Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird.
Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird s...
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ftcdlib:oai:escholarship.org:ark:/13030/qt40c0v12v 2023-11-12T04:24:04+01:00 Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. Sin, Simon Yung Wa Cloutier, Alison Nevitt, Gabrielle Edwards, Scott V Lawniczak, M iyab210 2022-02-04 application/pdf https://escholarship.org/uc/item/40c0v12v unknown eScholarship, University of California qt40c0v12v https://escholarship.org/uc/item/40c0v12v public Genetics, vol 220, iss 2 Biological Sciences Bioinformatics and Computational Biology Genetics Neurosciences Human Genome Biotechnology Genome Receptors Odorant Smell OR gene duplication multigene family evolution olfaction olfactory receptor genes procellariiform seabird storm-petrel Developmental Biology Biochemistry and cell biology article 2022 ftcdlib 2023-10-16T18:05:06Z Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird species thus far. Here, we assembled a high-quality genome and nasal epithelium transcriptome of the Leach's storm-petrel (Oceanodroma leucorhoa) to extensively characterize their OR repertoire. Using a depth-of-coverage-assisted counting method, we estimated over 160 intact OR genes (∼500 including OR fragments). This method reveals the highest number of intact OR genes and the lowest proportion of pseudogenes compared to other waterbirds studied, and suggests that rates of OR gene duplication vary between major clades of birds, with particularly high rates in passerines. OR expression patterns reveal two OR genes (OR6-6 and OR5-11) highly expressed in adults, and four OR genes (OR14-14, OR14-12, OR10-2, and OR14-9) differentially expressed between age classes of storm-petrels. All four genes differentially expressed between age classes were more highly expressed in chicks compared to adults, suggesting that OR genes may exhibit ontogenetic specializations. Three highly differentially expressed OR genes also had high copy number ratios, suggesting that expression variation may be linked to copy number in the genome. We provide better estimates of OR gene number by using a copy number-assisted counting method, and document ontogenetic changes in OR gene expression that may be linked to olfactory specialization. These results provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds. Article in Journal/Newspaper Oceanodroma leucorhoa University of California: eScholarship |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Biological Sciences Bioinformatics and Computational Biology Genetics Neurosciences Human Genome Biotechnology Genome Receptors Odorant Smell OR gene duplication multigene family evolution olfaction olfactory receptor genes procellariiform seabird storm-petrel Developmental Biology Biochemistry and cell biology |
spellingShingle |
Biological Sciences Bioinformatics and Computational Biology Genetics Neurosciences Human Genome Biotechnology Genome Receptors Odorant Smell OR gene duplication multigene family evolution olfaction olfactory receptor genes procellariiform seabird storm-petrel Developmental Biology Biochemistry and cell biology Sin, Simon Yung Wa Cloutier, Alison Nevitt, Gabrielle Edwards, Scott V Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. |
topic_facet |
Biological Sciences Bioinformatics and Computational Biology Genetics Neurosciences Human Genome Biotechnology Genome Receptors Odorant Smell OR gene duplication multigene family evolution olfaction olfactory receptor genes procellariiform seabird storm-petrel Developmental Biology Biochemistry and cell biology |
description |
Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird species thus far. Here, we assembled a high-quality genome and nasal epithelium transcriptome of the Leach's storm-petrel (Oceanodroma leucorhoa) to extensively characterize their OR repertoire. Using a depth-of-coverage-assisted counting method, we estimated over 160 intact OR genes (∼500 including OR fragments). This method reveals the highest number of intact OR genes and the lowest proportion of pseudogenes compared to other waterbirds studied, and suggests that rates of OR gene duplication vary between major clades of birds, with particularly high rates in passerines. OR expression patterns reveal two OR genes (OR6-6 and OR5-11) highly expressed in adults, and four OR genes (OR14-14, OR14-12, OR10-2, and OR14-9) differentially expressed between age classes of storm-petrels. All four genes differentially expressed between age classes were more highly expressed in chicks compared to adults, suggesting that OR genes may exhibit ontogenetic specializations. Three highly differentially expressed OR genes also had high copy number ratios, suggesting that expression variation may be linked to copy number in the genome. We provide better estimates of OR gene number by using a copy number-assisted counting method, and document ontogenetic changes in OR gene expression that may be linked to olfactory specialization. These results provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds. |
author2 |
Lawniczak, M |
format |
Article in Journal/Newspaper |
author |
Sin, Simon Yung Wa Cloutier, Alison Nevitt, Gabrielle Edwards, Scott V |
author_facet |
Sin, Simon Yung Wa Cloutier, Alison Nevitt, Gabrielle Edwards, Scott V |
author_sort |
Sin, Simon Yung Wa |
title |
Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. |
title_short |
Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. |
title_full |
Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. |
title_fullStr |
Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. |
title_full_unstemmed |
Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. |
title_sort |
olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. |
publisher |
eScholarship, University of California |
publishDate |
2022 |
url |
https://escholarship.org/uc/item/40c0v12v |
op_coverage |
iyab210 |
genre |
Oceanodroma leucorhoa |
genre_facet |
Oceanodroma leucorhoa |
op_source |
Genetics, vol 220, iss 2 |
op_relation |
qt40c0v12v https://escholarship.org/uc/item/40c0v12v |
op_rights |
public |
_version_ |
1782338647513628672 |