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

Volumn 56, Issue 1, 2010, Pages 53-61

  Xue, Jia Yu ^a,b   Liu, Yang ^a   Li, Libo ^a   Wang, Bin ^a   Qiu, Yin Long ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b NANJING UNIVERSITY   (China)

Author keywords

Evolution; Hornwort; Land plant; Mitochondrial genome; Phaeoceros laevis; Pseudogene

Indexed keywords

PLANT DNA; PLANT RNA; RIBOSOME RNA; SPACER DNA; TRANSFER RNA;

ARTICLE; BASE PAIRING; CHROMOSOME INVERSION; CHROMOSOME TRANSLOCATION; CONTROLLED STUDY; EXON; GENE DISRUPTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; HORNWORT; INTRON; LIVERWORT; MITOCHONDRIAL GENETICS; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PRIORITY JOURNAL; PSEUDOGENE; RNA SPLICING;

ANTHOCEROTOPHYTA; BASE SEQUENCE; EVOLUTION; GENES, PLANT; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; PSEUDOGENES;

ANTHOCEROTOPHYTA; BRYOPHYTES; EMBRYOPHYTA; EUKARYOTA; MARCHANTIOPHYTA; MEGACEROS AENIGMATICUS; PHAEOCEROS LAEVIS; SPERMATOPHYTA;

EID: 75049083803     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-009-0279-1     Document Type: Article

References (42)

1. KL Adams YL Qiu M Stoutemyer JD Palmer 2002 Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution Proc Natl Acad Sci USA 99 9905 9912 10.1073/pnas.042694899 1:CAS:528:DC%2BD38XlslKgsb0%3D 12119382 (Pubitemid 34831145)
2. JO Allen CM Fauron P Minx L Roark S Oddiraju GN Lin L Meyer H Sun K Kim CY Wang FY Du D Xu M Gibson J Cifrese SW Clifton KJ Newton 2007 Comparisons among two fertile and three male-sterile mitochondrial genomes of maize Genetics 177 1173 1192 10.1534/genetics.107.073312 1:CAS:528:DC%2BD2sXhtlyrs7vL 17660568 (Pubitemid 350005664)
3. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410 1:CAS:528:DyaK3MXitVGmsA%3D%3D 2231712
4. C Andre A Levy V Walbot 1992 Small repeated sequences and the structure of plant mitochondrial genomes Trends Genet 8 128 132 1:STN:280: DyaK38zjs1ektg%3D%3D 1631955
5. SM Chaw ACC Shih D Wang YW Wu SM Liu TY Chou 2008 The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites Mol Biol Evol 25 603 615 10.1093/molbev/msn009 1:CAS:528:DC%2BD1cXjt1Cltbs%3D 18192697 (Pubitemid 351301916)
6. O Dombrovska Y-L Qiu 2004 Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications Mol Phylogen Evol 32 246 263 10.1016/j.ympev.2003.12.013 1:CAS:528: DC%2BD2cXks1ektLk%3D (Pubitemid 38851943)
7. JJ Doyle JS Doyle 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue Phytochem Bull 19 11 15
8. RJ Duff JC Villarreal DC Cargill KS Renzaglia 2007 Progress and challenges toward developing a phylogeny and classification of the hornworts Bryologist 110 214 243 10.1639/0007-2745(2007)110[214:PACTDA]2.0.CO;2 (Pubitemid 46752704)
9. MW Gray BF Lang G Burger 2004 Mitochondria of protists Annu Rev Genet 38 477 524 10.1146/annurev.genet.37.110801.142526 1:CAS:528:DC%2BD2MXltlyjsQ%3D%3D 15568984 (Pubitemid 40013736)
10. M Groth-Malonek D Pruchner F Grewe V Knoop 2005 Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants Mol Biol Evol 22 117 125 10.1093/molbev/msh259 1:CAS:528:DC%2BD2cXhtFansrbK 15356283 (Pubitemid 39628548)
11. M Groth-Malonek U Wahrmund M Polsakiewicz V Knoop 2007 Evolution of a pseudogene: Exclusive survival of a functional mitochondrial nad7 gene supports Haplomitrium as the earliest liverwort lineage and proposes a secondary loss of RNA editing in Marchantiidae Mol Biol Evol 24 1068 1074 10.1093/molbev/msm026 1:CAS:528:DC%2BD2sXkslGrsLk%3D 17283365 (Pubitemid 46536718)
12. X Guo Z Zhang MB Gerstein D Zheng 2009 Small RNAs originated from pseudogenes: cis- or trans-acting? PLoS Comput Biol 5 e1000449 10.1371/journal.pcbi.1000449 19649160
13. H Handa 2003 The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana Nucleic Acids Res 31 5907 5916 10.1093/nar/gkg795 1:CAS:528:DC%2BD3sXotVCltr0%3D 14530439 (Pubitemid 37442317)
14. Kelch DG, Driskell A, Mishler BD (2004) Inferring phylogeny using genomic characters: a case study using land plant plastomes. In: Goffinet B, Hollowell V, Magill R (eds) Molecular systematics of bryophytes. Missouri Botanical Garden Press, St. Louis, pp 3-11
15. V Knoop 2004 The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective Curr Genet 46 123 139 10.1007/s00294-004-0522-8 1:CAS:528:DC%2BD2cXntlSqsLc%3D 15300404 (Pubitemid 39307201)
16. Kubo N, Arimura S-I (2009) Discovery of a functional rpl10 gene in diverse plant mitochondrial genomes and its functional replacement by a nuclear gene for chloroplast RPL10 in two lineages of angiosperms. DNA Res (in press)
17. M Kugita Y Yamamoto T Fujikawa T Matsumoto K Yoshinaga 2003 RNA editing in hornwort chloroplasts makes more than half the genes functional Nucleic Acids Res 31 2417 2423 10.1093/nar/gkg327 1:CAS:528:DC%2BD3sXjt1Ogtrc%3D 12711687 (Pubitemid 37442110)
18. S Kurtz JV Choudhuri E Ohlebusch C Schleiermacher J Stoye R Giegerich 2001 REPuter: The manifold applications of repeat analysis on a genomic scale Nucleic Acids Res 29 4633 4642 10.1093/nar/29.22.4633 1:CAS:528: DC%2BD3MXptV2iu74%3D 11713313
19. BF Lang G Burger CJ Okelly R Cedergren GB Golding C Lemieux D Sankoff M Turmel MW Gray 1997 An ancestral mitochondrial DNA resembling a eubacterial genome in miniature Nature 387 493 497 10.1038/387493a0 1:CAS:528: DyaK2sXjsF2huro%3D 9168110 (Pubitemid 27235465)
20. Lenz H, Rüdinger M, Volkmar U, FIscher S, Herres S, Grewe F, Knoop V (2009) Introducing PREPACT-the plant RNA editing prediction and analysis computer tool and an update on RNA editing site nomenclature. Curr Genet (in press)
21. L Li B Wang Y Liu Y-L Qiu 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 J Mol Evol 68 665 678 10.1007/s00239-009-9240-7 1:CAS:528:DC%2BD1MXmvV2rs7s%3D 19475442
22. M Lohse O Drechsel R Bock 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 10.1007/s00294-007-0161-y 1:CAS:528:DC%2BD2sXht1Oks7%2FN 17957369 (Pubitemid 350090630)
23. TM Lowe SR Eddy 1997 tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res 25 955 964 10.1093/nar/25.5.955 1:CAS:528:DyaK2sXhvVahtrk%3D 9023104 (Pubitemid 27298263)
24. O Malek V Knoop 1998 Trans-splicing group II introns in plant mitochondria: The complete set of cis-arranged homologs in ferns, fern allies, and a hornwort RNA 4 1599 1609 10.1017/S1355838298981262 1:CAS:528: DyaK1cXnvFOgs7s%3D 9848656 (Pubitemid 28555220)
25. F Michel B Dujon 1983 Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear-encoded members EMBO J 2 33 38 1:CAS:528:DyaL3sXosVekug%3D%3D 11894905
26. K Oda K Yamato E Ohta Y Nakamura M Takemura N Nozato K Akashi T Kanegae Y Ogura T Kohchi K Ohyama 1992 Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA-a primitive form of plant mitochondrial genome J Mol Biol 223 1 7 10.1016/0022-2836(92)90708-R 1:CAS:528:DyaK3sXhvVCls7s%3D 1731062
27. JD Palmer 1985 Comparative organization of chloroplast genomes Annu Rev Genet 19 325 354 10.1146/annurev.ge.19.120185.001545 1:CAS:528: DyaL28Xmt12ksg%3D%3D 3936406
28. JD Palmer KL Adams YR Cho CL Parkinson YL Qiu KM Song 2000 Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates Proc Natl Acad Sci USA 97 6960 6966 10.1073/pnas.97.13. 6960 1:CAS:528:DC%2BD3cXksVKisLs%3D 10860957 (Pubitemid 30431402)
29. D Pruchner S Beckert H Muhle V Knoop 2002 Divergent intron conservation in the mitochondrial nad2 gene: signatures for the three bryophyte classes (Mosses, liverworts, and hornworts) and the lycophytes J Mol Evol 55 265 271 10.1007/s00239-002-2324-2 1:CAS:528:DC%2BD38XmtlGhs7g%3D 12187380 (Pubitemid 34913538)
30. Y-L Qiu 2008 Phylogeny and evolution of charophytic algae and land plants J Syst Evol 46 287 306
31. Y-L Qiu YR Cho JC Cox JD Palmer 1998 The gain of three mitochondrial introns identifies liverworts as the earliest land plants Nature 394 671 674 10.1038/29286 1:CAS:528:DyaK1cXlsFKmsLY%3D 9716129 (Pubitemid 28389791)
32. Y-L Qiu LB Li B Wang ZD Chen V Knoop M Groth-Malonek O Dombrovska J Lee L Kent J Rest GF Estabrook TA Hendry DW Taylor CM Testa M Ambros B Crandall-Stotler RJ Duff M Stech W Frey D Quandt CC Davis 2006 The deepest divergences in land plants inferred from phylogenomic evidence Proc Natl Acad Sci USA 103 15511 15516 10.1073/pnas.0603335103 1:CAS:528:DC%2BD28XhtFCjtLnO 17030812 (Pubitemid 44625623)
33. Schuster RM (1992) The Hepaticae and Anthocerotae of North America, vol VI. Field Museum of Natural History, Chicago
34. W Schuster A Brennicke 1994 The plant mitochondrial genome-physical structure, information content, RNA editing, and gene migration to the nucleus Annu Rev Plant Physiol Plant Mol Biol 45 61 78 10.1146/annurev.pp.45.060194. 000425 1:CAS:528:DyaK2MXhslKruw%3D%3D
35. S Steinhauser S Beckert I Capesius O Malek V Knoop 1999 Plant mitochondrial RNA editing J Mol Evol 48 303 312 10.1007/PL00006473 1:CAS:528:DyaK1MXhs1ymuro%3D 10093219
36. K Terasawa M Odahara Y Kabeya T Kikugawa Y Sekine M Fujiwara N Sato 2007 The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants Mol Biol Evol 24 699 709 10.1093/molbev/msl198 1:CAS:528:DC%2BD2sXjtlersrk%3D 17175527 (Pubitemid 46355794)
37. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 4876 4882 10.1093/nar/25.24.4876 1:CAS:528:DyaK1cXntFyntQ%3D%3D 9396791 (Pubitemid 28022245)
38. M Turmel C Otis C Lemieux 2002 The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: Insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants Proc Natl Acad Sci USA 99 11275 11280 10.1073/pnas.162203299 1:CAS:528:DC%2BD38XmslSmtbs%3D 12161560 (Pubitemid 34920916)
39. M Turmel C Otis C Lemieux 2003 The mitochondrial genome of Chara vulgaris: Insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants Plant Cell 15 1888 1903 10.1105/tpc.013169 1:CAS:528:DC%2BD3sXms1Wlsbg%3D 12897260 (Pubitemid 37078342)
40. M Unseld JR Marienfeld P Brandt A Brennicke 1997 The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366, 924 nucleotides Nat Genet 15 57 61 10.1038/ng0197-57 1:CAS:528:DyaK2sXjsFSiuw%3D%3D 8988169 (Pubitemid 27014950)
41. B Wang J-Y Xue L Li L Liu Y-L Qiu 2009 The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts Curr Genet 55 601 609 10.1007/s00294-009-0273-7 1:CAS:528:DC%2BD1MXhsVeht7bL
42. Z Zhang M Gerstein 2004 Large-scale analysis of pseudogenes in the human genome Curr Opin Genet Dev 14 328 335 10.1016/j.gde.2004.06.003 1:CAS:528:DC%2BD2cXlsl2lsbw%3D 15261647 (Pubitemid 38903122)