ArticleGenome biology and evolution2020
Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses.
Article in Genome biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 90 citations in OpenAlex.
- Genomic and Structural Analysis of Gamete Recognition Proteins in a Broadcast Spawning Echinoderm Mesocentrotus franciscanus.Journal of molecular evolution · 2026Article
- The tuxedo sea urchinbioRxiv : the preprint server for biology · 2026Article
- Chromosome-level genome provides new insights into the fatty acid biosynthesis and metabolism of the sea urchin Strongylocentrotus intermedius.BMC genomics · 2026Article
- A stage and anatomy ontology for embryogenesis in indirect-developing echinoderms.Development (Cambridge, England) · 2026Article
- Chromosome-level genome assembly and annotation of the tropical sea cucumber Holothuria fuscocinerea.Scientific data · 2026Article
- Genetically tractable embryonic cell lines from sea urchins Lytechinus variegatus and Strongylocentrotus purpuratus.Communications biology · 2025Article
- Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma.Genome biology and evolution · 2025Article
- A chromosome-level genome assembly of tropical purple sea urchin Heliocidaris crassispina.Scientific data · 2024Article
- Reprogramming of cells during embryonic transfating: overcoming a reprogramming block.Development (Cambridge, England) · 2024Article
- Structure of Genes Encoding Oxidosqualene Cyclases-Key Enzymes of Triterpenoid Biosynthesis from Sea CucumberInternational journal of molecular sciences · 2024Article
- Anterior-Posterior Wnt Signaling Network Conservation between Indirect Developing Sea Urchin and Hemichordate Embryos.Integrative and comparative biology · 2024Article
- Structural and molecular distinctions of primary and secondary spines in the sea urchin Lytechinus variegatus.Scientific reports · 2024Article
- A molecular basis for spine color morphs in the sea urchin Lytechinus variegatus.Scientific reports · 2024Article
- Chromosomal-Level Genome Assembly of the Antarctic Sea Urchin Sterechinus neumayeri: A Model for Antarctic Invertebrate Biology.Genome biology and evolution · 2024Article
- The evolution of tenascins.BMC ecology and evolution · 2024Article
- Evolutionary origin of the chordate nervous system revealed by amphioxus developmental trajectories.Nature ecology & evolution · 2024Article
- The brittle star genome illuminates the genetic basis of animal appendage regeneration.Nature ecology & evolution · 2024Article
- Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758).DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchinbioRxiv : the preprint server for biology · 2024Article
- Assembly of continuous high-resolution draft genome sequence of Hemicentrotus pulcherrimus using long-read sequencing.Development, growth & differentiation · 2024Article
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Authors and funding
10 authors at 2 institutions in 3 countries.
Funding
Abstract
Lytechinus variegatus is a camarodont sea urchin found widely throughout the western Atlantic Ocean in a variety of shallow-water marine habitats. Its distribution, abundance, and amenability to developmental perturbation make it a popular model for ecologists and developmental biologists. Here, we present a chromosomal-level genome assembly of L. variegatus generated from a combination of PacBio long reads, 10× Genomics sequencing, and HiC chromatin interaction sequencing. We show L. variegatus has 19 chromosomes with an assembly size of 870.4 Mb. The contiguity and completeness of this assembly are reflected by a scaffold length N50 of 45.5 Mb and BUSCO completeness score of 95.5%. Ab initio and transcript-informed gene modeling and annotation identified 27,232 genes with an average gene length of 12.6 kb, comprising an estimated 39.5% of the genome. Repetitive regions, on the other hand, make up 45.4% of the genome. Physical mapping of well-studied developmental genes onto each chromosome reveals nonrandom spatial distribution of distinct genes and gene families, which provides insight into how certain gene families may have evolved and are transcriptionally regulated in this species. Lastly, aligning RNA-seq and ATAC-seq data onto this assembly demonstrates the value of highly contiguous, complete genome assemblies for functional genomics analyses that is unattainable with fragmented, incomplete assemblies. This genome will be of great value to the scientific community as a resource for genome evolution, developmental, and ecological studies of this species and the Echinodermata.
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