Whole genomes and transcriptomes reveal adaptation and domestication of pistachio
| Autor: | Ming-Shan Wang, Ali Esmailizadeh, Li-Li Ji, Bing-She Lu, Min Liu, Dong-Dong Wu, Hong Zhou, Lin Zeng, He Dai, Xiao-Long Tu, Hojjat Asadollahpour Nanaei, David M. Irwin, Fengming Han, Mehdi Mansouri, Xiao-Long Li, Ali Tajabadipour, Hong-Kun Zheng |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
lcsh:QH426-470
Population Adaptation Biological Genetic admixture Genome Domestication Evolution Molecular 03 medical and health sciences 0302 clinical medicine education lcsh:QH301-705.5 030304 developmental biology Local adaptation Pistacia vera 0303 health sciences Genetic diversity education.field_of_study Pistacia biology Research Artificial selection Salt Tolerance biology.organism_classification lcsh:Genetics lcsh:Biology (General) Evolutionary biology Multigene Family Crop domestication Adaptation Transcriptome 030217 neurology & neurosurgery Genome Plant |
| Zdroj: | Genome Biology, Vol 20, Iss 1, Pp 1-13 (2019) Genome Biology |
| Popis: | Background Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses. Results Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Particularly, a comparative transcriptomic analysis shows that the jasmonic acid (JA) biosynthetic pathway plays an important role in salt tolerance in pistachio. Moreover, we resequence 93 cultivars and 14 wild P. vera genomes and 35 closely related wild Pistacia genomes, to provide insights into population structure, genetic diversity, and domestication. We find that frequent genetic admixture occurred among the different wild Pistacia species. Comparative population genomic analyses reveal that pistachio was domesticated about 8000 years ago and suggest that key genes for domestication related to tree and seed size experienced artificial selection. Conclusions Our study provides insight into genetic underpinning of local adaptation and domestication of pistachio. The Pistacia genome sequences should facilitate future studies to understand the genetic basis of agronomically and environmentally related traits of desert crops. Electronic supplementary material The online version of this article (10.1186/s13059-019-1686-3) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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