Chloroplast DNA-based studies in molecular ecology may be compromised by nuclear-encoded plastid sequence

Molecular Ecology

Volumn 19, Issue 18, 2010, Pages 3853-3856

  Arthofer, Wolfgang ^a   SchÜler, Silvio ^b   Steiner, Florian M ^a   Schlick Steiner, Birgit C ^a  

^a UNIVERSITY OF INNSBRUCK   (Austria)

^b FEDERAL RESEARCH AND TRAINING CENTRE FOR FORESTS   (Austria)

Author keywords

chloroplast DNA; mitochondrial DNA; nuclear mitochondrial; nuclear plastid; phylogeny; phylogeography; population genetics; pseudogene

Indexed keywords

CHLOROPLAST DNA; MITOCHONDRIAL DNA; PLANT DNA;

DNA SEQUENCE; ECOLOGY; GENETICS; METHODOLOGY; PLANT; PLASTID; REVIEW;

DNA, CHLOROPLAST; DNA, MITOCHONDRIAL; DNA, PLANT; ECOLOGY; PLANTS; PLASTIDS; SEQUENCE ANALYSIS, DNA;

METAZOA;

EID: 77956586033     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04787.x     Document Type: Review

References (38)

1. Akbarova YY, Solovyev VV, Shahmuradov IA (2010) Possible functional and evolutionary role of plastid DNA insertions in rice genome. Applied and Computational Mathematics, 9, 19 33.
2. Arthofer W, Avtzis DN, Riegler M, Miller W, Stauffer C (2006) 'Pitfalls in Applying Mitochondrial Markers onto the scolytid species Pityogenes chalcographus'. In : Proceedings from the Third Workshop on Genetics of Bark Beetles and Associated Microorganism (eds Bentz B, Raffa K). 15 19, U.S. Department of Agriculture, Rocky Mountain Research Station.
3. Avise JC (2009) Phylogeography: retrospect and prospect. Journal of Biogeography, 36, 3 15.
4. Ayliffe MA, Timmis JN (1992) Tobacco nuclear DNA contains long tracts of homology to chloroplast DNA. Theoretical and Applied Genetics, 85, 229 238.
5. Beckenbach AT (2009) Numts and mitochondrial pseudogenes. Myrmecological News, 12, 217 218.
6. Benesh DP, Hasu T, Suomalainen LR, Tellervo Valtonen E, Tiirola M (2006) Reliability of mitochondrial DNA in an acanthocephalan: the problem of pseudogenes. International Journal for Parasitology, 36, 247 254.
7. Bensasson D, Zhang DX, Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends in Ecology & Evolution, 16, 314 321.
8. Clegg MT (1993) Chloroplast gene sequences and the study of plant evolution. Proceedings of the National Academy of Sciences of the USA, 90, 363 367.
9. Demesure B, Sodzi N, Petit RJ (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology, 4, 129 131.
10. Gilad Y, Pritchard JK, Thornton K (2009) Characterizing natural variation using next-generation sequencing technologies. Trends in Genetics, 25, 463 471.
11. Graham SW, Olmstead RG (2000) Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. American Journal of Botany, 87, 1712 1730.
12. Kejnovsky E, Kubat Z, Hobza R et al. (2006) Accumulation of chloroplast DNA sequences on the Y chromosome of Silene latifolia. Genetica, 128, 167 175.
13. Kleine T, Maier UG, Leister D (2009) DNA transfer from the organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annual Review of Plant Biology, 60, 115 138.
14. Kress WJ, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non- coding trnH-psbA spacer region. PLoS ONE, 6, e508.
15. Leister D (2005) Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends in Genetics, 21, 655 663.
16. Martin W, Herrmann RG (1998) Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiology, 118, 9 17.
17. Matsuo M, Ito Y, Yamauchi R, Obokata J (2005) The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux. The Plant Cell, 17, 665 675.
18. Meimberg H, Thalhammer S, Brachmann A, Heubl G (2006) Comparative analysis of a translocated copy of the trnK intron in carnivorous family Nepenthaceae. Molecular Phylogenetics and Evolution, 39, 478 490.
19. Moulton MJ, Song H, Whiting MF (2010) Assessing the effects of primer specificity on eliminating numt coamplification in DNA barcoding: a case study from Orthoptera (Arthropoda: Insecta). Molecular Ecology Resources, 10, 615 627.
20. Naciri Y, Manen JF (2010) Potential DNA transfer from the chloroplast to the nucleus in Eryngium alpinum. Molecular Ecology Resources, 10, 728 731.
21. Palmer JD (1987) Chloroplast DNA evolution and biosystematic uses of chloroplast DNA variation. The American Naturalist, 130, S6 S29.
22. Parducci L, Petit RJ (2004) Ancient DNA - unlocking plants' fossil secrets. New Phytologist, 161, 335 339.
23. Petit RJ, Kremer A, Wagner DB (1993) Geographic structure of chloroplast DNA polymorphisms in European oaks. Theoretical and Applied Genetics, 87, 122 128.
24. Petit RJ, Pineau E, Demesure B, Bacilieri R, Ducousso A, Kremer A (1997) Chloroplast DNA footprints of postglacial recolonization by oaks. Proceedings of the National Academy of Sciences of the USA, 94, 9996 10001.
25. Qiu Y-X, Guan B-C, Fu C-X, Comes HP (2009) Did glacials and/or interglacials promote allopatric incipient speciation in East Asian temperate plants? Phylogeographic and coalescent analyses on refugial isolation and divergence in Dysosma versipellis. Molecular Phylogenetics and Evolution, 51, 281 293.
26. Richly E, Leister D (2004) NUMTs in sequenced eukaryotic genomes. Molecular Biology and Evolution, 21, 1081 1084.
27. Savolainen V, Cuénoud P, Spichiger R, Martinez MDP, Crèvecoeur M, Manen JF (1995) The use of herbarium specimens in DNA phylogenetics: evaluation and improvement. Plant Systematics and Evolution, 197, 87 98.
28. Shamuradov IA, Akbarova YY, Solovyev VV, Aliyev JA (2003) Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis. Plant Molecular Biology, 52, 923 934.
29. Song H, Buhay JE, Whiting MF, Crandall KA (2008) Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the National Academy of Sciences of the USA, 105, 13486 13491.
30. Sorenson MD, Quinn TW (1998) Numts: a challenge for avian systematics and population biology. The Auk, 115, 214 221.
31. Stupar RM, Lilly JW, Town CD et al. (2001) Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proceedings of the National Academy of Sciences of the USA, 98, 5099 5103.
32. Taberlet P, Gielly L, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology, 17, 1105 1109.
33. Tautz D, Ellegren H, Weigel D (2010) Next generation molecular ecology. Molecular Ecology, 19, 1 3.
34. Thalmann O, Hebler J, Poinar HN, Pääbo S, Vigilant L (2004) Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Molecular Ecology, 13, 321 335.
35. Whittall JB, Syring J, Parks M et al. (2010) Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Molecular Ecology, 19, 100 114.
36. Wu CS, Wang YN, Liu SM, Chaw SM (2007) Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed slants. Molecular Biology and Evolution, 24, 1366 1379.
37. Yao YG, Kong QP, Salas A, Bandelt HJ (2008) Pseudomitochondrial genome haunts disease studies. Journal of Medical Genetics, 45, 769 772.
38. Zhang DX, Hewitt GM (1996) Nuclear integrations: challenges for mitochondrial DNA markers. Trends in Ecology & Evolution, 11, 247 251. W Arthofer, FM Steiner and BC Schlick-Steiner focus on terrestrial animals (insects, harvestmen, millipedes, spiders) and their symbionts (ascomycete fungi, bacteria) of the Alpine environment. Their research topics include Alpine endemism, biogeography, climate-change and conservation biology, morphology and integrative taxonomy and the development of markers for population genetics. S Schüler is interested in geno- and phenotypic variation of forest trees and the analysis of natural and anthropogenic influences shaping this variation. He utilizes molecular methods with the goal of developing guidelines for sustainable forest management.