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Journal of Plant Biochemistry and Biotechnology

, Volume 27, Issue 4, pp 478–487 | Cite as

Estimation of nuclear genome size and characterization of Ty1-copia like LTR retrotransposon in Mesua ferrea L.

  • Reshmi Das
  • Rahul G. Shelke
  • Latha Rangan
  • Sudip Mitra
Original Article

Abstract

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.

Keywords

Flow cytometry Mesua ferrea Ty1-copia Nuclear DNA content 

Notes

Acknowledgements

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.

Author contributions

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.

Supplementary material

13562_2018_457_MOESM1_ESM.doc (3.2 mb)
Figures Fig. A1: Dot plot of PI-stained gated nuclei of M. ferrea using P. pinnata as standard; (a) external standardization (b) internal standardization and (c) pseudo-internal standardization. Fig. A2: Correlation between genome size and geographical distribution of M. ferrea in Assam, India. Fig. A3: Somatic metaphase chromosome in different individuals of M. ferrea. Dispur (a); Tezpur (b); Jorhat (c); Dibrugarh (d); Silchar (e); Tinsukia (f); Kokrajhar (g); Halflong (h); IIT Guwahati campus (i). Fig. A4: Multiple sequence alignment of the nucleotide sequences corresponding to the RT-RH domain of the Ty1-copia element in M. ferrea clones using ClustalW. Shading was performed by Multiple Sequence Alignment Editor and Shading Utility (Genedoc, version 2.6.002: www.psc.edu/biomed/genedoc) in conservation mode. Darkest shading indicates residues that are 100 percent conserved and are identical in all sequences; lighter shading denotes residues that are identical in most of sequences or functionally identical in all of them. Clones are numbered as MFTY 1 to MFTY-18. Fig. A5: Dot blot hybridization conducted for the determination of Ty1-copia copy number in M. ferrea. (a) Different concentrations of RT-RH PCR product and (b) M. ferrea genomic DNA were serially diluted on row and dot spotted on a membrane (DOC 3290 kb)
13562_2018_457_MOESM2_ESM.doc (38 kb)
Table A1 Estimation of mean 2C nuclear DNA (pg) in ecotypes of M. ferrea using P. pinnata as reference standard (DOC 38 kb)

References

  1. 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
  2. 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
  3. Bainard JD, Fazekas AJ, Newmaster SG (2010) Methodology significantly affects genome size estimates: quantitative evidence using bryophytes. Cytom Part A 77A:725–732.  https://doi.org/10.1002/cyto.a.20902 CrossRefGoogle Scholar
  4. Bennett MD, Leitch IJ (2005) Plant genome size research: a field in focus. Ann Bot Lond 95:1–6.  https://doi.org/10.1093/aob/mci001 CrossRefGoogle Scholar
  5. Bennett MD, Leitch IJ (2010) Plant DNA C-values database (release 5.0, December 2010)Google Scholar
  6. Bennetzen JL (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot Lond 95:127–132.  https://doi.org/10.1093/aob/mci008 CrossRefGoogle Scholar
  7. Cheng X, Dongfeng D, Cheng Z, Keller B, Ling HQ (2009) A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event. Genetics 181:1183–1193.  https://doi.org/10.1534/genetics.108.099150 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 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
  9. Dolezel J, Bartos J (2005) Plant DNA flow cytometry and estimation of nuclear genome size. Ann Bot Lond 95:99–110.  https://doi.org/10.1093/aob/mci005 CrossRefGoogle Scholar
  10. Dolezel J, Bartos J, Voglmayr H, Greilhuber J (2003) Nuclear DNA content and genome size of trout and human. Cytometry 51:127–128.  https://doi.org/10.1002/cyto.a.10013 CrossRefPubMedGoogle Scholar
  11. Ebert I, Greilhuber J, Speta F (1996) Chromosome banding and genome size differentiation in Prospero (Hyacinthaceae): Diploids. Plant Syst Evol 203:143–177CrossRefGoogle Scholar
  12. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329–341.  https://doi.org/10.1038/nrg793 CrossRefPubMedGoogle Scholar
  13. Flavell AJ, Smith DB, Kumar A (1992) Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet 23:233–242Google Scholar
  14. 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
  15. Hill P, Burford D, Martin DM, Flavell AJ (2005) Retrotransposon populations of Vicia species with varying genome size. Mol Genet Genomics 273:371–381.  https://doi.org/10.1007/s00438-005-1141-x CrossRefPubMedGoogle Scholar
  16. Kesari V, Sudarshan M, Das A, Rangan L (2009) PCR amplification of the genomic DNA from the seeds of Ceylon Ironwood, Jatropha and Pongamia. Biomass Bioenerg 33:1724–1728.  https://doi.org/10.1016/j.biombioe.2009.08.005 CrossRefGoogle Scholar
  17. Kesari V, Das A, Rangan L (2010) Physico-chemical characterization and microbial assay from seed oil of Pongamia pinnata, potential biofuel crop. Biomass Bioenerg 34:108–115.  https://doi.org/10.1016/j.biombioe.2009 CrossRefGoogle Scholar
  18. Keskitalo M, Linden A, Valkonen JPT (1998) Genetic and morphological diversity of Finnish Tansy (Tanacetum vulgare L., Asteraceae). Theor Appl Genet 96:1141–1150.  https://doi.org/10.1007/s001220050850 CrossRefGoogle Scholar
  19. Kidwell MG (2002) Transposable elements and the evolution of genome size in eukaryotes. Genetica 115:49–63CrossRefPubMedGoogle Scholar
  20. Knight CA, Molinari NA, Petrov DA (2005) The large genome constraint hypothesis: evolution, ecology and phenotype. Ann Bot Lond 95:177–1902.  https://doi.org/10.1093/aob/mci011 CrossRefGoogle Scholar
  21. Kolano B, Siwinska D, Pando LG, Pulka JS, Maluszynska J (2012) Genome size variation in Chenopodium quinoa (Chenopodiaceae). Plant Syst Evol 298:251–255.  https://doi.org/10.1007/s00606-011-0534-z CrossRefGoogle Scholar
  22. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532.  https://doi.org/10.1146/annurev.genet.33.1.479 CrossRefPubMedGoogle Scholar
  23. Loureiro J, Rodriguez E, Dolezel J, Santos C (2007) Two new nuclear isolation buffers for plant DNA flow cytometry: a test with 37 species. Ann Bot Lond 100:875–888.  https://doi.org/10.1093/aob/mcm152 CrossRefGoogle Scholar
  24. Lysak MA, Rostkova A, Dixon JM, Rossi G, Dolezel J (2000) Limited genome size variation in Sesleria albicans. Ann Bot Lond 86:399–403.  https://doi.org/10.1006/anbo.2000.1200 CrossRefGoogle Scholar
  25. Ma Y, Sun H, Zhao G, Dai H, Gao X, Li H et al (2008) Isolation and characterization of genomic retrotransposons sequences from octoploid strawberry (Fragaria × ananassa Duch.). Plant Cell Rep 27:499–507.  https://doi.org/10.1007/s00299-007-0476-7 CrossRefPubMedGoogle Scholar
  26. Rajput MK, Upadhyaya KC (2010) Isolation and characterization of stress induced Ty1-copia like Retrotransposable elements in Chickpea (Cicer arietinum L.). Mol Biol 44:693–698.  https://doi.org/10.1134/s0026893310050031 CrossRefGoogle Scholar
  27. 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
  28. Rico-Cabanas L, Martinez-Izquierdo JA (2007) CIRE1, a novel transcriptionally, active Ty1-copia retrotransposons from Citrus sinensis. Mol Genet Genom 277:365–377.  https://doi.org/10.1007/s00438-006-0200-2 CrossRefGoogle Scholar
  29. Roychoudhury R, Basak S, Ramesh AM, Rangan L (2013) Nuclear DNA content of Pongamia pinnata L. and genome size stability of in vitro-regenerated plantlets. Protoplasma 251:703–709.  https://doi.org/10.1007/s00709-013-0545-4 CrossRefGoogle Scholar
  30. Ruhfel BR, Bittrich V, Bove CP, Mats GH, Philbrick CT, Rutishauser R, Xi Z (2011) Phylogeny of the clusioid clade (Malpighiales): Evidence from the plastid and mitochondrial genomes. Am J Bot 98:306–325.  https://doi.org/10.3732/ajb.1000354 CrossRefPubMedGoogle Scholar
  31. Schmuths H, Meister A, Horres R, Bachmann K (2004) Genome size variation among accessions of Arabidopsis thaliana. Ann Bot Lond 9:317–321.  https://doi.org/10.1093/aob/mch037 CrossRefGoogle Scholar
  32. Suda J, Leitch IJ (2010) The quest for suitable reference standards in genome size research. Cytom Part A 77A(717):720.  https://doi.org/10.1002/cyto.a.20907 CrossRefGoogle Scholar
  33. Suda J, Kyncl T, Freiova R (2003) Nuclear DNA amounts in Macaronesian angiosperms. Ann Bot Lond 92:153–164.  https://doi.org/10.1093/aob/mcg104 CrossRefGoogle Scholar
  34. Temsch EM, Temsch W, Ehrendorfer-Schratt L, Greilhuber J (2010) Heavy metal pollution, selection, and genome size: the species of the Zerjav study revisited with flow cytometry. J Bot 11:596542.  https://doi.org/10.1155/2010/596542 CrossRefGoogle Scholar
  35. Wang X, Zhang T, Wen Z, Xiao H, Yang Z, Chen G, Zhao X (2005) The chromosome number, karyotype and genome size of the desert plant diploid Reaumuria soongorica (Pall.) Maxim. Plant Cell Rep 30:955–964.  https://doi.org/10.1007/s00299-011-1020-3 CrossRefGoogle Scholar
  36. Zedek F, Smerda J, Smarda P, Bures P (2010) Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis. BMC Plant Biol 265:1–10.  https://doi.org/10.1186/1471-2229-10-265 CrossRefGoogle Scholar

Copyright information

© Society for Plant Biochemistry and Biotechnology 2018

Authors and Affiliations

  • Reshmi Das
    • 1
  • Rahul G. Shelke
    • 1
  • Latha Rangan
    • 1
    • 2
  • Sudip Mitra
    • 2
  1. 1.Department of Biosciences and BioengineeringIndian Institute of Technology GuwahatiGuwahatiIndia
  2. 2.Centre for Rural TechnologyIndian Institute of Technology GuwahatiGuwahatiIndia

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