TY - JOUR
T1 - The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation
AU - Rendón-Anaya, Martha
AU - Ibarra-Laclette, Enrique
AU - Méndez-Bravo, Alfonso
AU - Lan, Tianying
AU - Zheng, Chunfang
AU - Carretero-Paulet, Lorenzo
AU - Perez-Torres, Claudia Anahí
AU - Chacón-López, Alejandra
AU - Hernandez-Guzmán, Gustavo
AU - Chang, Tien Hao
AU - Farr, Kimberly M.
AU - Brad Barbazuk, W.
AU - Chamala, Srikar
AU - Mutwil, Marek
AU - Shivhare, Devendra
AU - Alvarez-Ponce, David
AU - Mitter, Neena
AU - Hayward, Alice
AU - Fletcher, Stephen
AU - Rozas, Julio
AU - Gracia, Alejandro Sánchez
AU - Kuhn, David
AU - Barrientos-Priego, Alejandro F.
AU - Salojärvi, Jarkko
AU - Librado, Pablo
AU - Sankoff, David
AU - Herrera-Estrella, Alfredo
AU - Albert, Victor A.
AU - Herrera-Estrella, Luis
N1 - Funding Information:
ACKNOWLEDGMENTS. 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. We thank the Fundación Salvador Sánchez Colín–Centro de Investigaciones Científicas y Tecnológicas de Aguacate en el Estado de Méx-ico, S.C. for providing avocado specimens. We also thank Araceli Fernandez and Emanuel Villafan, administrators of the high-performance computing systems at Laboratorio Nacional de Genomica para la Biodiversidad and Instituto Nacional de Ecología, respectively.
Funding Information:
This project was funded in large part by Grant 00126261from the Secretaria de Agr?cultura, Ganader?a, Recursos Pesqueros y Alimentos/Consejo Nacional de Ciencia y Tecnolog?a 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. We thank the Fundaci?n Salvador S?nchez Col?n?Centro de Investigaciones Cient?ficas y Tecnol?gicas de Aguacate en el Estado de M?xico, S.C. for providing avocado specimens. We also thank Araceli Fernandez and Emanuel Villafan, administrators of the high-performance computing systems at Laboratorio Nacional de Genomica para la Biodiversidad and Instituto Nacional de Ecolog?a, respectively.
Publisher Copyright:
© 2019 National Academy of Sciences. All rights reserved.
PY - 2019/8/20
Y1 - 2019/8/20
N2 - 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. Resequenc-ing 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.
AB - 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. Resequenc-ing 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.
KW - Angiosperm phylogeny
KW - Avocado genome
KW - Genome duplications
KW - Genome evolution
KW - Phytophthora
UR - http://www.scopus.com/inward/record.url?scp=85071332309&partnerID=8YFLogxK
U2 - 10.1073/pnas.1822129116
DO - 10.1073/pnas.1822129116
M3 - Article
C2 - 31387975
AN - SCOPUS:85071332309
VL - 116
SP - 17081
EP - 17089
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
IS - 34
ER -