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A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes.

Publication ,  Journal Article
Ketchum, RN; Davidson, PL; Smith, EG; Wray, GA; Burt, JA; Ryan, JF; Reitzel, AM
Published in: Genome biology and evolution
October 2022

Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly, we determined that the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. Ab initio and transcript-informed gene modeling and annotation identified 29,405 genes, including a conserved Hox cluster. E. sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared E. sp. EZ gene families and transcription factors associated with environmental stress response ("defensome") with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in E. sp. EZ noncoding elements near genes involved in environmental response pathways as well as losses of transcription factors important for environmental response. These data provide key insights into the biology of E. sp. EZ as well as the diversification of Echinometra more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond.

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Published In

Genome biology and evolution

DOI

EISSN

1759-6653

ISSN

1759-6653

Publication Date

October 2022

Volume

14

Issue

10

Start / End Page

evac144

Related Subject Headings

  • Transcription Factors
  • Sea Urchins
  • Regulatory Sequences, Nucleic Acid
  • Molecular Sequence Annotation
  • Developmental Biology
  • Chromosomes
  • Animals
  • 3105 Genetics
  • 3104 Evolutionary biology
  • 3101 Biochemistry and cell biology
 

Citation

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Ketchum, R. N., Davidson, P. L., Smith, E. G., Wray, G. A., Burt, J. A., Ryan, J. F., & Reitzel, A. M. (2022). A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes. Genome Biology and Evolution, 14(10), evac144. https://doi.org/10.1093/gbe/evac144
Ketchum, Remi N., Phillip L. Davidson, Edward G. Smith, Gregory A. Wray, John A. Burt, Joseph F. Ryan, and Adam M. Reitzel. “A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes.Genome Biology and Evolution 14, no. 10 (October 2022): evac144. https://doi.org/10.1093/gbe/evac144.
Ketchum RN, Davidson PL, Smith EG, Wray GA, Burt JA, Ryan JF, et al. A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes. Genome biology and evolution. 2022 Oct;14(10):evac144.
Ketchum, Remi N., et al. “A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes.Genome Biology and Evolution, vol. 14, no. 10, Oct. 2022, p. evac144. Epmc, doi:10.1093/gbe/evac144.
Ketchum RN, Davidson PL, Smith EG, Wray GA, Burt JA, Ryan JF, Reitzel AM. A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes. Genome biology and evolution. 2022 Oct;14(10):evac144.
Journal cover image

Published In

Genome biology and evolution

DOI

EISSN

1759-6653

ISSN

1759-6653

Publication Date

October 2022

Volume

14

Issue

10

Start / End Page

evac144

Related Subject Headings

  • Transcription Factors
  • Sea Urchins
  • Regulatory Sequences, Nucleic Acid
  • Molecular Sequence Annotation
  • Developmental Biology
  • Chromosomes
  • Animals
  • 3105 Genetics
  • 3104 Evolutionary biology
  • 3101 Biochemistry and cell biology