Mitochondrial genome recombination in the zone of contact between two hybridizing conifers

Genetics

Volumn 171, Issue 4, 2005, Pages 1951-1962

  Jaramillo Correa, Juan P ^a   Bousquet, Jean ^a  

^a UNIVERSITÉ LAVAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ALLOPATRY; ARTICLE; BLACK SPRUCE; CONIFER; CONTROLLED STUDY; DNA POLYMORPHISM; DNA RECOMBINATION; DNA SEQUENCE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC VARIABILITY; GEOGRAPHICAL VARIATION (SPECIES); GEOLOGICAL TIME; HETEROPLASMY; HYBRID; MITOCHONDRIAL GENETICS; MITOTYPE; NONHUMAN; NORTH AMERICA; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES DIVERSITY;

BASE SEQUENCE; CANADA; DNA, MITOCHONDRIAL; GEOGRAPHY; HAPLOTYPES; HYBRIDIZATION, GENETIC; MOLECULAR SEQUENCE DATA; NEW ENGLAND; PINUS; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

CONIFEROPHYTA; PICEA MARIANA; PICEA RUBENS;

EID: 33645129727     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.105.042770     Document Type: Article

References (69)

1. ALBERT, B., B. GODELLE and P.-H. GOUYON, 1998 Evolution of the plant mitochondrial genome: dynamics of duplication and deletion of sequences. J. Mol. Evol. 46: 155-158.
2. ANDERSON, J. B., C. WICKENS, M. KHAN, L. E. COWEN, N. FEDERSPIEL et al., 2001 Infrequent genetic exchange and recombination in the mitochondrial genome of Candida albicans. J. Bacteriol. 183: 865-872.
3. ARRIETA-MONTIEL, M., A. LYZNIK, M. WOLOSZYNSKA, H. JANSKA and S. MACKENZIE, 2001 Tracing evolutionary and developmental implications of mitochondrial stoichiometric shifting in the common bean. Genetics 158: 851-864.
4. ASMUSSEN, M. A., and C. J. BASTEN, 1994 Sampling theory for cytonuclear disequilibria. Genetics 138: 1351-1363.
5. ASMUSSEN, M. A., and C. J. BASTEN, 1996 Constraints and normalized measures for cytonuclear disequilibria. Heredity 76: 207-214.
6. AWADALLA, P., A. EYRE-WALKER and J. MAYNARD-SMITH, 1999 Linkage disequilibrium and recombination in hominid mitochondrial DNA. Science 286: 2524-2525.
7. BLUM, B. M., 1990 Red spruce, pp. 250-257 in Silvics of North America: Conifers, Vol. 1, edited by R. M. Burns and B. H. Honkala. U.S. Department of Agriculture, Washington, DC.
8. BURBAN, C., and R. J. PETIT, 2003 Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance. Mol. Ecol. 12: 1487-1495.
9. BUROKER, N. E., J. R. BROWN, T. A. GILBERT, P. J. O'HARA, A. T. BECKENBACH et al., 1990 Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model. Genetics 124: 157-163.
10. BURT, A., D. A. BROWN, G. L. KOENING, T. J.WHITE and J. W. TAYLOR, 1996 Molecular markers reveal cryptic sex in the human pathogen Coccidoides immitis. Proc. Natl. Acad. Sci. USA 93: 770-773.
11. CLEMENT, M. D., D. POSADA and K. CRANDALL, 2000 TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9: 1657-1660.
12. COYER, J. A., G. HOARAU, W. T. STAM and J. L. OLSEN, 2004 Geographically specific heteroplasmy of mitochondrial DNA in the seaweed, Fucus serratus (Heterokontophyta: Phaeophyceae, Fucales). Mol. Ecol. 13: 1323-1326.
13. CRANDALL, K. A., and A. R. TEMPLETON, 1993 Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134: 959-969.
14. DOWTON, M., L. R. CASTRO, S. L. CAMPBELL, S. D. BARGON and A. D. AUSTIN, 2003 Frequent mitochondrial gene rearrangements at the hymenopteran nad3-nad5 junction. J. Mol. Evol. 56: 517-526.
15. FAURON, C. M. R., B. MOORE and M. CASPER, 1995 Maize as a model of higher plant mitochondrial genome plasticity. Plant Sci. 112: 11-32.
16. GODBOUT, J., J. P. JARAMILLO-CORREA, J. BEAULIEU and J. BOUSQUET, 2005 A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer. Mol. Ecol. 14: 3497-3512.
17. GORDON, A. G., 1976 The taxonomy and genetics of Picea rubens and its relationship to Picea mariana. Can. J. Bot. 54: 781-813.
18. HALL, T. A., 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98.
19. HALLE, M. L., A. M. BORTLAND, M. H. G. GUSTAFSSON and K. WOLFF, 2004 Causes of size homoplasy among chloroplast microsatellites in closely related Clusia species. J. Mol. Evol. 58: 182-190.
20. HOARAU, G., S. HOLLA, R. LESCASSE, W. T. STAM and J. L. OLSEN, 2002 Heteroplasmy and evidence for recombination in the mitochondrial control region of the flatfish Platichthys flesus. Mol. Biol. Evol. 19: 2261-2264.
21. HUDSON, R. R., and N. L. KAPLAN, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
22. JARAMILLO-CORREA, J. P., and J. BOUSQUET, 2003 New evidence from mitochondrial DNA of a progenitor-derivative relationship between black spruce and red spruce (Pinaceae). Am. J. Bot. 90: 1801-1806.
23. JARAMILLO-CORREA, J. P., J. BOUSQUET, J. BEAULIEU, N. ISABEL, M. PERRON et al., 2003 Cross-species amplification of mitochondrial DNA sequence-tagged-site markers in conifers: the nature of polymorphism and variation within and among species in Picea. Theor. Appl. Genet. 106: 1353-1367.
24. JARAMILLO-CORREA, J. P., J. BEAULIEU and J. BOUSQUET, 2004 Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer. Mol. Ecol. 13: 2735-2747.
25. KREBS, C. J., 1999 Ecological Methodology.Wesley Longman, New York.
26. LADOUKAKIS, E. D., and E. ZOUROS, 2001 Direct evidence for homologous recombination in mussel (Mytilus galloprovincialis) mitochondrial DNA. Mol. Biol. Evol. 18: 1168-1175.
27. LANDGREN, M., and K. GLIMELIUS, 1994 A high frequency of intergenomic mitochondrial recombination and an overall biased segregation of B. campestris or recombined B. campestris mitochondria were found in somatic hybrids made within Brassicaceae. Theor. Appl. Genet. 87: 854-862.
28. LAROCHE, J., P. LI, L. MAGGIA and J. BOUSQUET, 1997 Molecular evolution of angiosperm mitochondrial introns and exons. Proc. Natl. Acad. Sci. USA 94: 5722-5727.
29. LASER, B., S. MOHR, W. ODENBACH, G. OETTLER and U. KUECK, 1997 Parental and novel copies of the mitochondrial orf25 gene in the hybrid crop-plant triticale: predominant transcriptional expression of the maternal gene copy. Curr. Genet. 32: 337-347.
30. LUDWIG, J. A., and J. F. REYNOLDS, 1988 Statistical Ecology. Wiley-Interscience, New York.
31. LUNT, H. D., and C. B. HYMAN, 1997 Animal mitochondrial DNA recombination. Nature 387: 247.
32. MANLEY, S. A. M., 1972 The occurrence of hybrid swarms of red and black spruces in central New Brunswick. Can. J. For. Res. 2: 381-391.
33. MARSHALL, H. D., C. NEWTON and K. RITLAND, 2001 Sequence repeat polymorphisms exhibit the signature of recombination in lodgepole pine chloroplast DNA. Mol. Biol. Evol. 18: 2136-2138.
34. MAYNARD SMITH, J., 1999 The detection and measurement of recombination from sequence data. Genetics 153: 1021-1027.
35. MAYNARD SMITH, J., and N. H. SMITH, 1998 Detecting recombination from gene trees. Mol. Biol. Evol. 15: 590-599.
36. MCCAULEY, D. E., M. F. BAILEY, N. A. SHERMAN and M. Z. DARNELL, 2005 Evidence for paternal transmission and heteroplasmy in the mitochondrial genome of Silene vulgaris, a gynodioedious plant. Heredity 95: 50-58.
37. MITTON, J. B., B. R. KREISER and R. G. LATTA, 2000 Glacial refugia of limber pine (Pinus flexilis James) inferred from the population structure of mitochondrial DNA. Mol. Ecol. 9: 91-97.
38. MOGENSEN, H. L., 1996 The hows and whys of cytoplasmic inheritance in seed plants. Am. J. Bot. 83: 383-404.
39. MORTON, B. R., and M. T. CLEGG, 1993 A chloroplast DNA mutational hotspot and gene conversion in a noncoding region near rbcL in the grass family (Poaceae). Curr. Genet. 24: 357-365.
40. OWENS, J. N., and S. J. MORRIS, 1991 Cytological basis for cytoplasmic inheritance in Pseudotsuga menziesii. II. Fertilization and proembryo. Am. J. Bot. 78: 1515-1527.
41. PALMER, J. D., and L. A. HERBON, 1988 Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J. Mol. Evol. 28: 87-97.
42. PERRON, M., and J. BOUSQUET, 1997 Natural hybridization between black spruce and red spruce. Mol. Ecol. 6: 725-734.
43. PERRON, M., A. G. GORDON and J. BOUSQUET, 1995 Species-specific RAPD fingerprints for the closely related Picea mariana and P. rubens. Theor. Appl. Genet. 91: 142-149.
44. PERRON, M., D. J. PERRY, C. ANDALO and J. BOUSQUET, 2000 Evidence from sequence-tagged-site markers of a recent progenitor derivative species pair in conifers. Proc. Natl. Acad. Sci. USA 97: 11331-11336.
45. PERRY, D. J., and J. BOUSQUET, 1998 Sequence-tagged site (STS) markers of arbitrary genes: development, characterization and analysis of linkage in black spruce. Genetics 149: 1089-1098.
46. PERRY, D. J., and J. BOUSQUET, 2001 Genetic diversity and mating system of post-fire and post-harvest black spruce: an investigation using codominant sequence-tagged-site (STS) markers. Can. J. For. Res. 31: 32-40.
47. POLASHOCK, J. J., P. J BEDKER and B. I. HILLMAN, 1997 Movement of a small mitochondrial double-stranded RNA element of Cryphonectria parasitica: ascospore inheritance and implications for mitochondrial recombination. Mol. Gen. Genet. 256: 566-571.
48. POSADA, D., and K. A. CRANDALL, 2002 The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54: 396-402.
49. RAJORA, O. P., A.MOSSELER and J. E. MAJOR, 2000 Indicators of population viability in red spruce, Picea rubens. II. Genetic diversity, population structure and mating behaviour. Can. J. Bot. 78: 941-956.
50. RICHARDSON, B. A., S. J. BRUNSFELD and N. B. KLOPFENSTEIN, 2002 DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetics structure of whitebark pine (Pinus albicaulis). Mol. Ecol. 11: 215-227.
51. ROKAS, A., E. LADOUKAKIS and E. ZOUROS, 2003 Animal mitochondrial DNA recombination revisited. Trends Ecol. Evol. 18: 411-417.
52. SAVILLE, B. J., Y. KOHLI and J. B. ANDERSON, 1998 MtDNA recombination in a natural population. Proc. Natl. Acad. Sci. USA 95: 1331-1335.
53. SEMERIKOV, V. L., and M. LASCOUX, 2003 Nuclear and cytoplasmic variation within and between Eurasian Larix (Pinaceae) species. Am. J. Bot. 90: 1113-1123.
54. SENJO, M., K. KIMURA, Y. WATANO, K. UEDA and T. SHIMIZU, 1999 Extensive mitochondrial introgression from Pinus pumila to P. parviflora var. pentaphylla (Pinaceae). J. Plant Res. 112: 97-105.
55. SIGURGEIRSSON, A., and A. E. SZMIDT, 1993 Phylogenetic and biogeographic implications of chloroplast DNA variation in Picea. Nord. J. Bot. 13: 233-246.
56. SLATE, J., and H. PHUA, 2003 Patterns of linkage disequilibrium in mitochondrial DNA of 16 ruminant populations. Mol. Ecol. 12: 597-608.
57. SMALL, I. D., P. G. ISAAC and C. J. LEAVER, 1987 Stoichiometric differences in DNA molecules containing the atpA gene suggest mechanisms for the generation of mitochondrial genome diversity in maize. EMBO J. 6: 865-869.
58. SPERISEN, C., U. BUCHLER, F. GUGERLI, G. MATYAS, T. GEBUREK et al., 2001 Tandem repeats in plant mitochondrial genomes: application to the analysis of population differentiation in the conifer Norway spruce. Mol. Ecol. 10: 257-263.
59. STÄDLER, T., and L. F. DELPH, 2002 Ancient mitochondrial haplotypes and evidence for intragenic recombination in a gynodioecious plant. Proc. Natl. Acad. Sci. USA 99: 11730-11735.
60. TEMPLETON, A. R., and C. F. SING, 1993 A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analysis with cladogram uncertainty and recombination. Genetics 134: 659-669.
61. TOTH, B., Z. HAMARI, L. FERENCZY, J. VARGA and F. KEVEI, 1998 Recombination of mitochondrial DNA without selection pressure among compatible strains of the Aspergillus niger species aggregate. Curr. Genet. 33: 199-205.
62. TSAOUSIS, A. D., D. P. MARTIN, E. D. LADOUKAKIS, D. POSADA and E. ZOUROS, 2005 Widespread recombination in published animal mtDNA sequences. Mol. Biol. Evol. 22: 925-933.
63. VIERECK, L. A., and W. F. JOHNSTON, 1990 Black spruce, pp. 227-237 in Silvics of North America: Conifers, Vol. 1, edited by R.M. Burns and B. H. Honkala. U.S. Department of Agriculture,Washington, DC.
64. VIJVERBERG, K., and K. BACHMANN, 1999 Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phlogenetic analysis. Mol. Biol. Evol. 16: 1329-1340.
65. WAGNER, D. B., J. DONG, M. R. CARLSON and A. D. YANCHUK, 1991 Paternal leakage of mitochondrial DNA in Pinus. Theor. Appl. Genet. 82: 510-514.
66. WENG, C., and S. T. JACKSON, 2000 Species differentiation of North American spruce (Picea) based on morphological and anatomical characteristics of needles. Can. J. Bot. 78: 1367-1383.
67. WOLFE, A. D., and C. P. RANDLE, 2004 Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: implications for plant molecular systematics. Syst. Bot. 29: 1011-1020.
68. WRIGHT, J. W., 1955 Species crossability in spruce in relation to distribution and taxonomy. For. Sci. 1: 319-349.
69. XU, Y. S., M. G. K. JONES, A. KARP and E. PEHU, 1993 Analysis of the mitochondrial DNA of the somatic hybrids of Solanum brevidens and S. tuberosum using non-radioactive digoxigenin-labelled DNA probes. Theor. Appl. Genet. 8: 1017-1022.