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

Abstract

Long non-coding RNAs (lncRNAs) play crucial roles in regulating gene expression in response to plant stresses. Given the importance regulatory roles of lncRNAs, providing methods for predicting the function of these molecules, especially in non-model plants, is strongly demanded by researchers. Here, we constructed a reference sequence for lncRNAs in P. vera (Pistacia vera L.) with 53220 transcripts. In total, we identified 1909 and 2802 salt responsive lncRNAs in Ghazvini, a salt tolerant cultivar, after 6 and 24 h salt treatment, respectively and 1820 lncRNAs in Sarakhs, a salt sensitive cultivar, after 6 h salt treatment. Functional analysis of these lncRNAs by several hybrid methods, revealed that salt responsive NAT-related lncRNAs associated with transcription factors, CERK1, LEA, Laccase genes and several genes involved in the hormone signaling pathways. Moreover, gene ontology (GO) enrichment analysis of salt responsive target genes related to top five selected lncRNAs showed their involvement in the regulation of ATPase, cation transporter, kinase and UDP-glycosyltransferases genes. Quantitative real-time PCR (qRT-PCR) experiment results of lncRNAs, pre-miRNAs and mature miRNAs were in accordance with our RNA-seq analysis. In the present study, a comparative analysis of differentially expressed lncRNAs and microRNA precursors between salt tolerant and sensitive pistachio cultivars provides valuable knowledge on gene expression regulation under salt stress condition. Pistacia belongs to Anacardiaceae family and contains 13 or more species, which among them pistachio (Pistacia vera L.) is the only cultivated and economically important species that is called as the 'green gold tree'. The other species are used mainly as a rootstock for pistachio cultivation 1,2. Like many other fruit trees, P. vera is hard to root and thus requires a rootstock for vegetative propagation 3. Pistachio is a deciduous (2n = 30), wind-pollinated tree species 4,5. Studies indicate that pistachio probably originated in the Middle East 6-8. It has a long history of cultivation (3000-4000 years) in Iran 9. In 2017, Iran has been ranked first in area harvested (429535 ha) and production quantity (574987 tons) of pistachio among United States, Turkey, and Syria as biggest pistachio producer countries 10. According to the number of pistachio genotypes, Iran is one of the rich countries in the world 7,8,11. In addition to fruit, other parts of plant, including leaf, flower and resins, have pharmacological properties 12,13. Salinity is major and ever-increasing problem in arid and semi-arid regions that affect plant production and growth throughout the world 14. The cultivated areas of pistachio in Iran are often in arid and semi-arid regions that the most important problem for economic crop production in these areas is high concentration of ions

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

“… Salinity lncRNA TCONS_00020253 Medtr1g081900 and Salinity TCONS_00116877 Medtr7g094600 Salinity Arabidosis – DRIR ANNAT7,NAC3 and Affecting fucosyltransferase or [ 37 ] WRKY8 NAC3 transcription factor Salinity Cotton SN91–11 lnc_388,lnc_883, Gh_A09G1182, Targeting Gh_A09G1182, [ 86 ] Gh_D03G0339 genes lnc_973 and lnc_253 and Gh_D03G0339 genes Regulating ghr-miR399 and ghr-156e by eTM Salinity Poplar P. euphratica Peu_00167161, Pal_00184400 HKT1 – P.alba var. pyramidalis Pal_00132209 fucosyltransferase or NAC3 Salinity Cotton SN91–11 lncRNA973 SOD, CAT, POD and P5CS, lncRNA973 regulate the [ 105 ] RBOHB, RBOHD, NHX7 ghr-miR399 and its target gene GhPHO2 MYB5, WRKY46, ERF62, NAC29 Salinity Pistacia vera L. Ghazvini and Sarakhs 5 NAT-lncRNAs CERK1, LEA, Laccase genes NAT-lncRNA regulate ATPase, [ 106 ] TF genes, ...…”

Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio

“…Differentially expressed coding or non-coding transcripts between tolerant and sensitive pistachio genotypes can be used to design FMs for more efficient salt tolerance screening and identifying successful salt tolerance mechanisms of tolerant genotypes 12 . In the present study, for the very first time, the SSR motifs in the specific early and late salt responsive genes of tolerant pistachio genotype were used for designing ISSR primers (Fig.…”

“…Comparative genomic analysis revealed that stress tolerance of P. vera is probably due to the chitinase gene families, and the expanded cytochrome P450 11 . Recently, the identification and characterization of long noncoding RNAs (lncRNAs) showed that these molecules act as transcriptional and post-transcriptional regulators by regulating the expression of transcription factor genes such as MYB , NAC , WRKY , ZIP , TCP and GRAS and several genes such as ATPase , LEA , Laccase , CERK1 and UGT in response to salt stress condition for pistachio adaptation 12 .…”

“…The first and only study of non-coding and regulatory sections of pistachio transcriptome led to the identification of 62 pistachio-specific pre-miRNA sequences. The expression and functional analysis of pistachio pre-miRNAs under salinity conditions showed the role of fourteen differentially expressed pre-miRNAs in the regulation of different transcription factors and transporters 12 .…”

Arabidopsis bZIP18 and bZIP52 Accumulate in Nuclei Following Heat Stress where They Regulate the Expression of a Similar Set of Genes

“…chinensis [ 40 ], Cucumis sativus [ 41 ], and Brassica juncea [ 42 ], however, the regulation of lncRNA expression by bZIP TFs under heat stress has not been reported yet. On the contrary, bZIP TFs were already reported to be targets of stress-regulated lncRNAs in Pistacia vera [ 43 ] and in Cleistogenes songorica [ 44 ]. Finaly, the lack of consistency among upregulated genes and a reasonable coherence among the downregulated genes, together with the upregulation of numerous lncRNAs suggests the possible mechanism of the upregulation of the downstream stress-responsive genes via lncRNAs alongside their direct transcription regulation.…”