Erratum to: Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants

Jo, Jihoon; Oh, Jooseong; Lee, Hyun-Gwan; Hong, Hyun-Hee; Lee, Sung-Gwon; Cheon, Seongmin; Kern, Elizabeth M.A.; Jin, Soyeong; Cho, Sung‐Jin; Park, Joong-Ki; Park, Chungoo

doi:10.1093/gigascience/gix069

Cited by 9 publications

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“…Here we present a high quality of the sea cucumber A . japonicus genome assembly and extensive transcriptomes, with the assembly quality comparable or superior to many previously published echinoderm genomes 8 , 11 , 12 . Our analysis of the sea cucumber genome revealed novel genomic features and molecular changes that may contribute to the evolutionary appearance of striking biological features.…”

Section: Discussionmentioning

confidence: 77%

“…We conducted a comprehensive comparison of our assembly with the two A . japonicus assemblies generated in previous studies 10 , 12 . In terms of assembly quality, ours and Zhang’s assembly is much better than Jo’s version (Supplementary Table S10 ).…”

Section: Resultsmentioning

confidence: 99%

“…Their superb adaptation attributes include several fascinating evolutionary innovations that are rarely seen in the animal kingdom such as a pentaradial body plan with rigid calcitic skeletons 4 , biosynthesis of saponins 5 , and extraordinary potential for regeneration 6 . However, our understanding of their biology and evolution is hindered by poor sampling of their genomes 7 – 10 , and their relatively large, highly heterozygous genomes generally challenge our ability to obtain high-quality assemblies 8 , 11 , 12 .…”

Section: Introductionmentioning

confidence: 99%

“…It is also among the best molecularly characterized sea cucumber species 27 – 30 , making it a good candidate for whole-genome sequencing. Recent sequencing efforts have been devoted to understanding its morphological evolution and visceral regeneration 10 , 12 , but their saponin synthesis and aestivation abilities remain poorly explored at whole genome levels. Here, we report sequencing of the genome and extensive transcriptomes of A .…”

Section: Introductionmentioning

confidence: 99%

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Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation

Wang

Xun

et al. 2018

Cell Discov

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Echinoderms exhibit several fascinating evolutionary innovations that are rarely seen in the animal kingdom, but how these animals attained such features is not well understood. Here we report the sequencing and analysis of the genome and extensive transcriptomes of the sea cucumber Apostichopus japonicus, a species from a special echinoderm group with extraordinary potential for saponin synthesis, aestivation and organ regeneration. The sea cucumber does not possess a reorganized Hox cluster as previously assumed for all echinoderms, and the spatial expression of Hox7 and Hox11/13b potentially guides the embryo-to-larva axial transformation. Contrary to the typical production of lanosterol in animal cholesterol synthesis, the oxidosqualene cyclase of sea cucumber produces parkeol for saponin synthesis and has “plant-like” motifs suggestive of convergent evolution. The transcriptional factors Klf2 and Egr1 are identified as key regulators of aestivation, probably exerting their effects through a clock gene-controlled process. Intestinal hypometabolism during aestivation is driven by the DNA hypermethylation of various metabolic gene pathways, whereas the transcriptional network of intestine regeneration involves diverse signaling pathways, including Wnt, Hippo and FGF. Decoding the sea cucumber genome provides a new avenue for an in-depth understanding of the extraordinary features of sea cucumbers and other echinoderms.

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Section: Discussionmentioning

confidence: 77%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation

Wang

Xun

et al. 2018

Cell Discov

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“…This species complex experiences cyclic population explosions where entire reefs can be decimated, taking decades to recover. Current technologies have enabled sequencing of the genomes of non-model organisms, including echinoderms such as the Japanese spiky sea cucumber, Apostichopus japonicas [ 20 ] and the purple sea urchin, Strongylocentrotus purpuratus [ 21 ]. The recent publication of the COTS genome [ 19 ] has facilitated the investigation of the molecular mechanisms underpinning COTS’ behaviours, including the identification of ‘ Acanthaster planci putative ORs’ (ApORs) [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

Putative chemosensory receptors are differentially expressed in the sensory organs of male and female crown-of-thorns starfish, Acanthaster planci

et al. 2018

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BackgroundChemosensation is a critical signalling process for all organisms and is achieved through the interaction between chemosensory receptors and their ligands. The Crown-of-thorns starfish, Acanthaster planci species complex (COTS), is a predator of coral polyps and Acanthaster cf. solaris is currently considered to be one of the main drivers of coral loss on the Great Barrier Reef in Queensland, Australia.ResultsThis study reveals the presence of putative variant Ionotropic Receptors (IRs) which are differentially expressed in the olfactory organs of COTS. Several other types of G protein-coupled receptors such as adrenergic, metabotropic glutamate, cholecystokinin, trace-amine associated, GRL101 and GPCR52 receptors have also been identified. Several receptors display male-biased expression within the sensory tentacles, indicating possible reproductive significance.ConclusionsMany of the receptors identified in this study may have a role in reproduction and are therefore key targets for further investigation. Based on their differential expression within the olfactory organs and presence in multiple tissues, it is possible that several of these receptor types have expanded within the Echinoderm lineage. Many are likely to be species-specific with novel ligand-binding affinity and a diverse range of functions. This study is the first to describe the presence of variant Ionotropic Glutamate Receptors in any Echinoderm, and is only the second study to investigate chemosensory receptors in any starfish or marine pest. These results represent a significant step forward in understanding the chemosensory abilities of COTS.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5246-0) contains supplementary material, which is available to authorized users.

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Euler common spatial patterns for EEG classification

Sun

Wei

Luo

et al. 2022

Med Biol Eng Comput

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Erratum to: Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants

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Cited by 9 publications

References 0 publications

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation

Putative chemosensory receptors are differentially expressed in the sensory organs of male and female crown-of-thorns starfish, Acanthaster planci

Euler common spatial patterns for EEG classification

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