Estimation of nuclear genome size and characterization of Ty1-copia like LTR retrotransposon in Mesua ferrea L.
- 114 Downloads
Mesua ferrea L. is a multipurpose versatile tree that is well known as a prospective feedstock biodiesel plant. The potentiality of M. ferrea as a sustainable source of feedstock for biodiesel industry is dependent on an extensive knowledge of the genome structure of the plant. However, to date, there has been no genomic research aimed at the exploitation of the biotechnological potential of this species. Flow cytometry with propidium iodide as the DNA stain was used to estimate the nuclear DNA content of Mesua and the 2C value is estimated to be 1.40 ± 0.02 pg. Somatic chromosome count from root-tip cells is found to be 2n = 30 corresponding to the diploid level (n = 15). Fold variation in genome size (1.14) is observed among the plants collected from different geographic locations in Assam and is attributed to reverse transcriptase-RNase H (RT-RH) domains of the Ty1-copia retrotransposons. Dot blot analysis revealed that Ty1-copia accounts for 2.5% of total haploid nuclear genome of Mesua and phylogenetic analyses showed that the RT-RH sequences are heterogeneous and resolved into 3 distinct groups. These results contribute to our understanding about genome organization of Mesua and will provide valuable information for its utilization in future.
KeywordsFlow cytometry Mesua ferrea Ty1-copia Nuclear DNA content
RD and RGS thank Ministry of Human Resources Development (MHRD), Government of India for student fellowship. Thanks also to Department of Biosciences and Bioengineering, IITG for instrumentation facility.
Conceived and designed the experiments: LR, RD, RGS, SM Performed the experiments: RD, RGS Analyzed the data: RD, RGS, SM Contributed reagents/materials/analysis tools: LR Manuscript preparation: LR, RD, RGS.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
- Ahmed S, Shafiuddin MD, Azam MS, Islam MDS, Ghosh A, Khan H (2011) Identification and characterization of jute LTR retrotransposons: their abundance, heterogeneity and transcriptional activity. Mob Genet Elements 1:18–28. https://doi.org/10.4161/mge.1.1.16433 CrossRefPubMedPubMedCentralGoogle Scholar
- Alipour A, Tsuchimoto S, Sakai H, Ohmido N, Fukui K (2013) Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. Biotechnol Biofuels 6:129. https://doi.org/10.1186/1754-6834-6-129 CrossRefPubMedPubMedCentralGoogle Scholar
- Bennett MD, Leitch IJ (2010) Plant DNA C-values database (release 5.0, December 2010)Google Scholar
- Das A, Kesari V, Vinod MS, Parida A, Mitra S, Rangan L (2013) Genetic diversity in ecotypes of the scarce wild medicinal crop Zingiber moran revealed by ISSR and AFLP marker analysis and chromosome number assessment. Plant Biosyst 149:111–120. https://doi.org/10.1080/11263504.2013.795197 CrossRefGoogle Scholar
- Flavell AJ, Smith DB, Kumar A (1992) Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet 23:233–242Google Scholar
- Gresshoff PM, Rangan L, Indrasumunar A, Scott PT (2017) Development of a new bioenergy crop based on oil-rich seeds from the legume tree Pongamia pinnata. Energy Emiss Control Technol 4:1–8Google Scholar
- Ramesh AM, Basak S, Choudhury RR, Rangan L (2014) Development of flow cytometric protocol for nuclear DNA content estimation and determination of chromosome number in Pongamia pinnata L., a valuable biodiesel plant. Appl Biochem Biotechnol 172:533–548. https://doi.org/10.1007/s12010-013-0553-z CrossRefPubMedGoogle Scholar