De novo transcriptome analysis of Justicia adhatoda reveals candidate genes involved in major biosynthetic pathway
Authors
Deepthi Padmanabhan
Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, 603203 Kattankulathur, India
Adil Lateef
Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, 603203 Kattankulathur, India
Purushothaman Natarajan
Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, 603203 Kattankulathur, India
Senthilkumar Palanisamy
Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, 603203 Kattankulathur, India
Keywords:
RNA sequencing, De novo assembly, Annotation, SALMON, SSR, qRT-PCR.
Abstract
Justicia adhatoda is an important medicinal plant traditionally used in the Indian system of medicine and the absence of molecular-level studies in this plant hinders its wide use, hence the study was aimed to analyse the genes involved in its various pathways.
Methods and results
The RNA isolated was subjected to Illumina sequencing. De novo assembly was performed using TRINITY software which produced 171,064 transcripts with 55,528 genes and N50 value of 2065 bp, followed by annotation of unigenes against NCBI, KEGG and Gene ontology databases resulted in 105,572 annotated unigenes and 40,288 non-annotated unigenes. A total of 5980 unigenes were mapped to 144 biochemical pathways, including the metabolism and biosynthesis pathways. The pathway analysis revealed the major transcripts involved in the tryptophan biosynthesis with TPM values of 6.0903, 33.6854, 11.527, 1.6959, and 8.1662 for Anthranilate synthase alpha, Anthranilate synthase beta, Arogenate/Prephenate dehydratase, Chorismate synthase and Chorismate mutase, respectively. The qRT-PCR validation of the key enzymes showed up-regulation in mid mature leaf when compared to root and young leaf tissue. A total of 16,154 SSRs were identified from the leaf transcriptome of J. Adhatoda ,which could be helpful in molecular breeding.
Conclusions
The study aimed at identifying transcripts involved in the tryptophan biosynthesis pathway for its medicinal properties, as it acts as a precursor to the acridone alkaloid biosynthesis with major key enzymes and their validation. This is the first study that reports transcriptome assembly and annotation of J. adhatoda plant.
Supplementary Information
The online version contains supplementary material available at 10.1007/s11033-022-07784-5.
Keywords: RNA sequencing, De novo assembly, Annotation, SALMON, SSR, qRT-PCR.
Author Biography
Purushothaman Natarajan, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, 603203 Kattankulathur, India
Associate Faculty Member, Department of Biology, , West Virginia State University, 225, Hamblin Hall, 25112-1000 Institute, WV USA
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