The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation
The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
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2021
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| Online Access: | https://hdl.handle.net/10356/148808 |
| _version_ | 1824454652169551872 |
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| author | Rendón-Anaya, Martha Ibarra-Laclette, Enrique Méndez-Bravo, Alfonso Lan, Tianying Zheng, Chunfang Carretero-Paulet, Lorenzo Perez-Torres, Claudia Anahí Chacón-López, Alejandra Hernandez-Guzmán, Gustavo Chang, Tien-Hao Farr, Kimberly M Barbazuk, W Brad Chamala, Srikar Mutwil, Marek Shivhare, Devendra Alvarez-Ponce, David Mitter, Neena Hayward, Alice Fletcher, Stephen Rozas, Julio Sánchez Gracia, Alejandro Kuhn, David Barrientos-Priego, Alejandro F Salojärvi, Jarkko Librado, Pablo Sankoff, David Herrera-Estrella, Alfredo Albert, Victor A Herrera-Estrella, Luis |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Rendón-Anaya, Martha Ibarra-Laclette, Enrique Méndez-Bravo, Alfonso Lan, Tianying Zheng, Chunfang Carretero-Paulet, Lorenzo Perez-Torres, Claudia Anahí Chacón-López, Alejandra Hernandez-Guzmán, Gustavo Chang, Tien-Hao Farr, Kimberly M Barbazuk, W Brad Chamala, Srikar Mutwil, Marek Shivhare, Devendra Alvarez-Ponce, David Mitter, Neena Hayward, Alice Fletcher, Stephen Rozas, Julio Sánchez Gracia, Alejandro Kuhn, David Barrientos-Priego, Alejandro F Salojärvi, Jarkko Librado, Pablo Sankoff, David Herrera-Estrella, Alfredo Albert, Victor A Herrera-Estrella, Luis |
| author_sort | Rendón-Anaya, Martha |
| collection | NTU |
| description | The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent "tuning knobs" in the genome adaptive landscapes of given species. |
| first_indexed | 2025-02-19T03:25:43Z |
| format | Journal Article |
| id | ntu-10356/148808 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-02-19T03:25:43Z |
| publishDate | 2021 |
| record_format | dspace |
| spelling | ntu-10356/1488082023-02-28T17:09:40Z The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation Rendón-Anaya, Martha Ibarra-Laclette, Enrique Méndez-Bravo, Alfonso Lan, Tianying Zheng, Chunfang Carretero-Paulet, Lorenzo Perez-Torres, Claudia Anahí Chacón-López, Alejandra Hernandez-Guzmán, Gustavo Chang, Tien-Hao Farr, Kimberly M Barbazuk, W Brad Chamala, Srikar Mutwil, Marek Shivhare, Devendra Alvarez-Ponce, David Mitter, Neena Hayward, Alice Fletcher, Stephen Rozas, Julio Sánchez Gracia, Alejandro Kuhn, David Barrientos-Priego, Alejandro F Salojärvi, Jarkko Librado, Pablo Sankoff, David Herrera-Estrella, Alfredo Albert, Victor A Herrera-Estrella, Luis School of Biological Sciences Science::Biological sciences Avocado Genome Angiosperm Phylogeny The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent "tuning knobs" in the genome adaptive landscapes of given species. Published version This project was funded in large part by Grant 00126261from the Secretaria de Agrícultura, Ganadería, Recursos Pesqueros y Alimentos/Consejo Nacional de Ciencia y Tecnología sectorial program to L.H.-E.; Grant 05-2018 from the Governor University Research Initiative program from the state of Texas; Howard Hughes Medical Institute Grant 55005946 to L.H.-E.; Grants 0922742 and 1442190 to V.A.A., N.M., and A.H. from the National Science Foundation; Horticulture Innovation Australia Ltd; and the Australian Bureau of Agricultural and Resource Economics and Sciences. 2021-05-07T07:13:22Z 2021-05-07T07:13:22Z 2019 Journal Article Rendón-Anaya, M., Ibarra-Laclette, E., Méndez-Bravo, A., Lan, T., Zheng, C., Carretero-Paulet, L., Perez-Torres, C. A., Chacón-López, A., Hernandez-Guzmán, G., Chang, T., Farr, K. M., Barbazuk, W. B., Chamala, S., Mutwil, M., Shivhare, D., Alvarez-Ponce, D., Mitter, N., Hayward, A., Fletcher, S., ...Herrera-Estrella, L. (2019). The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. Proceedings of the National Academy of Sciences, 116(34), 17081-17089. https://dx.doi.org/10.1073/pnas.1822129116 0027-8424 https://hdl.handle.net/10356/148808 10.1073/pnas.1822129116 31387975 2-s2.0-85071332309 34 116 17081 17089 en Proceedings of the National Academy of Sciences © 2019 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution-NonCommercialNoDerivatives License 4.0 (CC BY-NC-ND). application/pdf |
| spellingShingle | Science::Biological sciences Avocado Genome Angiosperm Phylogeny Rendón-Anaya, Martha Ibarra-Laclette, Enrique Méndez-Bravo, Alfonso Lan, Tianying Zheng, Chunfang Carretero-Paulet, Lorenzo Perez-Torres, Claudia Anahí Chacón-López, Alejandra Hernandez-Guzmán, Gustavo Chang, Tien-Hao Farr, Kimberly M Barbazuk, W Brad Chamala, Srikar Mutwil, Marek Shivhare, Devendra Alvarez-Ponce, David Mitter, Neena Hayward, Alice Fletcher, Stephen Rozas, Julio Sánchez Gracia, Alejandro Kuhn, David Barrientos-Priego, Alejandro F Salojärvi, Jarkko Librado, Pablo Sankoff, David Herrera-Estrella, Alfredo Albert, Victor A Herrera-Estrella, Luis The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation |
| title | The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation |
| title_full | The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation |
| title_fullStr | The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation |
| title_full_unstemmed | The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation |
| title_short | The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation |
| title_sort | avocado genome informs deep angiosperm phylogeny highlights introgressive hybridization and reveals pathogen influenced gene space adaptation |
| topic | Science::Biological sciences Avocado Genome Angiosperm Phylogeny |
| url | https://hdl.handle.net/10356/148808 |
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