling intervals over 178 days) across temperature changes of more than 18 degrees C. On 5 September, which represented the peak of inactivity and lack of feeding, A. japonicus decreased its body mass, gut mass and gut length by 50%, 85%, and 70%, respectively, in comparison to values for these parameters preceding the inactive period. The activities of amylase, cellulase and lipase decreased by 77%, 98%, and 35% respectively, in comparison to mean values for these enzymes in June, whereas pepsin activity increased two-fold during the inactive phase. Alginase and trypsin activities were variable and did not change significantly across the 178-day experiment. With the exception of amylase and cellulase, all body size indices and digestive enzyme activities recovered and even surpassed the mean values preceding the inactive phase during the latter part of the experiment (October-November). Principal Component Analysis (PCA) utilizing the digestive enzyme activity and body size index data divided the physiological state of this cucumber into four phases: an active stage, prophase of inactivity, peak inactivity, and a reversion phase. These phases are all consistent with previously suggested life stages for this species, but our data provide more defined characteristics of each phase. A. japonicus clearly exhibits phenotypic plasticity (or life-cycle staging) of the digestive tract during its annual inactive period.

Stichopin-containing nerves and secretory cells specific to connective tissues of the sea cucumber.

Stichopin, a 17-amino acid peptide isolated from a sea cucumber, affects the stiffness change of the body-wall catch connective tissues and the contraction of the body-wall muscles. The localization of stichopin in sea cucumbers was studied by indirect immunohistochemistry using antiserum against stichopin. Double staining was performed with both stichopin antiserum and 1E11, the monoclonal antibody specific to echinoderm nerves. A stichopin-like immunoreactivity (stichopin-LI) was exclusively found in the connective tissues of various organs. Many fibres and cells with processes were stained by both the anti-stichopin antibody and 1E11. They were found in the body-wall dermis and the connective tissue layer of the cloacae and were suggested to be connective tissue-specific nerves. Oval cells with stichopin-LI (OCS) without processes were found in the body-wall dermis, the connective tissue sheath of the longitudinal body-wall muscles, the connective tissue layer of the tube feet and tentacles, and the connective tissue in the radial nerves separating the ectoneural part from the hyponeural part. Electron microscopic observations of the OCSs in the radial nerves showed that they were secretory cells. The OCSs were located either near the well-defined neural structures or near the water-filled cavities, such as the epineural sinus and the canals of the tube feet. The location near the water-filled cavities might suggest that stichopin was secreted into these cavities to function as a hormone.