Whole genomes and transcriptomes reveal adaptation and domestication of pistachio

Abstract

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.

A genome-wide identification, characterization and functional analysis of salt-related long non-coding RNAs in non-model plant Pistacia vera L. using transcriptome high throughput sequencing

“…Thus, the cerk1 mutant was more salt sensitive than the wild type under NaCl treatment 95 . In accordance with our results, differentially expressed genes were also found to be enriched in 'chitin binding' in pistachio under salt stress condition 36 .…”

“…Through comparative transcriptome analysis, a similar result was obtained in pistachio. This result indicated that the biosynthetic pathway of jasmonic acid (JA) plays an essential role in salt stress tolerance in pistachio 36 . Therefore, it can be concluded that lncRNAs in NAT pairs use different ways to modulate salt stress tolerance responses in pistachio seedlings including gene expression regulation of transcription factors, LEA, Laccases, and CERK1, and controlling the signaling pathways of plant hormones.…”

Transcriptome analysis of a medicinal plant, Pistacia chinensis

“…However, compared to reports from other plant species, the number of unigenes reported by Dong et al (2016) is very high, so further verification may be needed. On the other hand, the number of unigenes in our study is about 60% of the number of predicted genes from P. vera genome, in which 31,784 genes were reported by Zeng et al (2019). Many unigenes from the present study showed higher similarity to those of Citrus sinensis.…”

“…2), suggesting that P. chinensis is closely related to C. sinensis. Genome evolution analysis using gene families from P. vera showed a similar results among nine species from different genus, in which P. chinensis and C. sinensis showed that they diverged more recently among tested nine species (Zeng et al 2019).…”

The genome evolution and domestication of tropical fruit mango

“…Mango belongs to the genus Mangifera which can be classified under the tribe Anacardieae. Despite the availability of molecular systematics data of Anacardiaceae [55], a detailed molecular clock dating of the species within the family is lacking, and no other chromosome-level Anacardiaceae genome is currently available [56], which hamper our detailed estimation of WGD event time. However, we observed preferential post-WGD retaining of duplicated genes involved in energy metabolism, such as photosynthesis and lipid biosynthesis.…”