The Mitochondrial Genome of an Aquatic Plant, Spirodela polyrhiza

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Wang, Wenqin ^a   Wu, Yongrui ^a   Messing, Joachim ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROPLAST DNA; MITOCHONDRIAL DNA;

ALISMATALES; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENE INSERTION; GENE LOSS; MITOCHONDRIAL GENE; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENE; PSEUDOGENE; RICE; RNA EDITING; SPIRODELA POLYRHIZA; SYNTENY;

ALISMATIDAE; DNA, PLANT; GENOME, MITOCHONDRIAL; GENOME, PLANT; OPEN READING FRAMES; PHYLOGENY; RNA EDITING;

ALISMATALES; LILIOPSIDA; POALES; SPIRODELA; SPIRODELA POLYRRHIZA;

EID: 84867137384     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046747     Document Type: Article

References (52)

1. Logan DC, (2006) The mitochondrial compartment. J Exp Bot 57: 1225-1243.
2. Mackenzie S, McIntosh L, (1999) Higher plant mitochondria. Plant Cell 11: 571-586.
3. Keeling PJ, Palmer JD, (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9: 605-618.
4. Sloan DB, Alverson AJ, Storchova H, Palmer JD, Taylor DR, (2010) Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia. BMC Evol Biol 10: 274.
5. Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, et al. (2010) Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol 27: 1436-1448.
6. Palmer JD, Adams KL, Cho Y, Parkinson CL, Qiu YL, et al. (2000) Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc Natl Acad Sci U S A 97: 6960-6966.
7. Fang Y, Wu H, Yang M (2012) A Complete Sequence and Transcriptomic Analysis of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome. NCBI GenBank NC_0167401.
8. Cabrera LI, Salazar GA, Chase MW, Mayo SJ, Bogner J, et al. (2008) Phylogenetic relationships of aroids and duckweeds (Araceae) inferred from coding and noncoding plastid DNA. Am J Bot 95: 1153-1165.
9. Stomp AM, (2005) The duckweeds: A valuable plant for biomanufacturing. Biotechnology Annual Review 11: 69-99.
10. Ljaz S, (2010) Plant mitochondrial genome: "A sweet and safe home" for transgene. African Journal of Biotechnology 9: 4.
11. Wang W, Messing J, (2011) High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PLoS One 6: e24670.
12. Zhang T, Zhang X, Hu S, Yu J, (2011) An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform. Plant Methods 7: 38.
13. Lutz K, Wang W, Zdepski A, Michael T, (2011) Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing. BMC Biotechnology 11: 54.
14. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
15. Zerbino DR, Birney E, (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.
16. 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.
17. Stothard P (2000) The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28: 1102, 1104.
18. Rice P, Longden I, Bleasby A, (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
19. Mower JP, (2009) The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucleic Acids Res 37: W253-259.
20. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, et al. (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29: 4633-4642.
21. Bergman CM, Quesneville H, (2007) Discovering and detecting transposable elements in genome sequences. Brief Bioinform 8: 382-392.
22. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
23. Revanna KV, Chiu CC, Bierschank E, Dong Q, (2011) GSV: a web-based genome synteny viewer for customized data. BMC Bioinformatics 12: 316.
24. Les DH, Crawford DJ, Landolt E, Gabel JD, Kimball RT, (2002) Phylogeny and Systematics of Lemnaceae, the Duckweed Family. Systematic Botany 27: 221-240.
25. Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, et al. (2002) The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Genet Genomics 268: 434-445.
26. Clifton SW, Minx P, Fauron CM, Gibson M, Allen JO, et al. (2004) Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol 136: 3486-3503.
27. Malek O, Knoop V, (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.
28. Unseld M, Marienfeld JR, Brandt P, Brennicke A, (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat Genet 15: 57-61.
29. Chaw SM, Shih AC, Wang D, Wu YW, Liu SM, et al. (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.
30. Zhang T, Fang Y, Wang X, Deng X, Zhang X, et al. (2012) The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes. PLoS One 7: e30531.
31. Giege P, Brennicke A, (1999) RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci 96: 15324-15329.
32. Takenaka M, Verbitskiy D, van der Merwe JA, Zehrmann A, Brennicke A, (2008) The process of RNA editing in plant mitochondria. Mitochondrion 8: 35-46.
33. Woodson JD, Chory J, (2008) Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 9: 383-395.
34. Schneider A, (2011) Mitochondrial tRNA import and its consequences for mitochondrial translation. Annu Rev Biochem 80: 1033-1053.
35. Mower JP, Sloan DB, Alverson AJ (2012) Plant Mitochondrial Genome Diversity: The Genomics Revolution In: Wendel JF, Greilhuber J, Dolezel J, Leitch IJ, editors. Plant Genome Diversity: Springer Vienna. 123-144.
36. Handa H, (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.
37. Satoh M, Kubo T, Nishizawa S, Estiati A, Itchoda N, et al. (2004) 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 272: 247-256.
38. Satoh M, Kubo T, Mikami T, (2006) The Owen mitochondrial genome in sugar beet (Beta vulgaris L.): possible mechanisms of extensive rearrangements and the origin of the mitotype-unique regions. Theor Appl Genet 113: 477-484.
39. Lilly JW, Havey MJ, (2001) Small, repetitive DNAs contribute significantly to the expanded mitochondrial genome of cucumber. Genetics 159: 317-328.
40. McDermott P, Connolly V, Kavanagh TA, (2008) The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) contains an integrated linear plasmid-like element. Theor Appl Genet 117: 459-470.
41. Alverson AJ, Zhuo S, Rice DW, Sloan DB, Palmer JD, (2011) The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS One 6: e16404.
42. Janssen T, Bremer K (2004) The age of major monocot groups inferred from 800+ rbcL sequences. Botanical Journal of the Linnean Society: 4.
43. Stockey RA, (2006) The fossil record of basal monocots. 22: 16.
44. Borsch T, Hilu KW, Quandt D, Wilde V, Neinhuis C, et al. (2003) Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J Evol Biol 16: 558-576.
45. Perrotta G, Grienenberger JM, Gualberto JM, (2002) Plant mitochondrial rps2 genes code for proteins with a C-terminal extension that is processed. Plant Mol Biol 50: 523-533.
46. Adams KL, Rosenblueth M, Qiu YL, Palmer JD, (2001) Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution. Genetics 158: 1289-1300.
47. Adams KL, Song K, Roessler PG, Nugent JM, Doyle JL, et al. (1999) Intracellular gene transfer in action: Dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes. Proc Natl Acad Sci 96: 13863-13868.
48. Goremykin VV, Salamini F, Velasco R, Viola R, (2009) Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol Biol Evol 26: 99-110.
49. Knoop V, Unseld M, Marienfeld J, Brandt P, Sunkel S, et al. (1996) copia-, gypsy- and LINE-like retrotransposon fragments in the mitochondrial genome of Arabidopsis thaliana. Genetics 142: 579-585.
50. Smit A, Hubley R, Green P (1996-2010) RepeatMasker Open-3.0. Available: http://www.repeatmasker.org. Accessed 2012 Sep 11.
51. Terasawa K, Odahara M, Kabeya Y, Kikugawa T, Sekine Y, et al. (2007) The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Mol Biol Evol 24: 699-709.
52. Chang S, Yang T, Du T, Huang Y, Chen J, et al. (2011) Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica. BMC Genomics 12: 497.