Preprint / Version 1

TinoTranscriptDB: A Database of Transcripts and Microsatellite Markers of Tinospora cordifolia, an Important Medicinal Plant

Authors

  • Rakesh Singh ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
  • Ajay Mahato The Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
  • Akshay Singh ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
  • Rajesh Kumar ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
  • Amit Singh ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
  • Sundeep Kumar ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
  • Soma Marla ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
  • Ashok Kumar ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
  • Nagendra Singh ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi 110012, India

Keywords:

Tinospora, markers, simple sequence repeats (SSRs), transcriptome, gene ontology (GO), transcription factors (TFs)

Abstract

Tinospora cordifolia, commonly known as “Giloe” in India, is a shrub belonging to the family Menispermaceae. It is an important medicinal plant known for its antipyretic, anti-inflammatory, antispasmodic, and antidiabetic properties and is used in the treatment of jaundice, gout, and rheumatism. Despite its economic importance, the limited information related to its genomic resources prohibits its judicious exploitation through molecular breeding or biotechnological approaches. In this study, we generated a meta-transcriptome assembly of 43,090 non-redundant transcripts by merging the RNASeq data obtained from Roche 454 GS-FLX, and Illumina platforms, and report the first transcriptome-based database for simple sequence repeats and transcription factors (“TinoTranscriptDB” (Tinospora cordifolia Transcriptome Database)). We annotated 26,716 (62%) of the total transcripts successfully from National Center for Biotechnology Information non-redundant protein (NCBI-NR), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Swiss-Prot, and Pfam databases. This database contains information of 2620 perfect simple sequence repeats (P-SSRs) with a relative abundance of 340.12 (loci/Mb), and relative density of 6309.29 (bp/Mb). Excluding mono-nucleotides, the most abundant SSR motifs were tri-nucleotides (54.31%), followed by di-nucleotides (37.51%), tetra-nucleotides (4.54%), penta-nucleotides (3.16%) and hexa-nucleotides (0.45%). Additionally, we also identified 4,311 transcription factors (TFs) and categorized them into 55 sub-families. This database is expected to fill the gap in genomic resource availability in T. cordifolia and thus accelerate molecular breeding and related functional and other applied studies aimed towards genetic improvements of T. cordifolia and related species. Keywords: Tinospora, markers, simple sequence repeats (SSRs), transcriptome, gene ontology (GO), transcription factors (TFs)