Sizing up arthropod genomes: An evaluation of the impact of environmental variation on genome size estimates by flow cytometry and the use of qPCR as a method of estimation1

Genome

Volumn 56, Issue 9, 2013, Pages 505-510

  Gregory, T Ryan ^a   Nathwani, Paula ^a   Bonnett, Tiffany R ^b   Huber, Dezene P W ^b  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY OF NORTHERN BRITISH COLUMBIA   (Canada)

Author keywords

Arthropoda; Flow cytometry; Genome size; Polymerase chain reaction; Real time PCR

Indexed keywords

ANIMAL; ARTICLE; BEETLE; DROSOPHILA MELANOGASTER; FLOW CYTOMETRY; GENETICS; GENOME SIZE; HOUSE FLY; HUMIDITY; INSECT GENOME; METHODOLOGY; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; TEMPERATURE; TRIBOLIUM;

ANIMALS; BEETLES; DROSOPHILA MELANOGASTER; FLOW CYTOMETRY; GENOME SIZE; GENOME, INSECT; HOUSEFLIES; HUMIDITY; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; TEMPERATURE; TRIBOLIUM;

EID: 84887501144     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/gen-2013-0044     Document Type: Article

References (31)

1. Adams M.D. Celniker S. Holt R. Evans C. Gocayne J.D. Amatides P.G. et al 2000. The genome sequence of Drosophila melanogaster. Science, 287 (5461): 2185-2195. 10.1126/science.287.5461.2185. 10731132.
2. Bennett, M.D., and Leitch, I.J. 2012. Plant DNA C-values database. Available from http://data.kew.org/cvalues/ [accessed 19 September 2013].
3. Bennett M.D. Leitch I.J. Price H.J. Johnston J.S. 2003. Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb. Ann. Bot. 91: 547-557. 10.1093/aob/mcg057. 12646499.
4. Bennett M.D. Price H.J. Johnston J.S. 2008. Anthocyanin inhibits propidium iodide DNA fluorescence in Euphorbia pulcherrima: implications for genome size variation and flow cytometry. Ann. Bot. 101: 777-790. 10.1093/aob/mcm303. 18158306.
5. DeSalle R. Gregory T.R. Johnston J.S. 2005. Preparation of samples for comparative studies of arthropod chromosomes: visualization, in situ hybridization, and genome size estimation. Methods Enzymol. 395: 460-488. 10.1016/S0076-6879(05)95025-8. 15865980.
6. Dolezel J. Bartos J. 2005. Plant DNA flow cytometry and estimation of nuclear genome size. Ann. Bot. 95: 99-110. 10.1093/aob/mci005. 15596459.
7. Dolezel J. Binarová P. Lucretti S. 1989. Analysis of nuclear DNA content in plant cells by flow cytometry. Biol. Plant. (Praha), 31: 113-120.
8. Dolezel J. Bartos J. Voglmayr H. Greilhuber J. 2003. Nuclear DNA content and genome size of trout and human. Cytometry, 51A: 127-128. 10.1002/cyto.a.10013.
9. Gao J. Scott J.G. 2006. Use of quantitative real-time polymerase chain reaction to estimate the size of the house-fly Musca domestica genome. Insect Mol. Biol. 15 (6): 835-837. 10.1111/j.1365-2583.2006.00690.x. 17201775.
10. Goffeau A. Barrell B.G. Bussey H. Davis R.W. Dujon B. Feldmann H. et al 1996. Life with 6000 genes. Science, 274: 546-567. 10.1126/science.274.5287.546. 8849441.
11. Gomulski, L.M., Dimopoulos, G., Xi, Z., Soares, M.B., Bonaldo, M.F., Malacrida, A.R., and Gasperi, G. 2008. Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata. BMC Genomics, 23: 243. http://www.biomedcentral.com/1471-2164/9/243.
12. Gregory T.R. 2005. Synergy between sequence and size in large-scale genomics. Nat. Rev. Genet. 6: 699-708. 10.1038/nrg1674. 16151375.
13. Gregory, T.R. 2013. Animal genome size database. Available from http://www.genomesize.com [accessed 19 September 2013].
14. Gregory T.R. Johnston J.S. 2008. Genome size diversity in the family Drosophilidae. Heredity, 101: 228-238. 10.1038/hdy.2008.49. 18523443.
15. Hardie D.C. Gregory T.R. Hebert P.D.N. 2002. From pixels to picograms: a beginners' guide to genome quantification by Feulgen image analysis densitometry. J. Histochem. Cytochem. 50: 735-749. 10.1177/002215540205000601. 12019291.
16. Hare, E.E., and Johnston, J.S. 2011. Genome size determination using flow cytometry of propidium iodide-stained nuclei. In Molecular methods for evolutionary genetics. Edited by V. Orgogozo and M.V. Rockman. Methods in Molecular Biology, vol. 772. pp. 3-12.
17. Hoy M.A. 2009. The predatory mite Metaseiulus occidentalis: mitey small and mitey large genomes. BioEssays, 31: 581-590. 10.1002/bies.200800175. 19334003.
18. International Human Genome Sequencing Consortium 2004. Finishing the euchromatic sequence of the human genome. Nature, 431: 931-945. 10.1038/nature03001. 15496913.
19. Jeyaprakash A. Hoy M. 2009. The nuclear genome is the phytoseiid Metaseiulus occidentalis (Acari: Phytoseiidae) is among the smallest known in arthropods. Exp. Appl. Acarol. 47: 263-273. 10.1007/s10493-008-9227-x. 19137405.
20. Kaewkong W. Imtawil K. Maleewong W. Intapan P.M. Sri-Aroon P. Wongkham S. Wongkham C. 2012. Genome size estimation of liver fluke Opisthorchis viverrini by real-time polymerase chain reaction based method. Parasitol. Int. 61: 77-80. 10.1016/j.parint.2011.06.025. 21757028.
21. Keeling C.I. Yuen M.M.S. Liao N.Y. Docking T.R. Chan S.K. Taylor G.A. et al 2013. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biol. 14: R27. 10.1186/gb-2013-14-3-r27. 23537049.
22. Loureiro J. Rodriguez E. Dolezel J. Santos C. 2006. Flow cytometric and microscopic analysis of the effect of tannic acid on plant nuclei and estimation of DNA content. Ann. Bot. 98: 515-527. 10.1093/aob/mcl140. 16820406.
23. Mounsey K.E. Willis C. Burgess S.T.G. Holt D.C. McCarthy J. Fischer K. 2012. Quantitative PCR-based genome size estimation of the astigmatid mites Sarcoptes scabiei, Psoroptes ovis and Dermatophagoides pteronyssinus. Parasites and Vectors, 5: 3. 10.1186/1756-3305-5-3. 22214472.
24. Nardon C. Weiss M. Vieira C. Blemont C. 2003. Variation of the genome size estimate with environmental conditions in Drosophila melanogaster. Cytometry, 55: 43-49. 12938187.
25. Noirot M. Barre P. Duperray C. Louarn J. Hamon S. 2003. Effects of caffeine and chlorogenic acid on propidium iodide accessibility to DNA: consequences on genome size evaluation in coffee tree. Ann. Bot. 92: 259-264. 10.1093/aob/mcg139. 12876189.
26. Rasch E.M. Barr H.J. Rasch R.W. 1971. The DNA content of sperm of Drosophila melanogaster. Chromosoma, 33: 1-18. 10.1007/BF00326379. 5574762.
27. Scott J.G. Liu N. Kristensen M. Clark A.G. 2009. A case for sequencing the genome of Musca domestica (Diptera: Muscidae). J. Med. Entomol. 46: 175-182. 10.1603/033.046.0202. 19351068.
28. Tribolium Genome Sequencing Consortium 2008. The genome of the model beetle and pest Tribolium castaneum. Nature, 452: 949-955. 10.1038/nature06784.
29. Tsoumani K.T. Mathiopoulos K.D. 2012. Genome size estimation with quantitative real-time PCR in two Tephritidae species: Ceratitis capitata and Bactrocera oleae. J. Appl. Entomol. 136: 626-631. 10.1111/j.1439-0418.2011. 01684.x.
30. Wilhelm, J., and Hahn, M. 2004. Measuring genome sizes by absolute quantification. In Rapid cycle real-time PCR-methods and applications. Edited by C. Wittwer, M. Hahn, and K. Kaul. Springer, Berlin. pp. 31-41.
31. Wilhelm J. Pingoud A. Hahn M. 2003. Real-time PCR based method for the estimation of genome size. Nucleic Acids Res. 31: e56. 10.1093/nar/gng056