The complete chloroplast and mitochondrial genome sequences of boea hygrometrica: Insights into the evolution of plant organellar genomes

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Zhang, Tongwu ^a,b   Fang, Yongjun ^a,b   Wang, Xumin ^b   Deng, Xin ^c   Zhang, Xiaowei ^b   Hu, Songnian ^b   Yu, Jun ^b  

^a ZHEJIANG UNIVERSITY   (China)

^b Chinese Academy of Sciences and China National Center for Bioinformation   (China)

^c INSTITUTE OF BOTANY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOSPERM; ARTICLE; BOEA HYGROMETRICA; CHLOROPLAST; CONTROLLED STUDY; GENE MAPPING; GENE SEQUENCE; GENE TRANSFER; GENETIC CODE; GENETIC CONSERVATION; LAMIALES; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT EVOLUTION; PLANT GENE; PLANT GENOME; PLANT SEED; RRN18 GENE; RRN26 GENE; RRN5 GENE; BIOLOGICAL MODEL; CELL ORGANELLE; CHLOROPLAST GENOME; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; HORIZONTAL GENE TRANSFER; METHODOLOGY; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PLASTID;

BOEA HYGROMETRICA; EMBRYOPHYTA; GESNERIACEAE; MAGNOLIOPHYTA; SELAGINELLA PILIFERA; SPERMATOPHYTA;

TRANSFER RNA;

ANGIOSPERMS; BASE SEQUENCE; CHLOROPLASTS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENES, PLANT; GENOME, CHLOROPLAST; GENOME, MITOCHONDRIAL; GENOME, PLANT; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; ORGANELLES; PLASTIDS; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA;

EID: 84856082699     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030531     Document Type: Article

References (53)

1. Olmstead R, Palmer J, (1994) Chloroplast DNA systematics: A review of methods and data analysis. American journal of botany 81: 1205-1224.
2. Qiu Y-L, Li L, Wang B, Xue J-Y, Hendry TA, et al. (2010) Angiosperm phylogeny inferred from sequences of four mitochondrial genes. Journal of Systematics and Evolution 48: 391-425.
3. Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, et al. (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. Molecular Biology and Evolution 23: 2175-2190.
4. Yang M, Zhang XW, Liu GM, Yin YX, Chen KF, et al. (2010) The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.). Plos One 5.
5. Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, et al. (2007) Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol Phylogenet Evol 45: 547-563.
6. Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, et al. (2006) The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Molecular Biology and Evolution 23: 279-291.
7. Ogihara Y, Yamazaki Y, Murai K, Kanno A, Terachi T, et al. (2005) Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic acids research 33: 6235-6250.
8. Li LB, Wang B, Liu Y, Qiu YL, (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.
9. Liu Y, Xue JY, Wang B, Li L, Qiu YL, (2011) The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: dynamic and conservative evolution. Plos One 6: e25836.
10. Alverson AJ, Wei XX, 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). Molecular Biology and Evolution 27: 1436-1448.
11. Palmer JD, Herbon LA, (1988) Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. Journal of Molecular Evolution 28: 87-97.
12. Goremykin VV, Salamini F, Velasco R, Viola R, (2009) Mitochondrial DNA of Vitis vinifera and the Issue of Rampant Horizontal Gene Transfer. Molecular Biology and Evolution 26: 99-110.
13. Lonsdale DM, Brears T, Hodge TP, Melville SE, Rottmann WH, (1988) The Plant Mitochondrial Genome: Homologous Recombination as a Mechanism for Generating Heterogeneity. Philosophical Transactions of the Royal Society of London B, Biological Sciences 319: 149-163.
14. Fujii S, Kazama T, Yamada M, Toriyama K, (2010) Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes. Bmc Genomics 11.
15. Zhang TW, Zhang XW, Hu SN, 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 (In press).
16. Deng X, Hu ZA, Wang HX, (1999) mRNA differential display visualized by silver staining tested on gene expression in resurrection plant Boea hygrometrica. Plant Molecular Biology Reporter 17: 279-279.
17. Jiang GQ, Wang Z, Shang HH, Yang WL, Hu Z, et al. (2007) Proteome analysis of leaves from the resurrection plant Boea hygrometrica in response to dehydration and rehydration. Planta 225: 1405-1420.
18. Goulding S, Wolfe K, Olmstead R, Morden C, (1996) Ebb and flow of the chloroplast inverted repeat. Molecular and General Genetics MGG 252: 195-206.
19. Palmer J, (1991) Plastid chromosomes: structure and evolution. Cell Culture and Somatic Cell Genetics of Plants, vol 7A, The Molecular Biology of Plastids pp. 5-53.
20. Besnard G, Hernandez P, Khadari B, Dorado G, Savolainen V, (2011) Genomic profiling of plastid DNA variation in the Mediterranean olive tree. Bmc Plant Biology 11.
21. Unseld M, Marienfeld JR, Brandt P, Brennicke A, (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genetics 15: 57-61.
22. Sugiyama Y, Watase Y, Nagase M, Makita N, Yagura S, et al. (2005) The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Molecular Genetics and Genomics 272: 603-615.
23. Tian XJ, Zheng J, Hu SN, Yu J, (2006) The rice mitochondrial genomes and their variations. Plant Physiology 140: 401-410.
24. Tang J, Xia H, Cao M, Zhang X, Zeng W, et al. (2004) A comparison of rice chloroplast genomes. Plant Physiology 135: 412-420.
25. Kubo T, Nishizawa S, Sugawara A, Itchoda N, Estiati A, et al. (2000) The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA). Nucleic acids research 28: 2571-2576.
26. 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. Molecular Genetics and Genomics 268: 434-445.
27. 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 research 31: 5907-5916.
28. Clifton SW, Minx P, Fauron CMR, Gibson M, Allen JO, et al. (2004) Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiology 136: 3486-3503.
29. Arrieta-Montiel M, Lyznik A, Woloszynska M, Janska H, Tohme J, et al. (2001) Tracing evolutionary and developmental implications of mitochondrial stoichiometric shifting in the common bean. Genetics 158: 851-864.
30. 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. Molecular Biology and Evolution 24: 699-709.
31. 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.
32. Hecht J, Grewe F, Knoop V, (2011) Extreme RNA editing in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes. Genome Biology and Evolution.
33. 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.
34. Linda B, (2008) Cis- and trans-splicing of group II introns in plant mitochondria. Mitochondrion 8: 26-34.
35. Qiu YL, Palmer JD, (2004) Many independent origins of trans splicing of a plant mitochondrial group II intron. Journal of Molecular Evolution 59: 80-89.
36. Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H, et al. (2007) The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: Organelle genomes of the smallest eukaryote are examples of compaction. Molecular Biology and Evolution 24: 956-968.
37. Small I, Suffolk R, Leaver CJ, (1989) Evolution of plant mitochondrial genomes via substoichiometric intermediates. Cell 58: 69-76.
38. Marechal-Drouard L, Guillemaut P, Cosset A, Arbogast M, Weber F, et al. (1990) Transfer RNAs of potato (Solanum tuberosum) mitochondria have different genetic origins. Nucleic acids research 18: 3689-3696.
39. Dombrovska O, Qiu Y-L, (2004) Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications. Mol Phylogenet Evol 32: 246-263.
40. Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD, (2011) Origins and Recombination of the Bacterial-Sized Multichromosomal Mitochondrial Genome of Cucumber. The Plant Cell Online.
41. Wang D, Wu Y-W, Shih AC-C, Wu C-S, Wang Y-N, et al. (2007) Transfer of Chloroplast Genomic DNA to Mitochondrial Genome Occurred At Least 300 MYA. Molecular Biology and Evolution 24: 2040-2048.
42. Matsuo M, Ito Y, Yamauchi R, Obokata J, (2005) The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast-Nuclear DNA Flux. The Plant Cell Online 17: 665-675.
43. Li L, Wang B, Liu Y, Qiu YL, (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.
44. Alexander J, (2010) Identification and quantification of genomic repeats and sample contamination in assemblies of 454 pyrosequencing reads.
45. Wyman SK, Jansen RK, Boore JL, (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255.
46. Lowe TM, Eddy SR, (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic acids research 25: 955-964.
47. Bock R, Lohse M, Drechsel O, (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.
48. 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 research 29: 4633-4642.
49. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32: 1792-1797.
50. Castresana J, (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540-552.
51. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, et al. (2010) New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology 59: 307-321.
52. Keane T, Creevey C, Pentony M, Naughton T, McLnerney J, (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. Bmc Evolutionary Biology 6: 29.
53. Chaw SM, Shih ACC, 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. Molecular Biology and Evolution 25: 603-615.