Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure

Plant Ecology and Evolution

Volumn 144, Issue 1, 2011, Pages 29-43

  Forrest, Laura L ^a   Wickett, Norman J ^b   Cox, Cymon J ^c   Goffinet, Bernard ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF ALGARVE   (Portugal)

Author keywords

454 technology; Chloroplast; Liverwort; Next generation sequencing; Plastid genome; Plastome; Ptilidium

Indexed keywords

BRYOPHYTA; BRYOPHYTES; EMBRYOPHYTA; MARCHANTIA; MARCHANTIOPHYTA; PTILIDIACEAE; PTILIDIUM; PTILIDIUM PULCHERRIMUM;

EID: 79955744844     PISSN: 20323913     EISSN: 20323921     Source Type: Journal    
DOI: 10.5091/plecevo.2011.535     Document Type: Article

References (98)

1. Barthet M.M., Hilu K.W. (2007) Expression of matK: functional and evolutionary implications. American Journal of Botany 94: 1402-1412. DOI: 10.3732%2Fajb.94.8.1402
2. Bidartondo M.I. (2005) The evolutionary ecology of myco-heterotrophy. New Phytologist 167: 335-352. DOI: 10.1111/j.1469-8137.2005.01429.x
3. Brundrett M.C. (2002) Coevolution of roots and mycorrhizas of land plants. New Phytologist 154: 275-304. DOI: 10.1046/j.1469-8137.2002.00397.x
4. Castoe T.A., Poole A.W., Gu W., de Koning A.P.J., Daza J.M., Smith E.N., Pollock D.D. (2010) Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun sequencing. Molecular Ecology Resources 10: 341-347. DOI: 10.1111/j.1755-0998.2009.02750.x
5. 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) 99: 45-56. [available at http://www.bioinfo.de/isb/gcb99/talks/chevreux/]
6. Cosner M.E., Raubeson L.A., Jansen R.K. (2004) Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evolutionary Biology 2004, 4: 27. DOI: 10.1186%2F1471-2148-4-27
7. Cronn R., Liston A., Parks M., Gernandt D.S., Shen R., Mockler, T. (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Research 36: e122. DOI: 10.1093/nar/gkn502
8. Cui L., Leebens-Mack J., Wang L.-S., Tang J., Rymarquis L., Stern D.B., dePamphilis C.W. (2006) Adaptive evolution of chloroplast genome structure inferred using a parametric boot-strap approach. BMC Evolutionary Biology 2006, 6: 13. DOI: 10.1186/1471-2148-6-13
9. Donaher N., Tanifuji G., Onodera N.T., Malfatti S.A., Chain P.S.G., Hara Y., Archibald J.M. (2009) The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biology and Evolution 1: 439-448. DOI: 10.1093/gbe/evp047
10. Drescher A., Ruf S., Calsa T. Jr, Carrer H., Bock. R. (2000) The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. The Plant Journal 22: 97-104. DOI: 10.1046/j.1365-313x.2000.00722.x
11. Faircloth B.C. (2008) MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8: 92-94. DOI: 10.1111/j.1471-8286.2007.01884.x
12. Fiz O., Vargas P., Alarcón M., Aedo C., García J.L., Aldasoro J.J. (2008) Phylogeny and historical biogeography of Geraniacae in relation to climate changes and pollination ecology. Systematic Botany 33: 326-342. DOI: 10.1600/036364408784571482
13. Forrest L.L., Crandall-Stotler B.J. (2005) Progress towards a robust phylogeny for the liverworts, with particular focus on the simple thalloids. Journal of the Hattori Botanical Laboratory 97: 127-159.
14. Forrest L.L., Davis E.C., Long D.G., Crandall-Stotler B.J., Hollingsworth, M.L., Clark A. (2006) Unravelling the evolutionary history of the liverworts (Marchantiophyta)-multiple taxa, genomes and analyses. The Bryologist 109: 303-334. DOI: 10.1639/0007-2745(2006)109[303:UTEHOT]2.0.CO;2
15. Freyer R., Kiefer-Meyer M.C., Kössel H. (1997) Occurrence of plastid RNA editing in all major lineages of land plants. Proceedings of the National Academy of Sciences of the USA 94: 6285-6290. DOI: http://dx.doi.org/10.1073/pnas.94.12.6285
16. Gao L., Yi X., Yang Y.-X., Su Y.-J., Wang T. (2009) Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evolutionary Biology 2009, 9: 130. DOI: 10.1186/1471-2148-9-130
17. Glime J.M. (2007) Bryophyte Ecology. Volume 1. Physiological Ecology. Ebook sponsored by Michigan Technological University and the International Association of Bryologists. Available from http://www.bryoecol.mtu.edu/ [accessed 7 Sep. 2010]
18. Goffinet B., Wickett N.J., Shaw A.J., Cox C.J. (2005) Phylogenetic significance of the rpoA loss in the chloroplast genome of mosses. Taxon 54: 353-360. DOI: 10.2307/25065363
19. Goffinet B., Wickett N.J., Werner O., Ros R.M., Shaw A.J., Cox C.J. (2007) Distribution and phylogenetic significance of the 71 kb inversion in the chloroplast genome in the Funariidae (Bryophyta). Annals of Botany 99: 747-753. DOI: 10.1093/ aob/mcm010
20. Goremykin V., Hirsch-Ernst K.I., Wölfl S., Hellwig F.H. (2003) The chloroplast genome of the "basal" angiosperm Calycanthus fertilis-structure and phylogenetic analyses. Plant Systematics and Evolution 242: 119-135. DOI: 10.1007/s00606-003-0056-4
21. Guisinger M.M., Kuehl J.V., Boore J.L., Jansen R.K. (2010) Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Molecular Biology and Evolution Advance Access 28: 583-600. DOI: 10.1093/molbev/msq229
22. Haberle R.C., Fourcade H.M., Boore J.L., Jansen R.K. (2008) Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. Journal of Molecular Evolution 66: 350-361. DOI: 10.1007/ s00239-008-9086-4
23. Heinrichs J., Gradstein S.R., Wilson R., Schneider H. (2005) Towards a natural classification of liverworts (Marchantiophyta) based on the chloroplast gene rbcL. Cryptogamie, Bryologie 26: 131-150.
24. Heinrichs J., Hentschel J., Wilson R., Feldberg K., Schneider H. (2007) Evolution of leafy liverworts (Jungermanniidae, Marchantiophyta): estimating divergence times from chloroplast DNA sequences using penalized likelihood with integrated fossil evidence. Taxon 56: 31-44. [available at http://www.ingentaconnect.com/content/iapt/tax/2007/00000056/00000001/art00004]
25. Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., Mori M., Kondo C., Honji Y., Sun C.-R., Meng B.-Y., Li Y.-Q., Kanno A., Nishizawa Y., Hirai A., Shinozaki K., Sugiura M. (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of cereals. Molecular and General Genetics 217: 185-194. DOI: 10.1007/BF02464880
26. Hollingsworth P.M., Forrest L.L., Spouge J.L., Hajibabaei M., Ratnasingham S., van der Bank M., Chase M.W., Cowan R.S., Erickson D.L., Fazekas A.J., Graham S.W., James K.E., Kim K.-J., Kress W.J., Schneider H., van AlphenStahl J., Barrett S.C.H., van den Berg C., Bogarin D., Burgess K.S., Cameron K.M., Carine M., Chacón J., Clark A., Clarkson J.J., Conrad F., Devey D.S., Ford C.S., Hedderson T.A.J., Hollingsworth M.L., Husband B.C., Kelly L.J., Kesanakurti P.R., Kim J.S., Kim Y.-D., Lahaye R., Lee H.-L., Long D.G., Madriñán S., Maurin O., Meusnier I., Newmaster S.G., Park C.-W., Percy D.M., Petersen G., Richardson J.E., Salazar G.A., Savolainen V., Seberg O., Wilkinson M.J., Yi D.-K., Little D.P. (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the USA 106: 12794-12797. DOI: 10.1073/pnas.0905845106
27. Huang X., Madan A. (1999) CAP3: A DNA sequence assembly program. Genome Research 9: 868-877. DOI: 10.1101/gr.9.9.868
28. Jansen R.K., Palmer J.D. (1987) A chloroplast DNA inversion marks an ancient split in the sunflower family Asteraceae. Proceedings of the National Academy of Sciences of the USA 84: 5818-5822. DOI: 10.1073/pnas.84.16.5818
29. Kallas T., Spiller S., Malkin R. (1988) Primary structure of cotranscribed genes encoding the Rieske Fe-S and cytochrome f proteins of the cyanobacterium Nostoc PCC 7906. Proceedings of the National Academy of Sciences of the USA 85: 5794-5798. DOI: 10.1073/pnas.85.16.5794
30. Kelch D.G., Driskell A., Mishler B.D. (2004) Inferring phylogeny using genomic characters: a case study using land plant plastomes. Monographs in Systematic Botany from the Missouri Botanical Garden 68: 3-12.
31. Knoop V. (2004) The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Current Genetics 46: 123-139. DOI: 10.1007/s00294-004-0522-8
32. Knoop V. (2010) Looking for sense in the nonsense: a short review of non-coding organellar DNA elucidating the phylogeny of bryophytes. Tropical Bryology 31: 51-60. [available at http://tropical-bryology.org/online/V31_35]
33. Kugita M., Kaneko A., Yamamoto Y., Takeya Y., Matsumoto T., Yoshinaga K. (2003) The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants. Nucleic Acids Research 31: 716-721. DOI: 10.1093/nar/gkg155
34. Kumar A., Bennetzen J.L. (1999) Plant retrotransposons. Annual Review of Genetics 33: 479-532. DOI: 10.1146/annurev. genet.33.1.479
35. Kurtz S., Schleiermacher C. (1999) REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics 15: 426-427. DOI: 10.1093/bioinformatics/15.5.426
36. Lee H.L., Jansen R.K., Chumley T.W., Kim K.-J. (2007) Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Molecular Biology and Evolution 24: 1161-1180. DOI: 10.1093/molbev/ msm036
37. Li L., Wang B., Liu Y., Qiu Y.L. (2009) The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. Journal of Molecular Evolution 68: 665-678. DOI: 10.1007/s00239-009-9240-7
38. Li W., Zhang P., Fellers J.P., Friebe B., Gill B.S. (2004) Sequence composition, organization, and evolution of the core Triticeae genome. The Plant Journal 40: 500-11. DOI: 10.1111/j.1365-313X.2004.02228.x
39. 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. Current Genetics 52: 267-274. DOI: 10.1007/s00294-007-0161-y
40. Magain N., Forrest L.L., Sérusiaux E., Goffinet B. (publ. online 2010) Microsatellite primers in the Peltigera dolichorhiza complex (lichenized ascomycete, Peltigerales). American Journal of Botany. DOI: 10.3732/ajb.1000283
41. Maier R.M., Neckermann K., Igloi G.L., Kössel H. (1995) Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. Journal of Molecular Biology 251: 614-628. DOI: 10.1006/jmbi.1995.0460
42. Marco A., Marín I. (2005) Retrovirus-like elements in plants. Recent Research Developments in Plant Science 3: 15-24. [available at http://www.uv.es/genomica/spa/PDF/27.pdf]
43. Maul J.E., Lilly J.W., Cui L., dePamphilis C.W., Miller W., Harris E.H., Stern D.B. (2002) The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. The Plant Cell 14: 2659-2679. DOI: 10.1105/tpc.006155
44. McNeal J.R., Leebens-Mack J.H., Arumuganathan K., Kuehl J.V., Boore J.L., dePamphilis C.W. (2006) Using partial genomic fosmid libraries for sequencing complete organellar genomes. BioTechniques 41: 69-73. DOI: 10.2144/000112202
45. Milligan B.G., Hampton J.N., Palmer J.D. (1989) Dispersed repeats and structural reorganization in subclover chloroplast DNA. Molecular Biology and Evolution 6: 355-368. [available at http://mbe.oxfordjournals.org/content/6/4/355.full.pdf]
46. Mishler B.D., Kelch D.G. (2009) Phylogenomics and early land plant evolution. In: Goffinet B., Shaw A.J. (eds) Bryophyte Biology (Ed. 2): 173-197. Cambridge, Cambridge University Press.
47. Monde R.A., Schuster G., Stern D.B. (2000) Processing and degradation of chloroplast mRNA. Biochimie 82: 573-582. DOI: 10.1016/S0300-9084%2800%2900606-4
48. Moore M.J., Dhingra A., Soltis P.S., Shaw R., Farmerie W.G., Folta K.M., Soltis D.E. (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biology 2006, 6: 17. DOI: 10.1186/1471-2229-6-17
49. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., Copley R., Courcelle E., Das U., Daugherty L., Dibley M., Finn R., Fleischmann W., Gough J., Haft D., Hulo N., Hunter S., Kahn D., Kanapin A., Kejariwal A., Labarga A., Langendijk-Genevaux P.S., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McAnulla C., McDowall J., Mistry J., Mitchell A., Nikolskaya A.N., Orchard S., Orengo C., Petryszak R., Selengut J.D., Sigrist C.J.A., Thomas P.D., Valentin F., Wilson D., Wu C.H., Yeats C. (2007) New developments in the InterPro database. Nucleic Acids Research 35: D224-D228. DOI: 10.1093/nar/gkl841
50. Nawrocki E.P., Kolbe D.L., Eddy S.R. (2009) Infernal 1.0: Inference of RNA alignments. Bioinformatics 25: 1335-1337. DOI: 10.1093/bioinformatics/btp157
51. Oda K., Yamato K., Ohta E., Nakamura Y., Takemura M., Nozato N., Akashi K., Kanegae T., Ogura Y., Kohchi T., Ohyama K. (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA-a primitive form of plant mitochondrial genome. Journal of Molecular Biology 223: 1-7. DOI: 10.1016/0022-2836%2892%2990708-R
52. Ohyama K., Fukuzawa H., Kohchi T., Sano T., Shirai H., Umesono K., Shiki Y., Takeuchi M., Chang Z, Atoa S.I., Inokuchi H., Ozeki H. (1988) Structure and organization of Marchantia polymorpha chloroplast genome. I. Cloning and gene identification. Journal of Molecular Biology 203: 281-298. DOI: 10.1016/0022-2836%2888%2990001-0
53. Ohyama K., Fukuzawa H., Kohchi T., Shirai H., Sano T., Sano S., Umesono K., Shiki Y., Takeuchi M., Chang Z., Aota S.-I., Inokuchi H., Ozeki H. (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322: 572-574. DOI: 10.1038/322572a0
54. Oliver M.J., Murdock A.G., Mishler B.D., Kuehl J.V., Boore J.L., Mandoli D.F., Everett K.D.E., Wolf P.G., Duffy A.M., Karol K.G. (2010) Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural rearrangement relative to other green plant chloroplast genomes. BMC Genomics 11: 143. DOI: 10.1186/1471-2164-11-143
55. Pyke K. (2009) Plastid Biology. Cambridge, U.K., Cambridge University Press.
56. Qiu Y.-L., Li L., Wang B., Chen Z., Knoop V., Groth-Malonek M., Dombrovska O., Lee J., Kent L., Rest J., Estabrook G.F., Hendry T.A., Taylor D.W., Testa C.M., Ambros M., Crandall-Stotler B., Duff R.J., Stech M., Frey W., Quandt D., Davis C.C. (2006) The deepest divergences in land plants inferred from phylogenomic evidence. Proceedings of the National Academy of Sciences of the USA 103: 15511-15516. DOI: 10.1073/ pnas.0603335103
57. Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. (2005) InterProScan: protein domains identifier. Nucleic Acids Research 33: W116-W120. DOI: 10.1093/nar/gki442
58. Raubeson L.A., Jansen R.K. (1992) Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255: 1697-1699. DOI: 10.1126/science.255.5052.1697
59. Raubeson L.A., Jansen R.K. (2005) Chloroplast genomes of plants. In: Henry R.J. (ed) Plant diversity and evolution: genotypic and phenotypic variation in higher plants: 45-68. Wallingford, UK, CAB International.
60. Raubeson L.A., Peery R., Chumley T.W., Dziubek C., Fourcade H.M., Boore J.L., Jansen R.K. (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 2007, 8: 174. DOI: 10.1186/1471-2164-8-174
61. Ravi V., Khurana J.P., Tyagi A.K., Khurana P. (2006) The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis. Tree Genetics and Genomes 3: 49-59. DOI: 10.1007/s11295-006-0051-3
62. Read, D.J., Duckett J.D., Francis R., Ligrone R., Russell A. (2000) Symbiotic fungal associations in 'lower' land plants. Philosophical Transactions of the Royal Society of London Ser. B. 355: 815-830. DOI: 10.1098/rstb.2000.0617
63. Rensing S.A., Lang D., Zimmer A.D., Terry A., Salamov A., Shapiro H., Nishiyama T., Perroud P.-F., Lindquist E.A., Kamisugi Y., Tanahashi T., Sakakibara K., Fujita T., Oishi K., Shin I T., Kuroki Y., Toyoda A., Suzuki Y., Hashimoto S.-I., Yamaguchi K., Sugano S., Kohara Y., Fjiyama A., Anterola A., Aoki S., Ashton N., Barbazuk W.B., Barker E., Bennetzen J.L., Blankenship R., Cho S.H., Dutcher, S.K. Estelle M., Fawcett J.A., Gundlach H., Hanada K., Heyl A., Hicks K.A., Hughes J., Lohr M., Mayer K., Melkozernov A., Murata T., Nelson D.R., Pils B., Prigge M., Reiss B., Renner T., Rombauts S., Rushton P.J., Sanderfoot A., Schween G., Shiu S.-H., Stueber K., Theodoulou F.L., Tu H., Van de Peer Y., Verrier P.J., Waters E., Wood A., Yang L., Cove D., Cuming A.C., Hasebe M., Lucas S., Mishler B.D., Reski R., Grigoriev I.V., Quatrano, R.S., Boore J.L. (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69. DOI: 10.1126/science.1150646
64. Roquet C., Sanmartín I., Garcia-Jacas N., Sáez L., Susanna A., Wikström N., Aldasoro J.J. (2009) Reconstructing the history of Campanulaceae with a Bayesian approach to molecular dating and dispersal-vicariance analyses. Molecular Phylogenetics and Evolution 52: 575-587. DOI: 10.1016/j.ympev.2009.05.014
65. Rozen S., Skaletsky H.J. (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S., Misener S. (eds) Bioinformatics methods and protocols: methods in molecular biology: 365-386. Totowa, NJ, Humana Press.
66. SanMiguel P., Bennetzen J.L. (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Annals of Botany 82(Suppl. A): 37-44. DOI: 10.1006/anbo.1998.0746
67. Schmitz-Linneweber C., Barkan A. (2007) RNA splicing and RNA editing in chloroplasts. In: Bock R. (ed.) Topics in current genetics 19: cell and molecular biology of plastids: 213-248. Berlin, Springer-Verlag.
68. Schmuths H., Meister A., Horres R., Bachmann K. (2004) Genome size variation among accessions of Arabidopsis thaliana. Annals of Botany 93: 317-321. DOI: 10.1093/aob/mch037
69. Schuster R.M. (1966) Ptilidium. In: Schuster R.M. (ed.) (1966-1993) Hepaticae and Anthocerotae of North America East of the Hundredth Meridian. Vol. 1: 760-780. New York, Columbia University Press.
70. Schuster R.M. (1992) The Hepaticae and Anthocerotae of North America, Vol. V. Chicago IL., Field Museum of Natural History.
71. Schween G., Gorr G., Hohe A., Reski R. (2003) Unique tissue-specific cell cycle in Physcomitrella. Plant Biology 5: 50-58. DOI: 10.1055/s-2003-37984
72. Squirrell J., Hollingsworth P.M., Woodhead M., Russell J., Lowe A., Gibby M., Powell W. (2003) How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology 12: 1339-1348. DOI: 10.1046/j.1365-294X.2003.01825.x
73. Stein D.B., Conant D.S., Ahearn M.E., Jordan E.T., Kirch S.A., Hasebe M., Iwatsuki K., Tan M.K., Thomson J.A. (1992) Structural rearrangements of the chloroplast genome provide and important phylogenetic link in ferns. Proceedings of the National Academy of Sciences of the USA 89: 1856-1860. DOI: 10.1073/pnas.89.5.1856
74. Stenøien H.K. (2008) Slow molecular evolution in 18S rDNA, rbcL and nad5 genes of mosses compared with higher plants. Journal of Evolutionary Biology 21: 566-571. DOI: 10.1111/j.1420-9101.2007.01479.x
75. Stern D.B., Goldschmidt-Clermont M., Hanson M.R. (2010) Chloroplast RNA metabolism. Annual Review of Plant Biology 61L: 125-155. DOI: 10.1146/annurev-arplant-042809-112242
76. Sugita M., Sugiura C., Arkkawa T., Higuchi M. (2004) Molecular evidence of an rpoA gene in the basal moss chloroplast genomes: rpoA is a useful marker for phylogenetic analysis of mosses. Hikobia 14: 171-175.
77. Sugiura C., Kobayashi Y., Aoki S., Sugita C., Sugita M. (2003) Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucleic Acids Research 31: 5324-5331. DOI: 10.1093/nar/gkg726
78. Tangphatsornruang S., Sangsrakru D., Chanprasert J., Uthaipaisanwong, P., Yoocha T., Jomchai N., Tragoonrung S. (2010) The chloroplast genome sequence of mungbean (Vinga radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Research 17: 11-22. DOI: 10.1093/dnares/dsp025
79. Temsch E.M., Greilhuber J., Krisai R. (2010) Genome size in liverworts. Preslia 82: 63-80.
80. Terasawa K., Odahara M., Kabeya Y., Kikugawa T., Sekine Y., Fujiwara, M., Sato N. (2006) The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Molecular Biology and Evolution 24: 699-709. DOI: 10.1093/molbev/msl198
81. The InterPro Consortium (Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D.R., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J.A., Zdobnov E.M.) (1999) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29: 37-40. DOI: 10.1093/nar/29.1.37
82. Tsuji S., Ueda K., Nishiyama T., Hasebe M., Yoshikawa S., Konagaya A., Nishiuchi T., Yamaguchi K. (2007) The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses. Journal of Plant Research 120: 281-290. DOI: 10.1007/ s10265-006-0055-y
83. Van Aller Hernick L., Landing E., Bartowski K.E. (2008) Earth's oldest liverworts-Metzgeriothallus sharonae sp. nov. from the Middle Devonian (Givetian) of Eastern New York. Review of Palaeobotany & Palynology 148: 154-162. DOI: 10.1016/j. revpalbo.2007.09.002
84. von Konrat M., Söderströmm L., Renner M.A.M., Hagborg A., Briscoe L., Engel J.J. (2010) Early Land Plants Today (ELPT): how many liverwort species are there? Phytotaxa 9: 22-40. [available at http://www.mapress.com/phytotaxa/taxa/Bryophytes.htm]
85. Wahrmund U., Groth-Malonek M., Knoop V. (2008) Tracing plant mitochondrial DNA evolution: rearrangements of the ancient mitochondrial gene cluster trnA-trnT-nad7 in liverwort phylogeny. Journal of Molecular Evolution 66: 621-629. DOI: 10.1007/s00239-008-9114-4
86. Wang B., Xue J., Li L., Qiu Y.-L. (2009) The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts. Current Genetics 55: 601-609. DOI: 10.1007/ s00294-009-0273-7
87. Wicker T., Schlagenhauf E., Graner A., Close T.J., Keller B., Stein N. (2006) 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7: 275. DOI: 10.1186/1471-2164-7-275
88. Wickett N.J., Fan Y., Lewis P.O., Goffinet B. (2008a) Distribution and evolution of pseudogenes, gene losses and a gene rearrangement in the plastid genome of the non-photosynthetic liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida). Journal of Molecular Evolution 67: 111-122. DOI: 10.1007/ s00239-008-9133-1
89. Wickett N.J., Zhang Y., Hansen S.K., Roper J.M., Kuehl J.V., Plock S.A., Wolf P.G., dePamphilis C.W., Boore J.L., Goffinet B. (2008b) Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis. Molecular Biology and Evolution 25: 393-401. DOI 10.1093/molbev/msm267
90. Wolf P.G., Karol K.G., Mandoli D.F., Kuehl J., Arumuganathan K., Ellis M.W., Mishler B.D., Kelch D.G., Olmstead R.G., Boore J.L. (2005) The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene 350: 117-128. DOI: 10.1016/j.gene.2005.01.018
91. Wolf P.G., Der J.P., Duffy A.M., Davidson J.B., Grusz A.L., Pryer K.M. (2010) The evolution of chloroplast genes and genomes in ferns. Plant Molecular Biology. DOI:10.1007/s11103-010-9706-4
92. Woodbury N.W., Roberts L.L., Palmer J.D., Thompson W.F. (1988) A transcription map of the pea chloroplast genome. Current Genetics 14: 75-89. DOI: 10.1007/BF00405857
93. Wu C.-S., Wang Y.-N., Liu S.-M., Chaw S.-M. (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 plants. Molecular Biology and Evolution 24: 1366-1379. DOI: 10.1093/molbev/msm059
94. Wyman S.K., Jansen R.K., Boore, J.L. (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255. DOI: 10.1093/bioinformatics/bth352
95. Xue J.-Y., Liu Y., Li L., Wang B. (2009) The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Current Genetics 56: 53-61. DOI: 10.1007/s00294-009-0279-1
96. Yoshinaga K., Iinuma H., Masuzawa T., Uedal K. (1996) Extensive editing of C to U substitution in the rbcL transcripts of hornwort chloroplasts and the origin of RNA editing in green plants. Nucleic Acids Research 24: 1008-1014. DOI: 10.1093/ nar/24.6.1008
97. Zane L., Bargelloni L., Patarnello T. (2002) Strategies for microsatellite isolation: a review. Molecular Ecology 11: 1-16. DOI: 10.1046/j.0962-1083.2001.01418.x
98. Zoschke R., Nakamura M., Liere K., Sugiura M., Börner T., Schmitz-Linneweber C. (2010) An organellar maturase associates with multiple group II introns. Proceedings of the National Academy of Sciences of the USA 107: 3245-3250. DOI: 10.1073/pnas.0909400107