Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome
Background: Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, eit...
Published in: | BMC Genomics |
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2020
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Online Access: | https://risweb.st-andrews.ac.uk/portal/en/researchoutput/reconstruction-of-ancient-homeobox-gene-linkages-inferred-from-a-new-highquality-assembly-of-the-hong-kong-oyster-magallana-hongkongensis-genome(94c69e85-6c7b-4b55-ba2e-13f84ea35c6a).html https://doi.org/10.1186/s12864-020-07027-6 https://research-repository.st-andrews.ac.uk/bitstream/10023/20800/1/Li_2020_BMCGenomics_reconstructionancient_VoR_CCBY.pdf |
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ftunstandrewcris:oai:risweb.st-andrews.ac.uk:publications/94c69e85-6c7b-4b55-ba2e-13f84ea35c6a 2023-05-15T15:59:02+02:00 Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome Li, Yiqian Nong, Wenyan Baril, Tobias Yip, Ho Yin Swale, Thomas Hayward, Alexander Ferrier, David Ellard Keith Hui, Jerome 2020-10-15 application/pdf https://risweb.st-andrews.ac.uk/portal/en/researchoutput/reconstruction-of-ancient-homeobox-gene-linkages-inferred-from-a-new-highquality-assembly-of-the-hong-kong-oyster-magallana-hongkongensis-genome(94c69e85-6c7b-4b55-ba2e-13f84ea35c6a).html https://doi.org/10.1186/s12864-020-07027-6 https://research-repository.st-andrews.ac.uk/bitstream/10023/20800/1/Li_2020_BMCGenomics_reconstructionancient_VoR_CCBY.pdf eng eng info:eu-repo/semantics/openAccess Li , Y , Nong , W , Baril , T , Yip , H Y , Swale , T , Hayward , A , Ferrier , D E K & Hui , J 2020 , ' Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome ' , BMC Genomics , vol. 21 , 713 . https://doi.org/10.1186/s12864-020-07027-6 article 2020 ftunstandrewcris https://doi.org/10.1186/s12864-020-07027-6 2022-06-02T07:52:13Z Background: Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. However, homeobox gene organization remains to be fully elucidated in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians. Results: Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~758Mb, scaffold N50 = 72.3Mb). Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al (2020), which was scaffolded using the Crassostrea gigas assembly. A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated in our genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data for other mollusc lineages. Conclusions: The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. Also, our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a ... Article in Journal/Newspaper Crassostrea gigas University of St Andrews: Research Portal BMC Genomics 21 1 |
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University of St Andrews: Research Portal |
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ftunstandrewcris |
language |
English |
description |
Background: Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. However, homeobox gene organization remains to be fully elucidated in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians. Results: Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~758Mb, scaffold N50 = 72.3Mb). Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al (2020), which was scaffolded using the Crassostrea gigas assembly. A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated in our genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data for other mollusc lineages. Conclusions: The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. Also, our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a ... |
format |
Article in Journal/Newspaper |
author |
Li, Yiqian Nong, Wenyan Baril, Tobias Yip, Ho Yin Swale, Thomas Hayward, Alexander Ferrier, David Ellard Keith Hui, Jerome |
spellingShingle |
Li, Yiqian Nong, Wenyan Baril, Tobias Yip, Ho Yin Swale, Thomas Hayward, Alexander Ferrier, David Ellard Keith Hui, Jerome Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome |
author_facet |
Li, Yiqian Nong, Wenyan Baril, Tobias Yip, Ho Yin Swale, Thomas Hayward, Alexander Ferrier, David Ellard Keith Hui, Jerome |
author_sort |
Li, Yiqian |
title |
Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome |
title_short |
Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome |
title_full |
Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome |
title_fullStr |
Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome |
title_full_unstemmed |
Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome |
title_sort |
reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the hong kong oyster ( magallana hongkongensis ) genome |
publishDate |
2020 |
url |
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/reconstruction-of-ancient-homeobox-gene-linkages-inferred-from-a-new-highquality-assembly-of-the-hong-kong-oyster-magallana-hongkongensis-genome(94c69e85-6c7b-4b55-ba2e-13f84ea35c6a).html https://doi.org/10.1186/s12864-020-07027-6 https://research-repository.st-andrews.ac.uk/bitstream/10023/20800/1/Li_2020_BMCGenomics_reconstructionancient_VoR_CCBY.pdf |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_source |
Li , Y , Nong , W , Baril , T , Yip , H Y , Swale , T , Hayward , A , Ferrier , D E K & Hui , J 2020 , ' Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster ( Magallana hongkongensis ) genome ' , BMC Genomics , vol. 21 , 713 . https://doi.org/10.1186/s12864-020-07027-6 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1186/s12864-020-07027-6 |
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BMC Genomics |
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21 |
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1 |
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1766394820963598336 |