Identification and characterization of dwarf mistletoe responding genes in Ziarat juniper tree (Juniperus excelsa M.Bieb) through suppression subtractive hybridization and deep sequencing
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A total of 1279 dwarf mistletoe responding genes, for the first time, were identified and characterized in the Ziarat juniper tree. These are involved in various significant biological processes.
Ziarat juniper tree (Juniperus excelsa M. Bieb) is an evergreen and dominant species of Balochistan juniper forest. It provides many benefits to regional ecosystems and surrounding populations. Unfortunately, the Ziarat juniper forest is in an endangered condition because of the large numbers of biotic and abiotic stresses including dwarf mistletoe (Arceuthobium oxycedri), an obligate parasite with an endophytic root system. The dwarf mistletoe responding genes showing differential expression might be a good source to reveal potential candidate-resistant genes in the juniper tree. The current research aims to identify and characterize dwarf mistletoe responding genes in Ziarat juniper tree (J. excelsa). For this purpose, the dwarf mistletoe infested and non-infested shoots were subjected to suppression subtractive hybridization (SSH) for construction of forward (F-SSH) and reversed (R-SSH) libraries followed by deep sequencing as well as bioinformatics analysis. A total of 1279 dwarf mistletoe responding genes were identified with 985 differentially expressed genes (DEGs) from dwarf mistletoe infested and 294 DEGs from dwarf mistletoe non-infested shoots of juniper tree. Some of the significant DEGs are heat shock proteins, galactinol synthase, metallothionein-related genes, leucine-rich repeat receptor kinases, zinc finger proteins, MYB transcription factors, serine/ threonine kinase and GATA transcription factor. Randomly selected 14 genes are subjected and validated through RT-qPCR. All the identified responding genes are further functionally characterized using gene ontology (GO). The responding genes are observed to be involved in various significant functions such as, stress, metabolism, transcription factor, signaling pathway and structural proteins. These results will be useful in preparing the juniper trees against dwarf mistletoe and other stresses.
KeywordsDifferentially expressed genes Dwarf mistletoe Juniperus excelsa Suppression subtractive hybridization
This paper is a part of the research project (HEC-NRPU Project 20-1867/R&D/11) financed by the higher education commission (HEC) of Pakistan, Islamabad. The authors are highly thankful and acknowledge the financial support of the higher education commission (HEC) of Pakistan, Islamabad.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
Data archiving statement
The sequenced raw data for both F-SSH and R-SSH were deposited in the Sequence Read Archive (SRA) at NCBI (ncbi.nlm.nih.gov/sra) under accession number SRP082133. The transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GFIA00000000. The version described in this paper is the first version, GFIA00000000.1.
- Ahmed M, Siddiqui MF, Ahmed A, Sarangzai AM, Abbas T, Hussain MI (2015) Present state and multivariate analysis of a few Juniper forests of Balochistan, Pakistan. Pak J Bot 47:135–140Google Scholar
- Andrews GK (1989) Regulation of metallothionein gene expression. Prog Food Nutr Sci 14:193–258Google Scholar
- Beg AR, Jamal SM (1973) Survey of diseases of conifers and selected hardwoods. Pakistan Forest Institute, PL-480 project A 17-FS-15. Annual technical report, 7 ppGoogle Scholar
- Ciesla WM, Geils BW, Adams RP (2002) Hosts and geographic distribution of Arceuthobium oxycedri (p. 4). RMRS-RN-11WWW. Fort Collins, CO: US Department of Agriculture, Forest Service, Rocky Mountain Research Station. Available: https://www.fs.fed.us/rm/pubs/rmrs_rn11/. Return to RMRS-RN-11 Main Page Title: RMRS-RN-11WWW: Citation Electronic Publish Date: September 2001 Last Update
- Degenhardt J, Al-Masri AN, Kürkcüoglu S, Szankowski I, Gau AE (2005) Characterization by suppression subtractive hybridization of transcripts that are differentially expressed in leaves of apple scab-resistant and susceptible cultivars of Malus domestica. Mol Genet Genom 273:326–335CrossRefGoogle Scholar
- Insua VR (1987) Contribución al estudio de la biología de Arceuthobium oxicedri (DC.) M. Bieb. Boletín de sanidad vegetal Plagas 13:53–62Google Scholar
- Juniperus excelsa Bieb M (2015b) Optimization of total RNA extraction protocol from Ziarat Juniper. Pure Appl Biol 4:275–279. https://doi.org/10.19045/bspab.2015.42018
- Lee SH, Mun JY, Lee DG, Lee K (2014) Identification of Abiotic Stress-Induced Differentially Expressed Genes of Rye Leaves. Romanian Biotechnol Lett 19:9992–9996Google Scholar
- Marcoux A (2000) Population and Deforestation. SD Dimensions. Sustainable Development Department, Food and Agriculture Organization of the United Nations (FAO)Google Scholar
- Palma M, D’Agostino N, Proietti S, Bertini L, Lorito M, Ruocco M, Tucci M (2016) Suppression Subtractive Hybridization analysis provides new insights into the tomato (Solanum lycopersicum L.) response to the plant probiotic microorganism Trichoderma longibrachiatum MK1. J Plant Physiol 190:79–94CrossRefGoogle Scholar
- Sheikh IS (1985) Afforestation in Juniper forests of Balochistan. Pakistan Forest Institute, PeshawarGoogle Scholar