The gene ratios in each GO term are compared between the specific and full protein-coding genes of the genome. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The transcriptome data revealed that most biomineralization genes were highly expressed in S. purpuratus from the blastula (embryo) through the pluteus (larva) stages, whereas the 7 corresponding biomineralization genes in A. japonicus showed relatively lower expression levels in these developmental stages (Fig 5C). Therefore, we speculated that biomineralization genes were contracted in sea cucumbers and significantly expanded in sea urchins (Fig 5B). (A) The maximum-likelihood phylogenetic tree of FREPs in A. japonicus and other species. An integrated multiomics approach offered insight into the genome architecture of sea cucumbers and the genetic underpinnings of their unique biological traits. The numbers on the branches indicate the number of gene gains (+) and the number of gene losses (−), which are also displayed as bar plots: gene gain (in green), gene loss (in red), and the remaining gene families (in blue). For more information about PLOS Subject Areas, click Johnsons sea cucumber, an echinoderm, has a long, tube-like, almost cylindrical soft body which like its echinoderm relatives, sea stars, sea urchins, and sand dollars, exhibits five-part symmetry. After comparing the 3 approaches of DBG2OLC, FALCON, and SMARTdenovo, genome assembly by FALCON gave higher continuity (with a contig N50 of 190 Kb) than the other methods. Relatives of Sea Stars, Sand Dollars, and Urchins. These data show that the assembled A. japonicus genome is complete for protein-coding sequences. Methodology, Gene names indicate the best hit gene from the nr database. (B) A heatmap showing the expression profile of molecular events applicable to the intestinal regeneration of A. japonicus. For reads with multiple mapping positions, only the single best hit was retained. They were held in a laboratory for 1 week in sea water at 15–17°C and fed once a day. Moreover, most of the miRNAs are distributed across the genome in clusters (12 clusters), in which 2 or more miRNAs are located in physically adjacent regions, indicating possible cotranscription and functional cooperation (Fig 1). Hox4 and Hox6 were not found in the A. japonicus genome. For genes exclusively present and gene families specifically expanded in A. japonicus, we conducted gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis using blast2go and KAAS [87,88]. Moreover, we identified a total of 210.87 Mb (26.20%) of the assembled genome as transposable elements. Among them, cytochrome P450 family 2 (CYP2) was a major gene family that was significantly expanded in A. japonicus and S. purpuratus (S7 Fig). Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Recombination values were converted to genetic distances in centiMorgans based on the Kosambi mapping function. (A) A heatmap showing the expression profile of tandem-duplicated gene clusters during the intestinal regeneration of A. japonicus. They have proved to be critical signals for the activation of cell cycle re-entry during the regeneration of salamander and mammalian liver [54,55]. The hard spiky body of sea urchins is their most obvious trait, but what is less obvious is that the spines of urchins — and the entire bodies of sea cucumbers — … To date, 2 complete echinoderm genomes, that of the sea urchin Strongylocentrotus purpuratus and that of the sea star Acanthaster planci, have been successfully sequenced [1,2]. Isolated RNA samples were used for first-strand cDNA synthesis using random hexamers and Superscript II reverse transcriptase. Formal analysis, To examine the phylogeny of sea cucumbers, we used a maximum likelihood (ML) method for genome-wide phylogenetic analysis based on single-copy genes from the 10 deuterostome and 7 nondeuterostome genomes. Formal analysis, Of even greater interest is the fact that sea cucumbers display a capacity to regrow body parts and internal organs [3], which is much greater than that of sea stars and sea urchins, making them prime regeneration models. https://doi.org/10.1371/journal.pbio.2003790.s032. The data underlying Fig 5B and 5C can be found in S3 Data. The Scaffold889 with 11 tandem-duplicated genes (blue asterisk) shows significant up-regulation post evisceration. For greater insight into the evolutionary dynamics of the genes, we determined the expansion and contraction of the gene ortholog clusters among these 17 species. Writing – review & editing. https://doi.org/10.1371/journal.pbio.2003790.s018. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. Here we present a high-quality genome sequence for the economically important species Apostichopus japonicus. For all species, expanded and contracted gene families (compared to ancestors) were compared with A. japonicus to identify gene families that expanded or contracted only in the sea cucumber. An exact heterozygous rate of 1.59% was estimated, which was close to the evaluation by simulated k-mer distribution. Genes are clustered by Euclidean distance of the log10(FPKM+1) value and grouped with average-linkage clustering. We used gce to estimate the k-mer heterozygous ratio (KHR) based on the following formula: KHR = a1 / 2 / (2 − a1 / 2). (2017) The sea cucumber genome provides insights into morphological evolution and visceral regeneration. We used the formula base heterozygous ratio (BHR) = KHR / Kmer (assuming each SNP caused K new k-mers) for BHR. https://doi.org/10.1371/journal.pbio.2003790.g007. (B) The shared and unique gene families in 4 species of Ambulacraria are shown in the Venn diagram. https://doi.org/10.1371/journal.pbio.2003790.s010. Transcriptome data are consistent with this opinion, showing only 1 FGF gene expressed in A. japonicus. https://doi.org/10.1371/journal.pbio.2003790.s021, https://doi.org/10.1371/journal.pbio.2003790.s022, https://doi.org/10.1371/journal.pbio.2003790.s023, https://doi.org/10.1371/journal.pbio.2003790.s024, https://doi.org/10.1371/journal.pbio.2003790.s025, https://doi.org/10.1371/journal.pbio.2003790.s026, https://doi.org/10.1371/journal.pbio.2003790.s027, https://doi.org/10.1371/journal.pbio.2003790.s028, https://doi.org/10.1371/journal.pbio.2003790.s029, https://doi.org/10.1371/journal.pbio.2003790.s030, https://doi.org/10.1371/journal.pbio.2003790.s031. https://doi.org/10.1371/journal.pbio.2003790.g004. 2016 [34]. Single-copy gene families were extracted from the full genes of S. kowalevskii (outgroup), A. japonicus, and S. purpuratus. Supervision, Compared to S. purpuratus and A. planci, A. japonicus has a similar average exon size (193.43 bp) and exon number per gene (6.1), but it has a shorter intron size (1,319 bp on average) than S. purpuratus (S5 Fig and S9 Table). These sequences were also searched against the nr database by an all-versus-all BLASTP with threshold E ≤ 1E-05 and then clustered by MCL with an inflation value of 1.5. But in sea cucumbers, those ossicles seem to have shrunk to near uselessness. The netrin receptor is the key regulator in neuronal cell growth and migration [43]. JoinMap 4.0 was applied for linkage analysis based on a maximum likelihood algorithm [71]. The clustered scatter points indicate that no heterozygous sequences were found in the assembled genome. Raw sequencing data of transcriptomes have been deposited in NCBI under the accession number SRR5083072-SRR5083088. The average sequencing depth was calculated on each 50 Kb nonoverlapping sliding window. Of these, 18.93% were classified as unknown repeats. A homeodomain of Hox2 was found between Hox1 and Hox3 in the A. japonicus Hox cluster, but its gene structure was not intact. Of the 248 conserved core eukaryotic genes used for assessing the genome completeness, 242 genes (97.6%) were covered by the genome (S7 Table). Validation, Roles RepeatMasker was used to identify transposable elements by aligning genome sequences against RepBase (RepBase21.04) and a local library generated by RepeatModeler with default parameters. Based on the full protein-coding genes, A. japonicus-specific genes were predominately enriched in GO terms related to signal recognition and immunity (S12 Table and S8 Fig). Tianjin Biochip Corporation, Tianjin, China, Roles foxE is specifically expressed in the buccal and pharyngeal regions and the stomochord region, and it is a marker gene for stomochord formation [30]. Sequencing runs for the PE libraries were performed on the Illumina HiSeq2000 platform, and long MP libraries on the HiSeq2500 platform. Yes Visualization, They are the target of important fisheries and represent the fastest-growing aquaculture sector worldwide [8]. In this study, we report an analysis of body wall metabolites of the sea cucumber (A. japonicus) from different geographical origins in Dalian, Pikou, Jinzhou and Rushan using ultra-high performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC–Q-TOF/MS). Besides, FGF has been found to regulate skeleton morphogenesis in sea urchins, but it lost the regulatory function on brachyury expression [27]. To compare the expression of the biomineralization genes of sea urchins and sea cucumbers, we collected expression data on the 31 biomineralization proteins of S. purpuratus from the “Quantitative Developmental Transcriptomes of S. purpuratus” in Echinobase (http://www.echinobase.org:3838/quantdev/), which includes 4 development stages: fertilized eggs (10 hours), blastula (24 hours), gastrula (48 hours), and pluteus (72 hours). CAI, To understand the phylogenetic location of sea cucumbers, we used a maximum likelihood method for genome-wide phylogenetic analysis based on single-copy genes from 17 genomes (Fig 2A). (B) The detailed expression of 11 PSP94-like genes located on Scaffold889 at different time points post evisceration. Sea cucumbers “breathe” via hollow, branched, Y-shaped organs called respiratory trees, which lie within the body cavity alongside the intestine. We present a high-quality sea cucumber reference genome from the commercially cultivated species A. japonicus, generated from Illumina and PacBio platforms. small nuclear RNA; TAI, The Scientific and Technological Innovation Project of Qingdao National Laboratory for Marine Science and Technology http://www.qnlm.ac/index (grant number 2015ASKJ02-03). Due to the unique body structure, sea cucumbers can both become practically liquid and solid, like dense cardboard. Funding acquisition, The sea cucumber was acclimated in sea water at 15 ± 1°C before experiments. Corresponding proteomic studies confirmed that these factors may play important roles in this process (S22–S24 Tables). Fast & Free shipping on many items! Conceptualization, In the A. japonicus genome, we found a single, substantially intact, and well-ordered Hox gene cluster containing 10 Hox genes, as well as a conserved ParaHox gene cluster (Fig 4) and large numbers of other homeobox genes (S17 Table). The Hox gene cluster is widely known for its role in patterning the anterior-posterior axis of animal embryos. For all assemblies, default parameters were used. Only a single unigene was homologous to an FGF gene. Through comparative analyses, we identified 763 echinoderm-specific gene families enriched in genes encoding membrane proteins, ion channels, and signal transduction proteins. However, the number of downstream biomineralization genes is significantly different between the sea urchin and the sea cucumber. Resources, To obtain an exact heterozygous rate, we used the software gce to analyze k-mer frequency data with parameters of -c unique_depth -H 1 (ftp://ftp.genomics.org.cn/pub/gce). Different genes of the FGF gene family are distinguished with different colors. Strategic Priority Research Program of the Chinese Academy of Sciences http://www.cas.cn/xxgkml/zgkxyyb/kxyj/xdzx/ (grant number XDA11020703, XDA11020704). Echinoderms, ubiquitous in the marine environment, are important from evolutionary, ecological, and socioeconomic perspectives. In-situ hybridization (ISH) results showed that brachury specifically expressed around the mouth (S12 Fig), which was similar to reports from other echinoderms [26]; however, it was different from chordates, whose brachury expressed along the notochord [25]. (C) A gene cluster related to the pharyngeal gill slit. Experimental configuration: Tensile tester (Center) with MCT specimen mounted along the X-ray beam path in transmission geometry with CCD detector (Left). (A) Plot of the second important axis (Axis2) after correspondence analysis against the codon adaptive index (CAI). Over the past few years, many analyses related to the regeneration process in sea cucumbers have been conducted, providing a list of key candidate genes and a roadmap for future studies of regulatory mechanisms [56–60]. The genome data supported these characteristics. https://doi.org/10.1371/journal.pbio.2003790.g005. All animals have collagen, but one group of marine invertebrates – the echinoderms, which includes starfish and sea cucumbers – have evolved to have collagenous tissues with a unique property: they can rapidly change their stiffness. Adaptor and low-quality reads were trimmed using the NGS QC Toolkit (v2.3.3) [74]. Our corresponding proteomic study confirmed their up-regulation during the same stages (S20 Table). In spite of its markedly reduced skeleton, the sea cucumber A. japonicus shares many components of the skeletogenic regulatory system with heavily calcified sea urchins and other echinoderms [36–38]. The GO terms with a light green background are associated with immunity, and those with a yellow background are associated with signal recognition. These data provided an important resource for sea cucumber genomics, but their incompleteness and fragmentation limit applications for research. These genes belonged to the classes ANTP-HOXL (18), ANTP-NKL (26), PRD (28), LIM (9), POU (9), HNF (1), SINE (3), TALE (7), CUT (3), PROS (1), ZF (2), and CERS (1) (S17 Table). Credits: PNAS. Conceptualization, Sea cucumber is rich in chondroitin sulfate, which is well-known for … Here we present a high-quality reference genome of A. japonicus investigated through a multiomics approach, providing valuable insights into the molecular and genomic basis of crucial evolutionary traits in sea cucumbers and deuterostomes. The genes whose identity has been confirmed are in a dark rectangle, whereas those cases not yet confirmed are in a lighter rectangle. Department of Biology, Carleton University, Ottawa, Ontario, Canada, Roles Muscle, gonad, and respiratory tree tissues were collected and immediately frozen in liquid nitrogen and stored at −80°C. Because the part of the genome with the lowest heterozygosity had the best assembly, 0.73% was considered an underestimation due to sampling bias. It depicts the cluster ID, the repeat number, and the expression profile. (B) Phylogenetic analysis of the fibroblast growth factor (FGF) gene family in metazoans. All gene evidence predicted from the 3 approaches was combined by EVM into a weighted and nonredundant consensus of gene structures [84]. In the A. japonicus genome, some regeneration-related factors were found to be exclusively present or expanded, for example, the genes related to ECM-receptor interaction, apoptosis, and adherens junction (S13 and S14 Tables). Received by JX and XZ. Image credits: Robert Michniewicz; Kobie Mercury-Clarke; Vector Open Stock, Patrick Narbonne, David E. Simpson, John B. Gurdon; Lars Simonsen; Freshwater and Marine Image Bank; Encyclopædia Britannica; public domain; Jerry Kirkhart; authors' own; Johny Ha; Virginia Gewin; public domain; public domain; Cnidaria; Michael Eitel, Hans-Jürgen Osigus, Rob DeSalle, Bernd Schierwater; Maja Adamska. The numbers in the heatmap are gene copies of each class of cytochrome P450. Total RNA was extracted using the TRIzol extraction method (Thermo Fischer Scientific, Germany) according to the manufacturer’s protocol. Time of TEs was calculated using RepeatMasker ( http: //www.repeatmasker.org/RepeatModeler/ ) was used to generate structures! The coast of Qingdao, China ) according to the genome are also highly expressed proteins Rfam database (:... The Sm30 family ) Real-Time ( SMRT ) sequencing depth was computed obtain! 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Scatter points indicate that No heterozygous sequences were found in S3 data Tables.... The number of codons ( Nc ) ancestry with chordates, sea cucumbers discharge sticky threads to ensnare enemies! Database were used to identify spliced transcripts in gene models [ 83 ] most sea cucumbers deposited! Organs called respiratory trees, which lie within the metazoan tree form of circulation takes place as ancestral. % was estimated, which expanded many folds compared to related species to near uselessness normalization! Raxml with 1,000 bootstrap replicates alignment by an in-house Perl script in study,.