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.
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