A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis)

Liu, Jun; Zhou, Yang; Pu, Yujin; Zhang, Hai-Bin

doi:10.1038/s41597-023-02397-4

Cited by 4 publications

(2 citation statements)

References 56 publications

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“…These results indicate that, among Eleutherozoa, sea cucumbers and sea stars show the strongest conservation of ancestral bilaterian linkage groups, whereas the brittle star genome is highly reshuffled relative to the Bilaterian ancestor. Examination of additional sea stars and sea urchins genomes suggest that these trends might broadly extend to species within their respective classes ((Davidson et al 2023; Liu et al 2023; Marlétaz et al 2023); Figure S3 ), but, given the limited sampling, this should be re-examined as more chromosome-scale genome assemblies become available.…”

Section: Resultsmentioning

confidence: 99%

The brittle star genome illuminates the genetic basis of animal appendage regeneration

Parey,

Ortega-Martinez,

Delroisse

et al. 2023

Preprint

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Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here, we report a chromosome-scale genome assembly for the brittle starAmphiura filiformis.We show that the brittle star genome is the most rearranged amongst echinoderms sequenced to date, featuring a reorganised Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasise the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.

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Section: Resultsmentioning

confidence: 99%

The brittle star genome illuminates the genetic basis of animal appendage regeneration

Parey,

Ortega-Martinez,

Delroisse

et al. 2023

Preprint

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“…63 , Asterias rubens 64 , Patiria miniata 65 , Plazaster borealis 66 , and Zoroaster cf. ophiactis 67 were utilized to identify orthologous groups using OrthoFinder (v2.5.5) 68 with the parameters ‘-S diamond’, and the sea urchin Lytechinus variegatus 69 was selected as an outgroup. A total of 5,315 single-copy orthogroups were obtained for subsequent phylogenetic analysis.…”

Section: Methodsmentioning

confidence: 99%

Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis

Wang,

Yang

et al. 2023

Sci Data

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Asterias amurensis has attracted widespread concern because of its population outbreaks, which has impacted fisheries and aquaculture, as well as disrupting local ecosystems. A high-quality reference genome is necessary to better investigate mechanisms of outbreak and adaptive changes. Combining PacBio HiFi and Hi-C sequencing data, we generated a chromosome-level A. amurensis genome with a size of 491.53 Mb. The contig N50 and scaffold N50 were 8.05 and 23.75 Mb, respectively. The result of BUSCO analysis revealed a completeness score of 98.85%. A total of 16,531 protein-coding genes were predicted in the genome, of which 94.63% were functionally annotated. The high-quality genome assembly resulting from this study will provide a valuable genetic resource for future research on the mechanism of population outbreaks and invasion ecology.

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The brittle star genome illuminates the genetic basis of animal appendage regeneration

Parey,

Ortega-Martinez,

Delroisse

et al. 2024

Nat Ecol Evol

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Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star genome is the most rearranged among echinoderms sequenced so far, featuring a reorganized Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasize the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.

show abstract

A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis)

Cited by 4 publications

References 56 publications

The brittle star genome illuminates the genetic basis of animal appendage regeneration

The brittle star genome illuminates the genetic basis of animal appendage regeneration

Chromosome-level genome assembly of the northern Pacific seastar Asterias amurensis

The brittle star genome illuminates the genetic basis of animal appendage regeneration

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