Citation

Priyavathi P, Nagesh S, Kavitha VVK, Johnson C, Gopal P (2018) Comprehensive Leaf Transcriptome of a Non-model Plant, Abelmoschus esculentus for the Functional Genomics Studies. J Genet Genome Res 5:036. doi.org/10.23937/2378-3648/1410036

Copyright

© 2018 Priyavathi P, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

RESEARCH ARTICLE | OPEN ACCESS DOI: 10.23937/2378-3648/1410036

Comprehensive Leaf Transcriptome of a Non-model Plant, Abelmoschus esculentus for the Functional Genomics Studies

Padmanabhan Priyavathi1, Srikakulam Nagesh1, Velayudha Vimala Kumar Kavitha1, Christdas Johnson2 and Pandi Gopal1*

1Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Tamil Nadu, India

2Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Tamil Nadu, India

Abstract

Abelmoschus esculentus is widely cultivated and consumed across the globe for its nutritional and medicinal purpose. In spite of the growing demand, its cultivation is massively affected by various insects, fungi, nematodes and viruses. Due to lack of genomic and limited transcriptomic resources, genetic manipulation studies concerning the crop improvement against various environmental factors is scarce for this crop. Thereby, the present study aims to develop high quality transcriptome of A. esculentus by employing the Next-Generation based RNA sequencing of four cDNA libraries generated from the leaf samples. Sequencing yielded a total of 206.3 million paired-end clean reads with 66,382 assembled unigenes having a total length of 71.35 Mb, an average length of 1,074 bp and an N50 of 1,408 bp. About 56% of the unigenes were successfully annotated in four public databases including Pfam, GO, COG, and KEGG. GO analysis revealed that the majority of the annotated unigenes were involved in key biological processes like ATP binding, DNA binding, transcription, DNA-templated, and integral component of membrane. KEGG pathway analysis showed that 16,307 unigenes were assigned to 143 pathways in which majority of secondary metabolites related transcripts involving in phenylpropanoids, flavonoid and terpenoid biosynthesis pathway were identified. In addition, transcription factor and simple sequence repeats (SSRs) analyses revealed 76 transcription factor families and 9,578 potential SSRs in the A. esculentus leaf transcriptome. Furthermore, de novo assembled leaf transcriptome generated in the present study had longer transcripts with better N50 sizes and the quality of assembly was ensured by qRT-PCR analysis. The A. esculentus sequence information presented in this study will be a valuable resource for further molecular genetics and functional genomics studies for the improvement of this crop plant.