A scenario of mitochondrial genome evolution in maize based on rearrangement events

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Darracq, Aude ^a,b,c   Varré, Jean Stéphane ^b,c   Touzet, Pascal ^a  

^a CNRS   (France)

^b UNIV LILLE   (France)

^c INRIA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE DUPLICATION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC MODEL; GENETIC POLYMORPHISM; MAIZE; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENETICS; GENETICS; PLANT GENOME;

ANIMALIA; ZEA MAYS;

GENE DUPLICATION; GENOME, MITOCHONDRIAL; GENOME, PLANT; PHYLOGENY; ZEA MAYS;

EID: 77950685622     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-233     Document Type: Article

References (57)

1. Gray MW, Burger G, Lang BF. Mitochondrial Evolution. Science 1999, 283:1476-1481. 10.1126/science.283.5407.1476, 10066161.
2. Lynch M, Koskella B, Schaack S. Mutation Pressure and the Evolution of Organelle Genomic Architecture. Science 2006, 311:1727-1730. 10.1126/science.1118884, 16556832.
3. Boore JL. Animal mitochondrial genomes. Nucleic Acids Res 1999, 27(8):1767-1780. 10.1093/nar/27.8.1767, 148383, 10101183.
4. Boore JL. The use of genome-level characters for phylogenetic reconstruction. Trends Ecol Evol 2006, 21(8):439-446. 10.1016/j.tree.2006.05.009, 16762445.
5. Segawa RD, Aotsuka T. The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): Evidence for its evolution via gene duplication. Gene 2005, 355:28-39. 10.1016/j.gene.2005.05.020, 16039805.
6. Lavrov DV, Boore JL, Brown WM. Complete mtdna sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and nonrandom loss. Mol Biol Evol 2002, 19:163-169.
7. Wang X, Lavrov DV. Mitochondrial Genome of the Homoscleromorph Oscarella carmela (Porifera, Demospongiae) Reveals Unexpected Complexity in the Common Ancestor of Sponges and Other Animals. Mol Biol Evol 2007, 24(2):363-373. 10.1093/molbev/msl167, 17090697.
8. Inoue JG, Miya M, Tsukamoto K, Nishida M. Evolution of the Deep-Sea Gulper Eel Mitochondrial Genomes: Large-Scale Gene Rearrangements Originated Within the Eels. Mol Biol Evol 2003, 20(11):1917-1924. 10.1093/molbev/msg206, 12949142.
9. Lockridge Mueller R, Boore JL. Molecular Mechanisms of Extensive Mitochondrial Gene Rearrangement in Plethodontid Salamanders. Mol Biol Evol 2005, 22(10):2104-2112. 10.1093/molbev/msi204, 15987876.
10. Perseke M, Fritzsch G, Ramsch K, Bernt M, Merkle D, Middendorf M, Bernhard D, Stadler PF, Schlegel M. Evolution of mitochondrial gene orders in echinoderms. Mol Phylogenet Evol 2008, 47(2):855-864. 10.1016/j.ympev.2007.11.034, 18280182.
11. Palmer JD, Herbon LA. Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence. J Mol Evol 1988, 28(1):87-97. 10.1007/BF02143500, 3148746.
12. Lonsdale DM, Hodge TP, Fauron CMR. The physical map and organisation of the mitochondrial genome from the fertile cytoplasm of maize. Nucleic Acids Res 1984, 12(24):9249-9261. 10.1093/nar/12.24.9249, 320458, 6096824.
13. Fauron CMR, Casper M. A Second Type of Normal Maize Mitochondrial Genome: An Evolutionary Link. Genetics 1994, 137:875-882. 1206047, 8088531.
14. Kubo T, Newton KJ. Angiosperm mitochondrial genomes and mutations. Mitochondrion 2008, 8(1):5-14. 10.1016/j.mito.2007.10.006, 18065297.
15. Knoop V. The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr Genet 2004, 46:123-139. 10.1007/s00294-004-0522-8, 15300404.
16. Sankoff D, Leduc G, Antoine N, Paquin B, Lang B, Cedergren R. Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences 1992, 89:6575-6579.
17. Hannenhalli S, Pevzner P. Transforming men into mice (polynomial algorithm for genomic distance problem). proceedings of the 36th Annual Symposium on Foundations of Computer Science (FOCS'95) 1995, 581-592.
18. Bourque G, Pevzner PA. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res 2002, 12(1):26-36. 155248, 11779828.
19. Moret B, Tang J, Wang L, Warnow T. Steps toward accurate reconstruction of phylogenies from gene-order data. J Comput Syst Sci 2002, 65(3):508-525.
20. Sankoff D. Genome rearrangement with gene families. Bioinformatics 1999, 15(11):909-917. 10.1093/bioinformatics/15.11.909, 10743557.
21. Chen X, Zheng J, Fu Z, Nan P, Zhong Y, Lonardi S, Jiang T. Assignment of orthologous genes via genome rearrangement. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2005, 2(4):302-315.
22. Chauve C, Doyon J, El-Mabrouk N. Gene family evolution by duplication, speciation, and loss. Journal of Computational Biology 2008, 15(8):1043-1062. 10.1089/cmb.2008.0054, 18781833.
23. Gordon JL, Byrne KP, Wolfe KH. Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome. PLoS Genetics 2009, 5(5):e1000485. 10.1371/journal.pgen.1000485, 2675101, 19436716.
24. Allen JO, Fauron CM, Minx P, , et al. (16 co-authors) Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics 2007, 177:1173-1192. 10.1534/genetics.107.073312, 2034622, 17660568, (16 co-authors).
25. Tang J, Moret BME. Phylogenetic reconstruction from gene-rearrangement data with unequal gene content. Lecture Notes in Computer Science vol 2748 8th International Workshop on Algorithms and Data Structures (WABI 2003) 2003, 37-46.
26. Bernt M, Merkle D, Ramsch K, Fritzsch G, Perseke M, Detlef B, Schlegel M, Stadler P, Middendorf M. CREx: inferring genomic rearrangements based on common intervals. Bioinformatics 2007, 23(21):2957-2958. 10.1093/bioinformatics/btm468, 17895271.
27. Pring DR, Levings III CS. Heterogeneity of maize cytoplasmic genomes among male-sterile cytoplasms. Genetics 1978, 89:121-136. 1213822, 17248823.
28. Doebley J, Renfroe W, Blanton A. Restriction Site Variation in the Zea Chloroplast Genome. Genetics 1987, 117:139-147. 1203182, 17246395.
29. Fénart S, Touzet P, Arnaud JF, Cuguen J. Emergence of gynodioecy in wild beet (Beta vulgaris ssp. maritima L.): a genealogical approach using chloroplastic nucleotide sequences. Proc R Soc Lond B Biol Sci 2006, 273:1391-1398.
30. Satoh M, Kubo T, Nishizawa S, Estiati A, Itchoda N, Mikami T. The cytoplasmic male-sterile type and normal type mitochondrial genomes of sugar beet share the same complement of genes of known function but differ in the content of expressed ORFs. Mol Genet Genomics 2004, 272(3):247-256. 10.1007/s00438-004-1058-9, 15340837.
31. Doebley J. The Genetics Of Maize Evolution. Annu Rev Gene 2004, 38:37-59.
32. Stanton DJ, Daehler LL, Moritz CC, Brown WM. Sequences With the Potential to Form Stem-and-Loop Structures Are Associated With Coding-Region Duplications in Animal Mitochondrial DNA. Genetics 1994, 137:233-241. 1205940, 8056313.
33. Fujita MK, Boore JL, Moritz C. Multiple Origins and Rapid Evolution of Duplicated Mitochondrial Genes in Parthenogenetic Geckos (Heteronotia binoei; Squamata, Gekkonidae). Mol Biol Evol 2007, 24:2775-2786. 10.1093/molbev/msm212, 17921488.
34. San Mauro D, Gower DJ, Zardoya R, Wilkinson M. A Hotspot of Gene Order Rearrangement by Tandem Duplication and Random Loss in the Vertebrate Mitochondrial Genome. Mol Biol Evol 2006, 23(1):227-234. 10.1093/molbev/msj025, 16177229.
35. Carapelli A, Vannini L, Nardi F, Boore JL, Beani L, Dallai R, Frati F. The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera). Gene 2006, 376:248-259. 10.1016/j.gene.2006.04.005, 16766140.
36. Vallès Y, Boore JL. Lophotrochozoan mitochondrial genomes. Integr Comp Biol 2005, 46(4):544-557.
37. Grande C, Templado J, Zardoya R. Evolution of gastropod mitochondrial genome arrangements. BMC Evolutionary Biology 2008, 8:61-75. 10.1186/1471-2148-8-61, 2291457, 18302768.
38. Yu Z, Wei Z, Kong X, Shi W. Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of Tandem duplication-random loss for genome rearrangement in Crassostrea?. BMC Genomics 2008, 9:477-489. 10.1186/1471-2164-9-477, 2576254, 18847502.
39. Small I, Suffolk R, Leaver CJ. Evolution of plant mitochondrial genomes via substoichiometric intermediates. Cell 1989, 58(1):69-76. 10.1016/0092-8674(89)90403-0, 2752423.
40. Leblanc C, Boyen C, Richard O, Bonnard G, Grienenberger JM, Kloareg B. Complete Sequence of the Mitochondrial DNA of the Rhodophyte Chondrus crispus (Gigartinales). Gene Content and Genome Organization. J Mol Biol 1995, 250:484-495. 10.1006/jmbi.1995.0392, 7616569.
41. Burger G, Plante I, Lonergan KM, Gray MW. The Mitochondrial DNA of the Amoeboid Protozoon, Acanthamoeba castellanii: Complete Sequence, Gene Content and Genome Organization. J Mol Evol 1995, 245:522-537.
42. Signorovitch AY, Buss LW, Dellaporta SL. Comparative Genomics of Large Mitochondria in Placozoans. PLoS Genetics 2007, 3(1):44-50.
43. Darling AC, Mau B, Blatter FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14(7):1394-1403. 10.1101/gr.2289704, 442156, 15231754.
44. Noe L, Kucherov G. YASS: enhancing the sensitivity of dna similarity search. Nucleic Acids Res 2005, 33(2):W540-W543. 10.1093/nar/gki478, 1160238, 15980530.
45. Uno T, Yagiura M. Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 2000, 26(2):290-309.
46. Luc N, Risler JL, Bergeron A, Raffinot M. Gene teams: a new formalization of gene clusters for comparative genomics. Comp Biol Chemistry 2003, 27(1):59-67.
47. Watterson G, Ewens W, Hall T, Morgan A. The chromosome inversion problem. J Theor Biol 1982, 99:1-7.
48. Blanchette M, Bourque G, Sankoff D. Breakpoint phylogenies. Proceedings of the 8th Genome Informatics Workshop (GIW 1997) 1997, 25-34. University Academy Press. Tokyo.
49. Sankoff D, Bryant D, Deneault M, Lang F, Burger G. Early Eukaryote Evolution Based on Mitochondrial Gene Order Breakpoints. J Comput Biol 2000, 7(3-4):521-535. 10.1089/106652700750050925, 11108477.
50. Wang LS, Warnow T, Moret BME, Jansen RK, Raubeson LA. Distance-Based Genome Rearrangement Phylogeny. J Mol Evol 2006, 63(4):473-483. 10.1007/s00239-005-0216-y, 17021931.
51. Bader DA, Moret BME, Yan M. A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study. J Comput Biol 2001, 8(5):483-491. 10.1089/106652701753216503, 11694179.
52. Tesler G. GRIMM: genome rearrangements web server. Bioinformatics 2002, 18(3):492-493. 10.1093/bioinformatics/18.3.492, 11934753.
53. Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 1997, 14:685-695.
54. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504. 10.1093/bioinformatics/18.3.502, 11934758.
55. Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 1985, 22(2):160-174. 10.1007/BF02101694, 3934395.
56. Quenouille MH. Notes on bias in estimation. Biometrika 1956, 43:353-360.
57. Tukey JW. Bias and confidence in not quite large samples (Abstract). Annals of Mathematical Statistics 1958, 29:614.