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Chromosomal-Level Genome Assembly of the Painted Sea Urchin Lytechinus pictus: A Genetically Enabled Model System for Cell Biology and Embryonic Development.
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The painted urchin Lytechinus pictus is a sea urchin in the family Toxopneustidae and one of several sea urchin species that are routinely used as an experimental research organism. Recently, L. pictus has emerged as a tractable model system for establishing transgenic sea urchin lines due to its amenability to long term laboratory culture. We present the first published genome of L. pictus. This chromosomal-level assembly was generated using Illumina sequencing in conjunction with Oxford Nanopore Technologies long read sequencing and HiC chromatin conformation capture sequencing. The 998.9-Mb assembly exhibits high contiguity and has a scaffold length N50 of 46.0 Mb with 97% of the sequence assembled into 19 chromosomal-length scaffolds. These 19 scaffolds exhibit a high degree of synteny compared with the 19 chromosomes of a related species Lytechinus variegatus. Ab initio and transcript evidence gene modeling, combined with sequence homology, identified 28,631 gene models that capture 92% of BUSCO orthologs. This annotation strategy was validated by manual curation of gene models for the ABC transporter superfamily, which confirmed the completeness and accuracy of the annotations. Thus, this genome assembly, in conjunction with recent high contiguity assemblies of related species, positions L. pictus as an exceptional model system for comparative functional genomics and it will be a key resource for the developmental, toxicological, and ecological biology scientific communities.
Aleksanyan,
Terminal alpha-d-mannosides are critical during sea urchin gastrulation.
2016, Pubmed,
Echinobase
Aleksanyan,
Terminal alpha-d-mannosides are critical during sea urchin gastrulation.
2016,
Pubmed
,
Echinobase
Borst,
Mammalian ABC transporters in health and disease.
2002,
Pubmed
Bryan,
ABCC8 and ABCC9: ABC transporters that regulate K+ channels.
2007,
Pubmed
Cabanettes,
D-GENIES: dot plot large genomes in an interactive, efficient and simple way.
2018,
Pubmed
Cameron,
Initiation of metamorphosis in laboratory cultured sea urchins.
1974,
Pubmed
,
Echinobase
Campos,
Major challenges in cryopreservation of sea urchin eggs.
2021,
Pubmed
,
Echinobase
Cantarel,
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
2008,
Pubmed
Cary,
Echinoderm development and evolution in the post-genomic era.
2017,
Pubmed
,
Echinobase
Coffaro,
Immune response in the sea urchin Lytechinus pictus.
1977,
Pubmed
,
Echinobase
Davidson,
Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses.
2020,
Pubmed
,
Echinobase
Dean,
Evolution of the ATP-binding cassette (ABC) transporter superfamily in vertebrates.
2005,
Pubmed
Erkenbrack,
Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity.
2019,
Pubmed
,
Echinobase
Evans,
Cyclin: a protein specified by maternal mRNA in sea urchin eggs that is destroyed at each cleavage division.
1983,
Pubmed
,
Echinobase
Gökirmak,
Functional diversification of sea urchin ABCC1 (MRP1) by alternative splicing.
2016,
Pubmed
,
Echinobase
Goldstone,
The chemical defensome: environmental sensing and response genes in the Strongylocentrotus purpuratus genome.
2006,
Pubmed
,
Echinobase
Gottesman,
Overview: ABC transporters and human disease.
2001,
Pubmed
Hinegardner,
Growth and development of the laboratory cultured sea urchin.
1969,
Pubmed
,
Echinobase
Hogan,
The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes.
2020,
Pubmed
,
Echinobase
Hussain,
Individual female differences in chemoattractant production change the scale of sea urchin gamete interactions.
2017,
Pubmed
,
Echinobase
Kassmer,
Migration of germline progenitor cells is directed by sphingosine-1-phosphate signalling in a basal chordate.
2015,
Pubmed
Kinjo,
HpBase: A genome database of a sea urchin, Hemicentrotus pulcherrimus.
2018,
Pubmed
,
Echinobase
Li,
Inhibitory effects of neurotoxin β-N-methylamino-L-alanine on fertilization and early development of the sea urchin Lytechinus pictus.
2020,
Pubmed
,
Echinobase
Lieberman-Aiden,
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
2009,
Pubmed
Liu,
Establishment of knockout adult sea urchins by using a CRISPR-Cas9 system.
2019,
Pubmed
,
Echinobase
Luciani,
Cloning of two novel ABC transporters mapping on human chromosome 9.
1994,
Pubmed
Morris,
Early development of the feeding larva of the sea urchin Heliocidaris tuberculata: role of the small micromeres.
2019,
Pubmed
,
Echinobase
Nesbit,
Embryo, larval, and juvenile staging of Lytechinus pictus from fertilization through sexual maturation.
2020,
Pubmed
,
Echinobase
Nesbit,
The painted sea urchin, Lytechinus pictus, as a genetically-enabled developmental model.
2019,
Pubmed
,
Echinobase
Oliveri,
Global regulatory logic for specification of an embryonic cell lineage.
2008,
Pubmed
,
Echinobase
Peter,
Methods for the experimental and computational analysis of gene regulatory networks in sea urchins.
2019,
Pubmed
,
Echinobase
Petrásek,
Auxin transport routes in plant development.
2009,
Pubmed
Putnam,
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.
2016,
Pubmed
Queiroz,
Comparative study of coelomocytes from Arbacia lixula and Lythechinus variegatus: Cell characterization and in vivo evidence of the physiological function of vibratile cells.
2021,
Pubmed
,
Echinobase
Schumacher,
Peptide length and sequence specificity of the mouse TAP1/TAP2 translocator.
1994,
Pubmed
Shipp,
ATP-binding cassette (ABC) transporter expression and localization in sea urchin development.
2012,
Pubmed
,
Echinobase
Silverton,
Variation and evolution of the ABC transporter genes ABCB1, ABCC1, ABCG2, ABCG5 and ABCG8: implication for pharmacogenetics and disease.
2011,
Pubmed
Simão,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
2015,
Pubmed
Smith,
Sea urchin reproductive performance in a changing ocean: poor males improve while good males worsen in response to ocean acidification.
2019,
Pubmed
,
Echinobase
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Tarling,
Role of ABC transporters in lipid transport and human disease.
2013,
Pubmed
Wang,
Genetic basis for divergence in developmental gene expression in two closely related sea urchins.
2020,
Pubmed
,
Echinobase
Yaguchi,
Temnopleurus as an emerging echinoderm model.
2019,
Pubmed
,
Echinobase
Yaguchi,
Establishment of homozygous knock-out sea urchins.
2020,
Pubmed
,
Echinobase
Zigler,
Speciation on the coasts of the new world: phylogeography and the evolution of bindin in the sea urchin genus Lytechinus.
2004,
Pubmed
,
Echinobase
