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.
???displayArticle.abstract???
Echinometra lucunter, the rock-boring sea urchin, is a widely distributed echinoid and a model for ecological studies of reproduction, responses to climate change, and speciation. We present a near chromosome-level genome assembly of E. lucunter, including 21 scaffolds larger than 10 Mb predicted to represent each of the chromosomes of the species. The 760.4 Mb assembly includes a scaffold N50 of 30.0 Mb and BUSCO (benchmarking universal single-copy orthologue) single copy and a duplicated score of 95.8% and 1.4%, respectively. Ab-initio gene model prediction and annotation with transcriptomic data constructed 33,989 gene models composing 50.4% of the assembly, including 37,036 transcripts. Repetitive elements make up approximately 39.6% of the assembly, and unresolved gap sequences are estimated to be 0.65%. Whole genome alignment with Echinometra sp. EZ revealed high synteny and conservation between the two species, further bolstering Echinometra as an emerging genus for comparative genomics studies. This genome assembly represents a high-quality genomic resource for future evolutionary and developmental studies of this species and more broadly of echinoderms.
Adonin,
Sea Urchin as a Universal Model for Studies of Gene Networks.
2020, Pubmed,
Echinobase
Adonin,
Sea Urchin as a Universal Model for Studies of Gene Networks.
2020,
Pubmed
,
Echinobase Brůna,
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.
2021,
Pubmed Brůna,
GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins.
2020,
Pubmed Buchfink,
Fast and sensitive protein alignment using DIAMOND.
2015,
Pubmed Camacho,
BLAST+: architecture and applications.
2009,
Pubmed Davidson,
A genomic regulatory network for development.
2002,
Pubmed
,
Echinobase Davidson,
Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses.
2020,
Pubmed
,
Echinobase Davidson,
Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins.
2022,
Pubmed
,
Echinobase Dudchenko,
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
2017,
Pubmed Durand,
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.
2016,
Pubmed Durand,
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.
2016,
Pubmed Emms,
OrthoFinder: phylogenetic orthology inference for comparative genomics.
2019,
Pubmed Flynn,
RepeatModeler2 for automated genomic discovery of transposable element families.
2020,
Pubmed Geyer,
Lack of character displacement in the male recognition molecule, bindin, in Altantic sea urchins of the genus Echinometra.
2009,
Pubmed
,
Echinobase Geyer,
Conspecific sperm precedence in two species of tropical sea urchins.
2005,
Pubmed
,
Echinobase Guan,
Identifying and removing haplotypic duplication in primary genome assemblies.
2020,
Pubmed Ketchum,
A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes.
2022,
Pubmed
,
Echinobase Kinjo,
HpBase: A genome database of a sea urchin, Hemicentrotus pulcherrimus.
2018,
Pubmed
,
Echinobase Koren,
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
2017,
Pubmed Landry,
Recent speciation in the Indo-West Pacific: rapid evolution of gamete recognition and sperm morphology in cryptic species of sea urchin.
2003,
Pubmed
,
Echinobase Lessios,
Speciation genes in free-spawning marine invertebrates.
2011,
Pubmed
,
Echinobase Lessios,
GAMETIC INCOMPATIBILITY BETWEEN SPECIES OF THE SEA URCHIN ECHINOMETRA ON THE TWO SIDES OF THE ISTHMUS OF PANAMA.
1990,
Pubmed
,
Echinobase Li,
The Sequence Alignment/Map format and SAMtools.
2009,
Pubmed Lomsadze,
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm.
2014,
Pubmed McCartney,
Dispersal barriers in tropical oceans and speciation in Atlantic and eastern Pacific sea urchins of the genus Echinometra.
2000,
Pubmed
,
Echinobase McCartney,
Quantitative analysis of gametic incompatibility between closely related species of neotropical sea urchins.
2002,
Pubmed
,
Echinobase McCartney,
Adaptive evolution of sperm bindin tracks egg incompatibility in neotropical sea urchins of the genus Echinometra.
2004,
Pubmed
,
Echinobase McIntyre,
Short-range Wnt5 signaling initiates specification of sea urchin posterior ectoderm.
2013,
Pubmed
,
Echinobase Metz,
Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin.
1996,
Pubmed
,
Echinobase O'Leary,
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.
2016,
Pubmed Palumbi,
SPECIATION AND POPULATION GENETIC STRUCTURE IN TROPICAL PACIFIC SEA URCHINS.
1997,
Pubmed
,
Echinobase Palumbi,
Speciation and the evolution of gamete recognition genes: pattern and process.
2009,
Pubmed
,
Echinobase Palumbi,
Evolutionary animation: how do molecular phylogenies compare to Mayr's reconstruction of speciation patterns in the sea?
2005,
Pubmed
,
Echinobase Palumbi,
Strong reproductive isolation between closely related tropical sea urchins (genus Echinometra).
1991,
Pubmed
,
Echinobase Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase Stanke,
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.
2006,
Pubmed Walker,
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
2014,
Pubmed Wang,
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
2012,
Pubmed Warner,
Chromosomal-Level Genome Assembly of the Painted Sea Urchin Lytechinus pictus: A Genetically Enabled Model System for Cell Biology and Embryonic Development.
2021,
Pubmed
,
Echinobase Zigler,
Sea urchin bindin divergence predicts gamete compatibility.
2005,
Pubmed
,
Echinobase
