The evolution of chloroplast genes and genomes in ferns

Plant Molecular Biology

Volumn 76, Issue 3-5, 2011, Pages 251-261

  Wolf, Paul G ^a   Der, Joshua P ^a   Duffy, Aaron M ^a   Davidson, Jacob B ^a   Grusz, Amanda L ^b   Pryer, Kathleen M ^b  

^a UTAH STATE UNIVERSITY   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

Inversion; Phylogeny; Plastid; Plastome; RNA editing; Substitution rates

Indexed keywords

CHLOROPLAST; CLASSIFICATION; FERN; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; PLANT GENE; REVIEW;

CHLOROPLASTS; EVOLUTION, MOLECULAR; FERNS; GENES, PLANT; PHYLOGENY;

FILICOPHYTA; SPERMATOPHYTA;

EID: 79957877560     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-010-9706-4     Document Type: Review

References (65)

1. Bell CD, Soltis DE, Soltis PS (2010) The age and diversification of the angiosperms re-revisited. Amer J Bot 97: 1296-1303.
2. Cai ZQ, Guisinger M, Kim HG, Ruck E, Blazier JC, McMurtry V, Kuehl JV, Boore J, Jansen RK (2008) Extensive reorganization of the plastid genome of Trifoliumsubterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. J Mol Evol 67: 696-704.
3. Chateigner-Boutin A-L, Small I (2007) A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res 35: e114.
4. Chevreux B, Wetter T, Suhai S (1999) Genome sequence assembly using trace signals and additional sequence information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB), pp 45-56.
5. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14: 1147-1159.
6. Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, Jansen RK (2006) The complete chloroplast genome sequence of Pelargonium x hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol 23: 2175-2190.
7. Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36: e122.
8. Cui LY, Leebens-Mack J, Wang LS, Tang JJ, Rymarquis L, Stern DB, de Pamphilis CW (2006) Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evol Biol 6: 13.
9. Darling AC, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394-1403.
10. Der JP (2010) Genomic perspectives on evolution in bracken fern. Dissertation, Utah State University.
11. Drouin G, Daoud H, Xia J (2008) Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Mol Phylogen Evol 49: 827-831.
12. Drummond AJ, Ashton B, Cheung M, Heled J, Kearse M, Moir R, Stones-Havas S, Thierer T, Wilson A (2007) Geneious v3. 0. BioMatters LTD.
13. Duffy AM, Kelchner SA, Wolf PG (2009) Conservation of selection on matK following an ancient loss of its flanking intron. Gene 438: 17-25.
14. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
15. Ems SC, Morden CW, Dixon CK, Wolfe KH, de Pamphilis CW, Palmer JD (1995) Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagusvirginiana. Plant Mol Biol 29: 721-733.
16. Funk HT, Berg S, Krupinska K, Maier UG, Krause K (2007) Complete DNA sequences of the plastid genomes of two parasitic flowering plant species Cuscuta reflexa and Cuscuta gronovii. BMC Plant Biol 7: 45.
17. Gao L, Yi X, Yang YX, Su YJ, Wang T (2009) Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol Biol 9: 130.
18. Goffinet B, Wickett NJ, Werner O, Ros RM, Shaw AJ, Cox CJ (2007) Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta). Ann Bot 99: 747-753.
19. Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH (2003) Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol Biol Evol 20: 1499-1505.
20. Grusz AL, Windham MD, Pryer KM (2009) Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae). Amer J Bot 96: 1636-1645.
21. Guisinger MM, Chumley TW, Kuehl JV, Boore JL, Jansen RK (2010) Implications of the plastid genome sequence of Typha (Typhaceae, Poales) for understanding genome evolution in Poaceae. J Mol Evol 70: 149-166.
22. Haberle RC, Fourcade HM, Boore JL, Jansen RK (2008) Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J Mol Evol 66: 350-361.
23. Jansen RK, Raubeson LA, Boore JL, de Pamphilis CW, Chumley TW et al (2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol 395: 348-384.
24. Karol KG, Arumuganathan K, Boore JL, Duffy AM, Everett KDE, et al. (2010) Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages. BMC Evol Biol (in press).
25. Korall P, Schuettpelz E, Pryer KM (2010) Abrupt deceleration of molecular evolution linked to the origin of arborescence in ferns. Evolution 64 (in press).
26. Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T, Yoshinaga K (2003) RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res 31: 2417-2423.
27. Lee HL, Jansen RK, Chumley TW, Kim KJ (2007) Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol 24: 1161-1180.
28. Liere K, Link G (1995) RNA-binding activity of the matK protein encoded by the chloroplast trnK intron from mustard (Sinapis-alba L.). Nucleic Acids Res 23: 917-921.
29. Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52: 267-274.
30. McCoy SR, Kuehl JV, Boore JL, Raubeson LA (2008) The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. BMC Evol Biol 8.
31. McNeal JR, Leebens-Mack JH, Arumuganathan K, Kuehl JV, Boore JL, De Pamphilis CW (2006) Using partial genomic fosmid libraries for sequencing complete organellar genomes. BioTechniques 41: 69-73.
32. Milligan BG, Hampton JN, Palmer JD (1989) Dispersed repeats and structural reorganization in subclover chloroplast DNA. Mol Biol Evol 6: 355-368.
33. Moore MJ, Dhingra A, Soltis PS, Shaw R, Farmerie WG, Folta KM, Soltis DE (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol 6: 17.
34. Muse SV (2000) Examining rates and patterns of nucleotide substitution in plants. Plant Mol Biol 42: 25-43.
35. Muse SV, Gaut BS (1997) Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test. Genetics 146: 393-399.
36. Nock CJ, Waters DL, Edwards MA, Bowen SG, Rice N, Cordeiro GM, Henry RJ (2010) Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnol J DOI: 10. 1111/j. 1467-7652. 2010. 00558. x.
37. Pryer KM, Schneider H, Smith AR, Cranfill R, Wolf PG, Hunt JS, Sipes SD (2001) Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409: 618-622.
38. Pryer KM, Schuettpelz E, Wolf PG, Schneider H, Smith AR, Cranfill R (2004) Phylogeny and evolution of ferns (monophylytes) with a focus on the early leptosporangiate divergences. Amer J Bot 91: 1582-1598.
39. Qiu YL, Dombrovska O, Lee J, Li LB, Whitlock BA et al (2005) Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. Int J Plant Sci 166: 815-842.
40. Qiu YL, Li LB, Wang B, Chen ZD, Dombrovska O et al (2007) A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes. Int J Plant Sci 168: 691-708.
41. Ratan A (2009) Assembly algorithms for next-generation sequence data. Dissertation, Pennsylvania State University.
42. Raubeson LA, Jansen RK (1992) Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255: 1697-1699.
43. Schneider H, Schuettpelz E, Pryer KM, Cranfill R, Magallion S, Lupia R (2004) Ferns diversified in the shadow of angiosperms. Nature 428: 553-557.
44. Schuettpelz E, Pryer KM (2006) Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns. Syst Biol 55: 485-502.
45. Schuettpelz E, Pryer KM (2007) Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes. Taxon 56: 1037-1050.
46. Smith AR, Tuomisto H, Pryer KM, Hunt JS, Wolf PG (2001) Metaxya lanosa, a second species in the genus and fern family Metaxyaceae. Syst Bot (in press).
47. Smith AR, Pryer KM, Schuettpelz E, Korall P, Schneider H, Wolf PG (2006) A classification for extant ferns. Taxon 55: 705-731.
48. Stern DB, Goldschmidt-Clermont M, Hanson MR (2010) Chloroplast RNA metabolism. Annu Rev Plant Biol 61: 125-155.
49. Sugiura M (2008) RNA editing in chloroplasts. In: Goringer HU (ed) RNA Editing. Nucleic Acids Mol Biol 20: 123-142.
50. Takenaka M, Merwe JA, Verbitskiy D, Neuwirt J, Zehrmann A, Brennicke A (2008) RNA editing in plant mitochondria. In: Göringer HU (ed) RNA editing. Nucleic Acids Mol Biol 20: 1-18.
51. Tillich M, Lehwark P, Morton BR, Maier UG (2006) The evolution of chloroplast RNA editing. Mol Biol Evol 23: 1912-1921.
52. Toor N, Hausner G, Zimmerly S (2001) Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7: 1142-1152.
53. Vogel J, Hubschmann T, Borner T, Hess WR (1997) Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: support for matK as an essential splice factor. J Mol Biol 270: 179-187.
54. Vogel J, Borner T, Hess WR (1999) Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants. Nucleic Acids Res 27: 3866-3874.
55. Wei FS, Stein JC, Liang CZ, Zhang JW, Fulton RS et al (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet 5: e1000728.
56. Wickett NJ, Zhang Y, Hansen SK, Roper JM, Kuehl JV et al (2008) Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneuramirabilis. Mol Biol Evol 25: 393-401.
57. Wolf PG, Rowe CA, Sinclair RB, Hasebe M (2003) Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Res 10: 59-65.
58. Wolf PG, Rowe CA, Hasebe M (2004) High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris. Gene 339: 89-97.
59. Wolf PG, Karol KG, Mandoli DF, Kuehl J, Arumuganathan K et al (2005) The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene 350: 117-128.
60. Wolf PG, Duffy AM, Roper JM (2009) Phylogenetic use of inversions in fern chloroplast genomes. Am Fern J 99: 132-134.
61. Wolf PG, Roper JM, Duffy AM (2010) The evolution of chloroplast genome structure in ferns. Genome 53: 731-738.
62. Wolfe KH, Morden CW, Palmer JD (1992) Functions and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc Natl Acad Sci USA 89: 10648-10652.
63. Yang ZH (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Optim Appl 13: 555-556.
64. Yatabe Y, Takamiya M, Murakami N (1998) Variation in the rbcL sequence of Stegnogramma pozoi subsp. mollissima (Thelypteridaceae) in Japan. J Plant Res 111: 557-564.
65. Zoschke R, Nakamura M, Liere K, Sugiura M, Börner T, Schmitz-Linneweber C (2010) An organellar maturase associates with multiple group II introns. Proc Natl Acad Sci USA 107: 3245-3250.