Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea)
A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate...
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ftpubmed:oai:pubmedcentral.nih.gov:5174732 2023-05-15T13:32:13+02:00 Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea) Jue, Nathaniel K. Batta-Lona, Paola G. Trusiak, Sarah Obergfell, Craig Bucklin, Ann O’Neill, Michael J. O’Neill, Rachel J. 2016-09-13 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174732/ http://www.ncbi.nlm.nih.gov/pubmed/27624472 https://doi.org/10.1093/gbe/evw215 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174732/ http://www.ncbi.nlm.nih.gov/pubmed/27624472 http://dx.doi.org/10.1093/gbe/evw215 © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com CC-BY-NC Research Article Text 2016 ftpubmed https://doi.org/10.1093/gbe/evw215 2017-01-01T01:05:02Z A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S. thompsoni or any closely related urochordate species. Using a multiple-platform, multiple-individual approach, we have produced a 318,767,936-bp genome sequence, covering >50% of the estimated 602 Mb (±173 Mb) genome size for S. thompsoni. Using a nonredundant set of predicted proteins, >50% (16,823) of sequences showed significant homology to known proteins and ∼38% (12,151) of the total protein predictions were associated with Gene Ontology functional information. We have generated 109,958 SNP variant and 9,782 indel predictions for this species, serving as a resource for future phylogenomic and population genetic studies. Comparing the salp genome to available assemblies for four other urochordates, Botryllus schlosseri, Ciona intestinalis, Ciona savignyi and Oikopleura dioica, we found that S. thompsoni shares the previously estimated rapid rates of evolution for these species. High mutation rates are thus independent of genome size, suggesting that rates of evolution >1.5 times that observed for vertebrates are a broad taxonomic characteristic of urochordates. Tests for positive selection implemented in PAML revealed a small number of genes with sites undergoing rapid evolution, including genes involved in ribosome biogenesis and metabolic and immune process that may be reflective of both adaptation to polar, planktonic environments as well as the complex life history of the salps. Finally, we performed an initial survey of small RNAs, revealing the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. Collectively, these resources provide a genomic foundation ... Text Antarc* Antarctic Southern Ocean PubMed Central (PMC) Antarctic Indel’ ENVELOPE(35.282,35.282,66.963,66.963) Southern Ocean Genome Biology and Evolution 8 10 3171 3186 |
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Research Article Jue, Nathaniel K. Batta-Lona, Paola G. Trusiak, Sarah Obergfell, Craig Bucklin, Ann O’Neill, Michael J. O’Neill, Rachel J. Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea) |
topic_facet |
Research Article |
description |
A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S. thompsoni or any closely related urochordate species. Using a multiple-platform, multiple-individual approach, we have produced a 318,767,936-bp genome sequence, covering >50% of the estimated 602 Mb (±173 Mb) genome size for S. thompsoni. Using a nonredundant set of predicted proteins, >50% (16,823) of sequences showed significant homology to known proteins and ∼38% (12,151) of the total protein predictions were associated with Gene Ontology functional information. We have generated 109,958 SNP variant and 9,782 indel predictions for this species, serving as a resource for future phylogenomic and population genetic studies. Comparing the salp genome to available assemblies for four other urochordates, Botryllus schlosseri, Ciona intestinalis, Ciona savignyi and Oikopleura dioica, we found that S. thompsoni shares the previously estimated rapid rates of evolution for these species. High mutation rates are thus independent of genome size, suggesting that rates of evolution >1.5 times that observed for vertebrates are a broad taxonomic characteristic of urochordates. Tests for positive selection implemented in PAML revealed a small number of genes with sites undergoing rapid evolution, including genes involved in ribosome biogenesis and metabolic and immune process that may be reflective of both adaptation to polar, planktonic environments as well as the complex life history of the salps. Finally, we performed an initial survey of small RNAs, revealing the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. Collectively, these resources provide a genomic foundation ... |
format |
Text |
author |
Jue, Nathaniel K. Batta-Lona, Paola G. Trusiak, Sarah Obergfell, Craig Bucklin, Ann O’Neill, Michael J. O’Neill, Rachel J. |
author_facet |
Jue, Nathaniel K. Batta-Lona, Paola G. Trusiak, Sarah Obergfell, Craig Bucklin, Ann O’Neill, Michael J. O’Neill, Rachel J. |
author_sort |
Jue, Nathaniel K. |
title |
Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea) |
title_short |
Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea) |
title_full |
Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea) |
title_fullStr |
Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea) |
title_full_unstemmed |
Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea) |
title_sort |
rapid evolutionary rates and unique genomic signatures discovered in the first reference genome for the southern ocean salp, salpa thompsoni (urochordata, thaliacea) |
publisher |
Oxford University Press |
publishDate |
2016 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174732/ http://www.ncbi.nlm.nih.gov/pubmed/27624472 https://doi.org/10.1093/gbe/evw215 |
long_lat |
ENVELOPE(35.282,35.282,66.963,66.963) |
geographic |
Antarctic Indel’ Southern Ocean |
geographic_facet |
Antarctic Indel’ Southern Ocean |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174732/ http://www.ncbi.nlm.nih.gov/pubmed/27624472 http://dx.doi.org/10.1093/gbe/evw215 |
op_rights |
© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
op_rightsnorm |
CC-BY-NC |
op_doi |
https://doi.org/10.1093/gbe/evw215 |
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Genome Biology and Evolution |
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8 |
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10 |
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3171 |
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3186 |
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1766025087938461696 |