Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis
Creators
- 1. Institute for Multidisciplinary Research, Kneza Višeslava 1, University of Belgrade, 11030 Belgrade, Serbia
- 2. Institute for Biological Research "Siniša Stanković"- National Institute of Republic of Serbia, University of Belgrade, Bul. despota Stefana 142, 11060 Belgrade, Serbia
- 3. Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi (SA), Italy
Description
Six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) were sequenced and de novo assembled using Trinity .
CE_Assembly.tar.gz - Centaury referent transcriptome comprises of 160.839 Trinity transcripts grouped in 105.726 Trinity genes.
CE_Assembly_fpkm.tar.gz - fpkm normalized read counts of the assembled transcripts in the six sequenced centaury tissues.
nt.db_CE_assembly.tar.gz - annotation of assembled transcripts by mapping them against NCBI nucleotide (NT) database using BLASTn . The obtained results were filtered with E-value E ≤ 10-3.
swissprot.db_CE_assembly.tar.gz - annotation of assembled transcripts by mapping them against NCBI nucleotide (swissprot) database using BLASTx . The obtained results were filtered with E-value E ≤ 10-3.
pfam30.db_CE_assembly.tar.gz - annotation of assembled transcripts by mapping them against Pfam30 domain database using hmmer3. The obtained results were filtered with independent E-value E ≤ 10-3.
Files
Files
(199.9 MB)
Additional details
Funding
- Physiological, chemical and molecular analysis of the diversity of selected rare and endangered plant species and application of biotechnology for ex situ conservation and production of biologically active compounds 173024
- Ministry of Education, Science and Technological Development
- Modulation of antioxidative metabolism in plants for improvement of plant abiotic stress tolerance and identification of new biomarkers for application in remediation and monitoring of degraded biotopes 43010
- Ministry of Education, Science and Technological Development
- Development and application of biotechnological methods for obtaining healthy plants of ornamental species 31019
- Ministry of Education, Science and Technological Development