Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2016, Article ID 5040598, 18 pages
http://dx.doi.org/10.1155/2016/5040598
Research Article

Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches

1College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu, China
2Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
3The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, Jiangsu, China

Received 17 August 2016; Accepted 26 September 2016

Academic Editor: Xiaobai Li

Copyright © 2016 Changwei Bi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. W. Gray, G. Burger, and B. F. Lang, “Mitochondrial evolution,” Science, vol. 283, no. 5407, pp. 1476–1481, 1999. View at Publisher · View at Google Scholar · View at Scopus
  2. B. F. Lang, M. W. Gray, and G. Burger, “Mitochondrial genome evolution and the origin of eukaryotes,” Annual Review of Genetics, vol. 33, pp. 351–397, 1999. View at Publisher · View at Google Scholar · View at Scopus
  3. C. L. Hsu and B. C. Mullin, “Physical characterization of mitochondrial DNA from cotton,” Plant Molecular Biology, vol. 13, no. 4, pp. 467–468, 1989. View at Publisher · View at Google Scholar · View at Scopus
  4. T. Kubo and T. Mikami, “Organization and variation of angiosperm mitochondrial genome,” Physiologia Plantarum, vol. 129, no. 1, pp. 6–13, 2007. View at Publisher · View at Google Scholar · View at Scopus
  5. J. D. Palmer and L. A. Herbon, “Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence,” Journal of Molecular Evolution, vol. 28, no. 1-2, pp. 87–97, 1988. View at Publisher · View at Google Scholar · View at Scopus
  6. H. Handa, “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, vol. 31, no. 20, pp. 5907–5916, 2003. View at Publisher · View at Google Scholar · View at Scopus
  7. R. M. Mulligan, K. L. C. Chang, and C. C. Chou, “Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites,” Molecular Biology and Evolution, vol. 24, no. 9, pp. 1971–1981, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. D. M. Lonsdale, T. P. Hodge, and C. M.-R. Fauron, “The physical map and organisatlon of the mitochondrial genome from the fertile cytoplasm of maize,” Nucleic Acids Research, vol. 12, no. 24, pp. 9249–9261, 1984. View at Publisher · View at Google Scholar · View at Scopus
  9. A. J. Alverson, S. Zhuo, D. W. Rice, D. B. Sloan, and J. D. Palmer, “The mitochondrial genome of the legume vigna radiata and the analysis of recombination across short mitochondrial repeats,” PLoS ONE, vol. 6, no. 1, Article ID e16404, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. C. André, A. Levy, and V. Walbot, “Small repeated sequences and the structure of plant mitochondrial genomes,” Trends in Genetics, vol. 8, no. 4, pp. 128–132, 1992. View at Publisher · View at Google Scholar · View at Scopus
  11. S. Chang, Y. Wang, J. Lu et al., “The mitochondrial genome of soybean reveals complex genome structures and gene evolution at intercellular and phylogenetic levels,” PLoS ONE, vol. 8, no. 2, article e56502, 2013. View at Publisher · View at Google Scholar · View at Scopus
  12. B. Lei, S. Li, G. Liu et al., “Evolution of mitochondrial gene content: loss of genes, tRNAs and introns between Gossypium harknessii and other plants,” Plant Systematics and Evolution, vol. 299, no. 10, pp. 1889–1897, 2013. View at Publisher · View at Google Scholar · View at Scopus
  13. J. D. Palmer and L. A. Herbo, “Unicircular structure of the Brassica hirta mitochondrial genome,” Current Genetics, vol. 11, no. 6-7, pp. 565–570, 1987. View at Publisher · View at Google Scholar · View at Scopus
  14. D. B. Sloan, A. J. Alverson, J. P. Chuckalovcak et al., “Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates,” PLoS Biology, vol. 10, no. 1, article e1001241, 2012. View at Publisher · View at Google Scholar · View at Scopus
  15. O. Dombrovska and Y.-L. Qiu, “Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications,” Molecular Phylogenetics and Evolution, vol. 32, no. 1, pp. 246–263, 2004. View at Publisher · View at Google Scholar · View at Scopus
  16. Y. Tanaka, M. Tsuda, K. Yasumoto, H. Yamagishi, and T. Terachi, “A complete mitochondrial genome sequence of Ogura-type male-sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.),” BMC Genomics, vol. 13, no. 1, article 352, 2012. View at Publisher · View at Google Scholar · View at Scopus
  17. A. J. Alverson, D. W. Rice, S. Dickinson, K. Barry, and J. D. Palmer, “Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber,” Plant Cell, vol. 23, no. 7, pp. 2499–2513, 2011. View at Publisher · View at Google Scholar · View at Scopus
  18. Y. Notsu, S. Masood, T. Nishikawa et al., “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, vol. 268, no. 4, pp. 434–445, 2002. View at Publisher · View at Google Scholar · View at Scopus
  19. S. W. Clifton, P. Minx, C. M.-R. Fauron et al., “Sequence and comparative analysis of the maize NB mitochondrial genome,” Plant Physiology, vol. 136, no. 3, pp. 3486–3503, 2004. View at Publisher · View at Google Scholar · View at Scopus
  20. P. Cui, H. Liu, Q. Lin et al., “A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai), and fast evolving mitochondrial genes in higher plants,” Journal of Genetics, vol. 88, no. 3, pp. 299–307, 2010. View at Publisher · View at Google Scholar · View at Scopus
  21. A. J. Alverson, X. Wei, D. W. Rice, D. B. Stern, K. Barry, and J. D. Palmer, “Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae),” Molecular Biology and Evolution, vol. 27, no. 6, pp. 1436–1448, 2010. View at Publisher · View at Google Scholar · View at Scopus
  22. M. Unseld, J. R. Marienfeld, P. Brandt, and A. Brennicke, “The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides,” Nature Genetics, vol. 15, no. 1, pp. 57–61, 1997. View at Publisher · View at Google Scholar · View at Scopus
  23. T. Kubo, S. Nishizawa, A. Sugawara, N. Itchoda, A. Estiati, and T. Mikami, “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, vol. 28, no. 13, pp. 2571–2576, 2000. View at Publisher · View at Google Scholar · View at Scopus
  24. G. Raman and S. Park, “Analysis of the complete chloroplast genome of a medicinal plant, Dianthus superbus var. longicalyncinus, from a comparative genomics perspective,” PLoS ONE, vol. 10, no. 10, article e0141329, 2015. View at Publisher · View at Google Scholar · View at Scopus
  25. H. Chen, L. Deng, Y. Jiang, P. Lu, and J. Yu, “RNA editing sites exist in protein-coding genes in the chloroplast genome of Cycas taitungensis,” Journal of Integrative Plant Biology, vol. 53, no. 12, pp. 961–970, 2011. View at Publisher · View at Google Scholar · View at Scopus
  26. T. Zhang, Y. Fang, X. Wang et al., “The complete chloroplast and mitochondrial genome sequences of boea hygrometrica: insights into the evolution of plant organellar genomes,” PLoS ONE, vol. 7, no. 1, Article ID e30531, 2012. View at Publisher · View at Google Scholar · View at Scopus
  27. K. H. Wolfe, W. H. Li, and P. M. Sharp, “Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs,” Proceedings of the National Academy of Sciences of the United States of America, vol. 84, no. 24, pp. 9054–9058, 1987. View at Publisher · View at Google Scholar · View at Scopus
  28. P.-F. Ma, Z.-H. Guo, and D.-Z. Li, “Rapid sequencing of the bamboo mitochondrial genome using illumina technology and parallel episodic evolution of organelle genomes in grasses,” PLoS ONE, vol. 7, no. 1, Article ID e30297, 2012. View at Publisher · View at Google Scholar · View at Scopus
  29. Y.-L. Qiu, L. Li, B. Wang et al., “Angiosperm phylogeny inferred from sequences of four mitochondrial genes,” Journal of Systematics and Evolution, vol. 48, no. 6, pp. 391–425, 2010. View at Publisher · View at Google Scholar · View at Scopus
  30. D. B. Sloan, A. J. Alverson, H. Štorchová, J. D. Palmer, and D. R. Taylor, “Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia,” BMC Evolutionary Biology, vol. 10, no. 1, article 274, 2010. View at Publisher · View at Google Scholar · View at Scopus
  31. K. Wang, Z. Wang, F. Li et al., “The draft genome of a diploid cotton Gossypium raimondii,” Nature Genetics, vol. 44, no. 10, pp. 1098–1103, 2012. View at Publisher · View at Google Scholar · View at Scopus
  32. Y.-L. Ruan, D. J. Llewellyn, and R. T. Furbank, “Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development,” The Plant Cell, vol. 15, no. 4, pp. 952–964, 2003. View at Publisher · View at Google Scholar
  33. Y.-H. Shi, S.-W. Zhu, X.-Z. Mao et al., “Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation,” Plant Cell, vol. 18, no. 3, pp. 651–664, 2006. View at Publisher · View at Google Scholar · View at Scopus
  34. Y.-M. Qin and Y.-X. Zhu, “How cotton fibers elongate: a tale of linear cell-growth mode,” Current Opinion in Plant Biology, vol. 14, no. 1, pp. 106–111, 2011. View at Publisher · View at Google Scholar · View at Scopus
  35. G. Liu, D. Cao, S. Li et al., “The complete mitochondrial genome of gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes,” PLoS ONE, vol. 8, no. 8, article e69476, 2013. View at Publisher · View at Google Scholar · View at Scopus
  36. M. Tang, Z. Chen, C. E. Grover et al., “Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes,” BMC Genomics, vol. 16, no. 1, article 770, 2015. View at Publisher · View at Google Scholar · View at Scopus
  37. A. H. Paterson, J. F. Wendel, H. Gundlach et al., “Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres,” Nature, vol. 492, no. 7429, pp. 423–427, 2012. View at Publisher · View at Google Scholar
  38. T. Zhang, X. Zhang, S. Hu, and J. Yu, “An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform,” Plant Methods, vol. 7, no. 1, article 38, 2011. View at Publisher · View at Google Scholar · View at Scopus
  39. H. Li and R. Durbin, “Fast and accurate short read alignment with Burrows-Wheeler transform,” Bioinformatics, vol. 25, no. 14, pp. 1754–1760, 2009. View at Publisher · View at Google Scholar · View at Scopus
  40. P. Librado and J. Rozas, “DnaSP v5: a software for comprehensive analysis of DNA polymorphism data,” Bioinformatics, vol. 25, no. 11, pp. 1451–1452, 2009. View at Publisher · View at Google Scholar · View at Scopus
  41. T. M. Lowe and S. R. Eddy, “TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence,” Nucleic Acids Research, vol. 25, no. 5, pp. 955–964, 1997. View at Publisher · View at Google Scholar · View at Scopus
  42. M. Lohse, O. Drechsel, and R. Bock, “OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes,” Current Genetics, vol. 52, no. 5-6, pp. 267–274, 2007. View at Publisher · View at Google Scholar · View at Scopus
  43. G. Benson, “Tandem repeats finder: a program to analyze DNA sequences,” Nucleic Acids Research, vol. 27, no. 2, pp. 573–580, 1999. View at Publisher · View at Google Scholar · View at Scopus
  44. T. Thiel, W. Michalek, R. K. Varshney, and A. Graner, “Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.),” Theoretical and Applied Genetics, vol. 106, no. 3, pp. 411–422, 2003. View at Google Scholar · View at Scopus
  45. J. P. Mower, “The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments,” Nucleic Acids Research, vol. 37, no. 2, pp. W253–W259, 2009. View at Publisher · View at Google Scholar · View at Scopus
  46. K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, “MEGA6: molecular evolutionary genetics analysis version 6.0,” Molecular Biology and Evolution, vol. 30, no. 12, pp. 2725–2729, 2013. View at Publisher · View at Google Scholar · View at Scopus
  47. R. C. Edgar, “MUSCLE: multiple sequence alignment with high accuracy and high throughput,” Nucleic Acids Research, vol. 32, no. 5, pp. 1792–1797, 2004. View at Publisher · View at Google Scholar · View at Scopus
  48. R. Overbeek, M. Fonstein, M. D'Souza, G. D. Push, and N. Maltsev, “The use of gene clusters to infer functional coupling,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 6, pp. 2896–2901, 1999. View at Publisher · View at Google Scholar · View at Scopus
  49. A. Zhu, W. Guo, K. Jain, and J. P. Mower, “Unprecedented heterogeneity in the synonymous substitution rate within a plant genome,” Molecular Biology & Evolution, vol. 31, no. 5, pp. 1228–1236, 2014. View at Publisher · View at Google Scholar · View at Scopus
  50. M. Nakazono, H. Itadani, T. Wakasugi, N. Tsutsumi, M. Sugiura, and A. Hirai, “The rps3-rpl16-nad3-rps12 gene cluster in rice mitochondrial DNA is transcribed from alternative promoters,” Current Genetics, vol. 27, no. 2, pp. 184–189, 1995. View at Publisher · View at Google Scholar · View at Scopus
  51. K. Oda, K. Yamato, E. Ohta et al., “Transfer RNA genes in the mitochondrial genome from a liverwort, Marchantia polymorpha: the absence of chloroplast-like tRNAs,” Nucleic Acids Research, vol. 20, no. 14, pp. 3773–3777, 1992. View at Publisher · View at Google Scholar · View at Scopus
  52. S.-M. Chaw, A. Chun-Chieh Shih, D. Wang, Y.-W. Wu, S.-M. Liu, and T.-Y. Chou, “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 & Evolution, vol. 25, no. 3, pp. 603–615, 2008. View at Publisher · View at Google Scholar · View at Scopus
  53. Y. Ogihara, Y. Yamazaki, K. Murai et al., “Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome,” Nucleic Acids Research, vol. 33, no. 19, pp. 6235–6250, 2005. View at Publisher · View at Google Scholar · View at Scopus
  54. Y. Sugiyama, Y. Watase, M. Nagase et al., “The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants,” Molecular Genetics & Genomics, vol. 272, no. 6, pp. 603–615, 2005. View at Publisher · View at Google Scholar · View at Scopus
  55. R. Bock and M. S. Khan, “Taming plastids for a green future,” Trends in Biotechnology, vol. 22, no. 6, pp. 311–318, 2004. View at Publisher · View at Google Scholar · View at Scopus
  56. A. Zandueta-Criado and R. Bock, “Surprising features of plastid ndhD transcripts: addition of non-encoded nucleotides and polysome association of mRNAs with an unedited start codon,” Nucleic Acids Research, vol. 32, no. 2, pp. 542–550, 2004. View at Publisher · View at Google Scholar · View at Scopus
  57. T. Wakasugi, T. Hirose, M. Horihata, T. Tsudzuki, H. Kössel, and M. Sugiura, “Creation of a novel protein-coding region at the RNA level in black pine chloroplasts: the pattern of RNA editing in the gymnosperm chloroplast is different from that in angiosperms,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 16, pp. 8766–8770, 1996. View at Publisher · View at Google Scholar · View at Scopus
  58. Y. Sugiyama, Y. Watase, M. Nagase et al., “The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants,” Molecular Genetics and Genomics, vol. 272, no. 6, pp. 603–615, 2005. View at Publisher · View at Google Scholar · View at Scopus
  59. S.-M. Chaw, A. Chun-Chieh Shih, D. Wang, Y.-W. Wu, S.-M. Liu, and T.-Y. Chou, “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, vol. 25, no. 3, pp. 603–615, 2008. View at Publisher · View at Google Scholar · View at Scopus
  60. J. D. Palmer, K. L. Adams, Y. Cho, C. L. Parkinson, Y.-L. Qiu, and K. Song, “Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 13, pp. 6960–6966, 2000. View at Publisher · View at Google Scholar · View at Scopus
  61. G. Perrotta, J. M. Grienenberger, and J. M. Gualberto, “Plant mitochondrial rps2 genes code for proteins with a C-terminal extension that is processed,” Plant Molecular Biology, vol. 50, no. 3, pp. 523–533, 2002. View at Publisher · View at Google Scholar · View at Scopus