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.
Genes Genomics
2022 Dec 01;4412:1487-1498. doi: 10.1007/s13258-022-01322-0.
Show Gene links
Show Anatomy links
De novo genome assembly and annotation of Holothuria scabra (Jaeger, 1833) from nanopore sequencing reads.
Luo H
,
Huang G
,
Li J
,
Yang Q
,
Zhu J
,
Zhang B
,
Feng P
,
Zhang Y
,
Yang X
.
???displayArticle.abstract???
BACKGROUND: Holothuria scabra is a costly gourmet and traditional Chinese tonic medicine. However, the lack of high-quality genome information hinders the genetic, phylogenetic, and bioactivator researches.
OBJECTIVE: To construct high-quality genomic data of H. scabra and conduct genome-wide phylogenetic analysis.
METHODS: The whole genome of a male H. scabra was sequenced based on Nanopore MinION platform, and the sequence was assembled by wtdbg2. Transcriptome sequencing was used to aid the gene annotation. Repeat sequences, non-coding RNA, pseudogene and gene functional annotation were analyzed. 750 single-copy gene families from ten species were applied to construct phylogenetic tree for evolutionary analysis by using the ML method.
RESULTS: The H. scabra genome of 1.18 Gb (N50 = 1557,492 bp) with 500.42 Mb of putative repetitive sequences was assembled from a male H. scabra individual, and 16,642 protein-coding genes, 951 pseudogenes, 1791 motifs and 45,400 domains from the generated assembly were identified. The divergence time between H. scabra and its ancestor was estimated approximately 192.6 million years ago. H. scabra and A. japonicas joined together while sea urchin and sea star diverged about 440 Mya ago. Some key genes involved in notochord and gill slits development, skeleton degeneration and nervous system, as well as homeobox genes differ between H. scabra and Apostichopus japonicas.
CONCLUSION: We report the first whole genome of H. scabra with expectation that this will be a valuable resource for genetic, phylogenetic, breading, molecular biology and bioactivator studies of sea cucumbers and other invertebrates.
Altschul,
Basic local alignment search tool.
1990, Pubmed
Altschul,
Basic local alignment search tool.
1990,
Pubmed
Bahrami,
Structure elucidation of five novel isomeric saponins from the viscera of the sea cucumber Holothuria lessoni.
2014,
Pubmed
,
Echinobase
Birney,
GeneWise and Genomewise.
2004,
Pubmed
Boeckmann,
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
2003,
Pubmed
Bordbar,
High-value components and bioactives from sea cucumbers for functional foods--a review.
2011,
Pubmed
,
Echinobase
Burke,
A genomic view of the sea urchin nervous system.
2006,
Pubmed
,
Echinobase
Chalorak,
Holothuria scabra extracts exhibit anti-Parkinson potential in C. elegans: A model for anti-Parkinson testing.
2018,
Pubmed
,
Echinobase
Chin,
Phased diploid genome assembly with single-molecule real-time sequencing.
2016,
Pubmed
Dawson,
CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences.
2017,
Pubmed
De Bie,
CAFE: a computational tool for the study of gene family evolution.
2006,
Pubmed
Dimmer,
The UniProt-GO Annotation database in 2011.
2012,
Pubmed
Edgar,
PILER: identification and classification of genomic repeats.
2005,
Pubmed
Ettensohn,
Lessons from a gene regulatory network: echinoderm skeletogenesis provides insights into evolution, plasticity and morphogenesis.
2009,
Pubmed
,
Echinobase
Fritzenwanker,
The Fox/Forkhead transcription factor family of the hemichordate Saccoglossus kowalevskii.
2014,
Pubmed
,
Echinobase
Gough,
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments.
2002,
Pubmed
Griffiths-Jones,
miRBase: microRNA sequences, targets and gene nomenclature.
2006,
Pubmed
Griffiths-Jones,
Rfam: annotating non-coding RNAs in complete genomes.
2005,
Pubmed
Guindon,
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
2010,
Pubmed
Haas,
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
2008,
Pubmed
Haft,
The TIGRFAMs database of protein families.
2003,
Pubmed
Hall,
The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest.
2017,
Pubmed
,
Echinobase
Jattujan,
Holothuria scabra extracts possess anti-oxidant activity and promote stress resistance and lifespan extension in Caenorhabditis elegans.
2018,
Pubmed
,
Echinobase
Jiang,
Characterization of antimicrobial resistance of Vibrio parahaemolyticus from cultured sea cucumbers (Apostichopus japonicas).
2014,
Pubmed
,
Echinobase
Jo,
Erratum to: Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants.
2017,
Pubmed
,
Echinobase
Jurka,
Repbase Update, a database of eukaryotic repetitive elements.
2005,
Pubmed
Kanehisa,
KEGG: kyoto encyclopedia of genes and genomes.
2000,
Pubmed
Keilwagen,
Using intron position conservation for homology-based gene prediction.
2016,
Pubmed
Kerr,
In vivo and in vitro biosynthesis of saponins in sea cucumbers.
1995,
Pubmed
,
Echinobase
Kiew,
Jewel of the seabed: sea cucumbers as nutritional and drug candidates.
2012,
Pubmed
,
Echinobase
Koren,
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
2017,
Pubmed
Lees,
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.
2012,
Pubmed
Li,
OrthoMCL: identification of ortholog groups for eukaryotic genomes.
2003,
Pubmed
Li,
Isolation and characterization of polymorphic microsatellite loci in the sea cucumber Holothuria scabra.
2015,
Pubmed
,
Echinobase
Li,
Regulation mechanism of peptides derived from sea cucumber (Apostichopus japonicas) for modulation of learning and memory.
2016,
Pubmed
,
Echinobase
Livesey,
Netrins and netrin receptors.
1999,
Pubmed
Lowe,
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
1997,
Pubmed
Lyons,
Specification to biomineralization: following a single cell type as it constructs a skeleton.
2014,
Pubmed
,
Echinobase
Majoros,
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
2004,
Pubmed
Marchler-Bauer,
CDD: a Conserved Domain Database for the functional annotation of proteins.
2011,
Pubmed
Mi,
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.
2017,
Pubmed
Mitu,
Evidence for a Saponin Biosynthesis Pathway in the Body Wall of the Commercially Significant Sea Cucumber Holothuria scabra.
2017,
Pubmed
,
Echinobase
Nawrocki,
Infernal 1.1: 100-fold faster RNA homology searches.
2013,
Pubmed
Pandurangan,
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.
2019,
Pubmed
Pertea,
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
2016,
Pubmed
Price,
De novo identification of repeat families in large genomes.
2005,
Pubmed
Purcell,
Value, market preferences and trade of Beche-de-mer from Pacific Island sea cucumbers.
2014,
Pubmed
,
Echinobase
Satoh,
How was the notochord born?
2012,
Pubmed
She,
GenBlastA: enabling BLAST to identify homologous gene sequences.
2009,
Pubmed
Simão,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
2015,
Pubmed
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Stanke,
Gene prediction with a hidden Markov model and a new intron submodel.
2003,
Pubmed
Tang,
Identification of protein coding regions in RNA transcripts.
2015,
Pubmed
Tatusov,
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
2001,
Pubmed
Thomas,
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.
2003,
Pubmed
Walker,
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
2014,
Pubmed
Wen,
Chemical composition and nutritional quality of sea cucumbers.
2010,
Pubmed
,
Echinobase
Wicker,
A unified classification system for eukaryotic transposable elements.
2007,
Pubmed
Wu,
PIRSF: family classification system at the Protein Information Resource.
2004,
Pubmed
Wu,
Differentiation of dried sea cucumber products from different geographical areas by surface desorption atmospheric pressure chemical ionization mass spectrometry.
2009,
Pubmed
,
Echinobase
Xu,
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.
2007,
Pubmed
Yaghmour,
First record of Holothuria (Metriatyla) scabra Jaeger, 1833 (Echinodermata: Holothuroidea) from the coastal waters of the United Arab Emirates.
2018,
Pubmed
,
Echinobase
Zhang,
The sea cucumber genome provides insights into morphological evolution and visceral regeneration.
2017,
Pubmed
,
Echinobase
