Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce
Abstract Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and βglu-1 may provide a plausible mechanism underlying the constitutively v...
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-09978-6 |
| _version_ | 1827370011113553920 |
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| author | Tin Hang Hung Ernest T. Y. Wu Pauls Zeltiņš Āris Jansons Aziz Ullah Nadir Erbilgin Joerg Bohlmann Jean Bousquet Inanc Birol Sonya M. Clegg John J. MacKay |
| author_facet | Tin Hang Hung Ernest T. Y. Wu Pauls Zeltiņš Āris Jansons Aziz Ullah Nadir Erbilgin Joerg Bohlmann Jean Bousquet Inanc Birol Sonya M. Clegg John J. MacKay |
| author_sort | Tin Hang Hung |
| collection | DOAJ |
| description | Abstract Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and βglu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of βglu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of βglu-1 and Ugt5 genes. We observed very large copy numbers of βglu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of βglu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences. |
| first_indexed | 2024-03-08T10:01:04Z |
| format | Article |
| id | doaj.art-ae9e5796f89343dcba1075554de5ae52 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-08T10:01:04Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-ae9e5796f89343dcba1075554de5ae522024-01-29T10:59:35ZengBMCBMC Genomics1471-21642024-01-0125111610.1186/s12864-024-09978-6Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruceTin Hang Hung0Ernest T. Y. Wu1Pauls Zeltiņš2Āris Jansons3Aziz Ullah4Nadir Erbilgin5Joerg Bohlmann6Jean Bousquet7Inanc Birol8Sonya M. Clegg9John J. MacKay10Department of Biology, University of OxfordDepartment of Biology, University of OxfordLatvian State Forest Research Institute “Silava”Latvian State Forest Research Institute “Silava”Department of Renewable Resources, University of AlbertaDepartment of Renewable Resources, University of AlbertaMichael Smith Laboratories, University of British ColumbiaCanada Research Chair in Forest Genomics, Forest Research Centre, Université LavalCanada’s Michael Smith Genome Sciences Centre, BC Cancer AgencyDepartment of Biology, University of OxfordDepartment of Biology, University of OxfordAbstract Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and βglu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of βglu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of βglu-1 and Ugt5 genes. We observed very large copy numbers of βglu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of βglu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.https://doi.org/10.1186/s12864-024-09978-6Acetophenone pathwayTargeted capturePiceaCNVSecondary metabolismConifer genomics |
| spellingShingle | Tin Hang Hung Ernest T. Y. Wu Pauls Zeltiņš Āris Jansons Aziz Ullah Nadir Erbilgin Joerg Bohlmann Jean Bousquet Inanc Birol Sonya M. Clegg John J. MacKay Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce BMC Genomics Acetophenone pathway Targeted capture Picea CNV Secondary metabolism Conifer genomics |
| title | Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce |
| title_full | Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce |
| title_fullStr | Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce |
| title_full_unstemmed | Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce |
| title_short | Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce |
| title_sort | long insert sequence capture detects high copy numbers in a defence related beta glucosidase gene βglu 1 with large variations in white spruce but not norway spruce |
| topic | Acetophenone pathway Targeted capture Picea CNV Secondary metabolism Conifer genomics |
| url | https://doi.org/10.1186/s12864-024-09978-6 |
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