A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome

Justin B. Jiang, Andrea M. Quattrini*, Warren R. Francis, Joseph F. Ryan, Estefanía Rodríguez, Catherine S. McFadden

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Resumé

Background: More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral "forests," which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri. Findings: We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256-448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models. Conclusions: The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.

OriginalsprogEngelsk
Artikelnummergiz026
TidsskriftGigaScience
Vol/bind8
Udgave nummer4
Antal sider7
ISSN2047-217X
DOI
StatusUdgivet - apr. 2019

Fingeraftryk

Renilla
Genes
Sea Anemones
Cnidaria
Pacific Ocean
Genome Size
Haploidy
Luciferases
Research Personnel
Databases
Bioluminescence
Molecular biology

Citer dette

Jiang, J. B., Quattrini, A. M., Francis, W. R., Ryan, J. F., Rodríguez, E., & McFadden, C. S. (2019). A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome. GigaScience, 8(4), [giz026]. https://doi.org/10.1093/gigascience/giz026
Jiang, Justin B. ; Quattrini, Andrea M. ; Francis, Warren R. ; Ryan, Joseph F. ; Rodríguez, Estefanía ; McFadden, Catherine S. / A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome. I: GigaScience. 2019 ; Bind 8, Nr. 4.
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title = "A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome",
abstract = "Background: More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral {"}forests,{"} which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri. Findings: We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88{\%} of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66{\%} (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256-448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models. Conclusions: The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.",
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author = "Jiang, {Justin B.} and Quattrini, {Andrea M.} and Francis, {Warren R.} and Ryan, {Joseph F.} and Estefan{\'i}a Rodr{\'i}guez and McFadden, {Catherine S.}",
year = "2019",
month = "4",
doi = "10.1093/gigascience/giz026",
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Jiang, JB, Quattrini, AM, Francis, WR, Ryan, JF, Rodríguez, E & McFadden, CS 2019, 'A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome', GigaScience, bind 8, nr. 4, giz026. https://doi.org/10.1093/gigascience/giz026

A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome. / Jiang, Justin B.; Quattrini, Andrea M.; Francis, Warren R.; Ryan, Joseph F.; Rodríguez, Estefanía; McFadden, Catherine S.

I: GigaScience, Bind 8, Nr. 4, giz026, 04.2019.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome

AU - Jiang, Justin B.

AU - Quattrini, Andrea M.

AU - Francis, Warren R.

AU - Ryan, Joseph F.

AU - Rodríguez, Estefanía

AU - McFadden, Catherine S.

PY - 2019/4

Y1 - 2019/4

N2 - Background: More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral "forests," which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri. Findings: We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256-448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models. Conclusions: The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.

AB - Background: More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral "forests," which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri. Findings: We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256-448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models. Conclusions: The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.

KW - Augustus

KW - gene prediction

KW - hybrid assembly

KW - MaSuRCA

KW - octocoral

KW - PacBio

U2 - 10.1093/gigascience/giz026

DO - 10.1093/gigascience/giz026

M3 - Journal article

VL - 8

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 4

M1 - giz026

ER -