Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Sci Data
2023 Jul 13;101:454. doi: 10.1038/s41597-023-02368-9.
Show Gene links
Show Anatomy links
Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus.
Sun L
,
Jiang C
,
Su F
,
Cui W
,
Yang H
.
???displayArticle.abstract???
Sea cucumber is a morphologically diverse and ecologically important clade of echinoderms. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber. The initial assembly of the A. japonicus genome was released in 2017. However, this genome assembly is fragmented and lacks relative position information of genes on chromosomes. In this study, we produced a high-quality chromosome-level genome of A. japonicus using Pacbio HiFi long-reads and Hi-C sequencing data. The assembled A. japonicus genome spanned 671.60 Mb with a contig N50 size of 17.20 Mb and scaffold N50 size of 29.65 Mb. A total of 99.9% of the assembly was anchored to 23 chromosomes. In total, 19,828 genes were annotated, and 97.2% of BUSCO genes were fully represented. This high-quality genome of A. japonicus will not only aid in the development of sustainable aquaculture practices, but also lay a foundation for a deeper understanding of their genetic makeup, evolutionary history, and ecological adaptation.
???displayArticle.pubmedLink???
37443361
???displayArticle.link???Sci Data
Altschul,
Basic local alignment search tool.
1990, Pubmed
Altschul,
Basic local alignment search tool.
1990,
Pubmed
Ashburner,
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
2000,
Pubmed
Bairoch,
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.
2000,
Pubmed
Belton,
Hi-C: a comprehensive technique to capture the conformation of genomes.
2012,
Pubmed
Benson,
Tandem repeats finder: a program to analyze DNA sequences.
1999,
Pubmed
Birney,
GeneWise and Genomewise.
2004,
Pubmed
Blanco,
Using geneid to identify genes.
2007,
Pubmed
Bordbar,
High-value components and bioactives from sea cucumbers for functional foods--a review.
2011,
Pubmed
,
Echinobase
Buchfink,
Fast and sensitive protein alignment using DIAMOND.
2015,
Pubmed
Burge,
Prediction of complete gene structures in human genomic DNA.
1997,
Pubmed
Chen,
Evolution of heat-shock protein expression underlying adaptive responses to environmental stress.
2018,
Pubmed
Cheng,
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
2021,
Pubmed
Cui,
Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus).
2021,
Pubmed
,
Echinobase
Edgar,
PILER: identification and classification of genomic repeats.
2005,
Pubmed
Finn,
InterPro in 2017-beyond protein family and domain annotations.
2017,
Pubmed
Finn,
Pfam: the protein families database.
2014,
Pubmed
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Griffiths-Jones,
Rfam: annotating non-coding RNAs in complete genomes.
2005,
Pubmed
Haas,
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
2003,
Pubmed
Haas,
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
2008,
Pubmed
Huo,
Exosomal microRNAs regulate the heat stress response in sea cucumber Apostichopus japonicus.
2023,
Pubmed
,
Echinobase
Jurka,
Repbase Update, a database of eukaryotic repetitive elements.
2005,
Pubmed
Kanehisa,
KEGG as a reference resource for gene and protein annotation.
2016,
Pubmed
Korf,
Gene finding in novel genomes.
2004,
Pubmed
Li,
Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation.
2018,
Pubmed
,
Echinobase
Li,
Identification and expression characterization of WntA during intestinal regeneration in the sea cucumber Apostichopus japonicus.
2017,
Pubmed
,
Echinobase
Li,
Fast and accurate short read alignment with Burrows-Wheeler transform.
2009,
Pubmed
Lowe,
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
1997,
Pubmed
Lu,
Two adaptor molecules of MyD88 and TRAF6 in Apostichopus japonicus Toll signaling cascade: molecular cloning and expression analysis.
2013,
Pubmed
,
Echinobase
Majoros,
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
2004,
Pubmed
Mount,
Using the Basic Local Alignment Search Tool (BLAST).
2007,
Pubmed
Mu,
Long Non-Coding RNAs (lncRNAs) of Sea Cucumber: Large-Scale Prediction, Expression Profiling, Non-Coding Network Construction, and lncRNA-microRNA-Gene Interaction Analysis of lncRNAs in Apostichopus japonicus and Holothuria glaberrima During LPS Challenge and Radial Organ Complex Regeneration.
2016,
Pubmed
,
Echinobase
Mulder,
InterPro and InterProScan: tools for protein sequence classification and comparison.
2007,
Pubmed
Nawrocki,
Infernal 1.0: inference of RNA alignments.
2009,
Pubmed
Parra,
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
2007,
Pubmed
Price,
De novo identification of repeat families in large genomes.
2005,
Pubmed
Rao,
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
2014,
Pubmed
Rhie,
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
2020,
Pubmed
Salindeho,
Anticancer and anticholesterol attributes of sea cucumbers: An opinion in terms of functional food applications.
2022,
Pubmed
,
Echinobase
Simão,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
2015,
Pubmed
Stanke,
AUGUSTUS: ab initio prediction of alternative transcripts.
2006,
Pubmed
Sun,
Metabolic responses to intestine regeneration in sea cucumbers Apostichopus japonicus.
2017,
Pubmed
,
Echinobase
Sun,
Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicus.
2011,
Pubmed
,
Echinobase
Sun,
iTRAQ reveals proteomic changes during intestine regeneration in the sea cucumber Apostichopus japonicus.
2017,
Pubmed
,
Echinobase
Sun,
Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus.
2023,
Pubmed
,
Echinobase
Tarailo-Graovac,
Using RepeatMasker to identify repetitive elements in genomic sequences.
2009,
Pubmed
Tian,
Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus.
2015,
Pubmed
,
Echinobase
Topper,
A stem group echinoderm from the basal Cambrian of China and the origins of Ambulacraria.
2019,
Pubmed
,
Echinobase
Wallace,
On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics.
2018,
Pubmed
Wang,
Investigation of structural proteins in sea cucumber (Apostichopus japonicus) body wall.
2020,
Pubmed
,
Echinobase
Wang,
Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study.
2022,
Pubmed
,
Echinobase
Wingett,
HiCUP: pipeline for mapping and processing Hi-C data.
2015,
Pubmed
Xu,
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.
2007,
Pubmed
Yang,
Genome-Wide DNA Methylation Signatures of Sea Cucumber Apostichopus japonicus during Environmental Induced Aestivation.
2020,
Pubmed
,
Echinobase
Zhang,
iTRAQ-based proteomics reveals novel members involved in pathogen challenge in sea cucumber Apostichopus japonicus.
2014,
Pubmed
,
Echinobase
Zhang,
The sea cucumber genome provides insights into morphological evolution and visceral regeneration.
2017,
Pubmed
,
Echinobase
Zhang,
Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data.
2019,
Pubmed
Zhang,
Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
2018,
Pubmed
van Berkum,
Hi-C: a method to study the three-dimensional architecture of genomes.
2010,
Pubmed
