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A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery.

ABSTRACT: BACKGROUND:Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress. RESULTS:RNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. From this analysis, the contrasting expression pattern of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars. CONCLUSION:This study, as the first report on the whole transcriptome survey of P. vera, provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance.

SUBMITTER: Moazzzam Jazi M

PROVIDER: S-EPMC5559799 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery.

Moazzzam Jazi Maryam M Seyedi Seyed Mahdi SM Ebrahimie Esmaeil E Ebrahimi Mansour M De Moro Gianluca G Botanga Christopher C

BMC genomics 20170817 1

<h4>Background</h4>Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain ...[more]

PMID: 28814265

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Project description:BackgroundPistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species.ResultsTo explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species.ConclusionsThe results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia.

Project description:Background:Gut microbiota holds a key-role in numerous biological functions and has emerged as a driving force for the development of diabetes. Diet contributes to gut microbiota diversity and functionality providing a tool for the prevention and management of the disease. The study aimed to investigate the effect of a dietary intervention with pistachio nuts, a rich source of monounsaturated fatty acids, dietary fibers and phytochemicals on gut microbiota composition in the rat model of Type 1 Diabetes. Methods:Male Wistar rats were randomly assigned into four groups: healthy animals which received control diet (CD) or pistachio diet (PD), and diabetic animals which received control diet (DCD) or pistachio diet (DPD) for 4 weeks. Plasma biochemical parameters were determined and histological examination of liver and pancreas was performed at the end of the dietary intervention. Adherent intestinal microbiota populations in jejunum, ileum, caecum and colon were analyzed. Fecal microbiota populations at the beginning and the end of the study were determined by microbiological analysis and 16S rRNA sequencing. Results:Diabetic animals of both groups exhibited high plasma glucose and low insulin concentrations, as well as characteristic pancreatic lesions. Pistachio supplementation significantly increased lactobacilli and bifidobacteria populations in jejunum, ileum and caecum (p < 0.05) and normalized microbial flora in all examined intestinal regions of diabetic animals. After 4 weeks of supplementation, populations of bifidobacteria and lactobacilli were increased in feces of both healthy and diabetic animals, while enterococci levels were decreased (p < 0.05). Next Generation Sequencing of fecal samples revealed increased and decreased counts of Firmicutes and Bacteroidetes, respectively, in healthy animals that received the pistachio diet. Actinobacteria OTUs were higher in diabetic animals and increased over time in the pistachio treated groups, along with increased abundance of Bifidobacterium. Lactobacillus, Turicibacter and Romboutsia populations were elevated in healthy animals administered the pistachio nuts. Of note, relative abundance of Bacteroides was higher in healthy than in diabetic rats (p < 0.05). Conclusion:Dietary pistachio restored normal flora and enhanced the presence of beneficial microbes in the rat model of streptozotocin-induced diabetes.

Dataset Information

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery.

Publications

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery.

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