Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response
Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2024
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| Subjects: | |
| Online Access: | http://hdl.handle.net/20.500.11937/96866 |
| _version_ | 1848766201070616576 |
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| author | Lo, T. Coombe, L. Gagalova, Kristina Marr, A. Warren, R.L. Kirk, H. Pandoh, P. Zhao, Y. Moore, R.A. Mungall, A.J. Ritland, C. Pavy, N. Jones, S.J.M. Bohlmann, J. Bousquet, J. Birol, I. Thomson, A. |
| author_facet | Lo, T. Coombe, L. Gagalova, Kristina Marr, A. Warren, R.L. Kirk, H. Pandoh, P. Zhao, Y. Moore, R.A. Mungall, A.J. Ritland, C. Pavy, N. Jones, S.J.M. Bohlmann, J. Bousquet, J. Birol, I. Thomson, A. |
| author_sort | Lo, T. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation. |
| first_indexed | 2025-11-14T11:47:22Z |
| format | Journal Article |
| id | curtin-20.500.11937-96866 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| language | eng |
| last_indexed | 2025-11-14T11:47:22Z |
| publishDate | 2024 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-968662025-02-13T00:56:43Z Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response Lo, T. Coombe, L. Gagalova, Kristina Marr, A. Warren, R.L. Kirk, H. Pandoh, P. Zhao, Y. Moore, R.A. Mungall, A.J. Ritland, C. Pavy, N. Jones, S.J.M. Bohlmann, J. Bousquet, J. Birol, I. Thomson, A. Picea mariana black spruce conifer genome assembly and annotation gymosperm Phylogeny Picea North America Picea Phylogeny North America Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation. 2024 Journal Article http://hdl.handle.net/20.500.11937/96866 10.1093/g3journal/jkad247 eng http://creativecommons.org/licenses/by/4.0/ fulltext |
| spellingShingle | Picea mariana black spruce conifer genome assembly and annotation gymosperm Phylogeny Picea North America Picea Phylogeny North America Lo, T. Coombe, L. Gagalova, Kristina Marr, A. Warren, R.L. Kirk, H. Pandoh, P. Zhao, Y. Moore, R.A. Mungall, A.J. Ritland, C. Pavy, N. Jones, S.J.M. Bohlmann, J. Bousquet, J. Birol, I. Thomson, A. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response |
| title | Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response |
| title_full | Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response |
| title_fullStr | Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response |
| title_full_unstemmed | Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response |
| title_short | Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response |
| title_sort | assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response |
| topic | Picea mariana black spruce conifer genome assembly and annotation gymosperm Phylogeny Picea North America Picea Phylogeny North America |
| url | http://hdl.handle.net/20.500.11937/96866 |