A STUDY OF DIRECT REPEATS IN MICROEVOLUTION OF PLANT MITOCHONDRIA AND PLASTIDS BASED ON PROTEIN CLUSTERING
https://doi.org/10.1234/XXXX-XXXX-2013-1-8-13
Abstract
The study focuses on insertions of perfect direct repeats of words of arbitrary length in plastomes and mitochondriomes. The approach is exemplified on seed plants. Plastomes of close species were analyzed to further develop and refine published evidence on the evolution of non-coding DNA. The results suggest that insertions are common elementary events in microevolution of short noncoding DNA regions. The repeated word length is usually 5, the word length distribution is similar between plastomes and mitochondriomes.
About the Authors
O. A. ZverkovRussian Federation
L. Y. Rusin
Russian Federation
A. V. Seliverstov
Russian Federation
V. A. Lyubetsky
Russian Federation
References
1. Kurtz S., Choudhuri J.V., Ohlebusch E., Schleiermacher C., Stoye J., Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale // Nuc. Acids Res. 2001. Vol. 29. P. 4633—4642.
2. Yang M., Zhang X. et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.) // PLoS ONE. 2010. Vol. 5. 9. e12762.
3. Greiner S., Wang X., Rauwolf U., Silber M.V., Mayer K., Meurer J., Haberer G., Herrmann R.G. The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. Sequence evaluation and plastome evolution // Nuc. Acids Res. 2008. Vol. 36. N 7. P. 2366—2378.
4. Ogihara Y., Terachi T., Sasakuma T. Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species // Proc. Natl. Acad. Sci. USA. 1988. Vol. 85. N 22.P. 8573—8577.
5. Cai Z., Guisinger M., Kim H.G., Ruck E., Blazier J.C., McMurtry V., Kuehl J.V., Boore J., Jansen R.K. Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions // J. Mol. Evol. 2008. Vol. 67. N 6. P. 696—704.
6. Timme R.E., Kuehl J.V., Boore J.L., Jansen R.K. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats // Amer. J. Bot. 2007. Vol. 94. N 3. P. 302—312.
7. Moore M.J., Hassan N., Gitzendanner M.A., Bruenn R.A., Croley M., Vandeventer A., Horn J.W., Dhingra A., Brockington S.F., Latvis M., Ramdial J., Alexandre R., Pied- rahita A., Xi Z., Davis C.C., Soltis P.S., Soltis D.E. Phylogenetic analysis of the plastid inverted repeat for 244 species: insights into deeper-level angiosperm relationships from a long, slowly evolving sequence region // Intern. J. Plant Sci. 2011. Vol. 172. N 4. P. 541—558.
8. Honma Y., Yoshida Y., Terachi T., Toriyama K., Mikami T., Kubo T. Polymorphic minisatellites in the mitochondrial DNAs of Oryza and Brassica // Current genetics. 2011. Vol. 57. N 4. P. 261—270.
9. Borsch T., Quandt D. Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA // Plant Syst. Evol. 2009. Vol. 282. P. 169—199.
10. Kelchner S.A. The evolution of non-coding chloroplast DNA and its application in plant systematics // Ann. Missouri Bot. Garden. 2000. Vol. 87. P. 482—498.
11. Ingvarsson P.K., Ribstein S., Taylor D.R. Molecular evolution of insertions and deletion in the chloroplast genome of Silene // Mol. Biol. Evol. 2003. Vol. 20. N 11. P. 1737—1740.
12. Официальный сайт лаборатории Института проблем передачи информации им. А.А. Харкевича РАН (URL: http://lab6.iitp.ru/ru/repeats 25.08.2011).
13. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput // Nucleic Acids Res. 2004. Vol. 32. P. 1792—1797.
14. Официальный сайт лаборатории Института проблем передачи информации РАН (URL: http://lab6.iitp.ru/en/treeal/25.08.2011).
15. Зверков О.А., Селиверстов А.В., Любецкий В.А. Белковые семейства, специфичные для пластомов небольших таксономических групп водорослей и простейших // Молекулярная биология. 2012. Т. 46. № 5. С. 799—809.
16. Селиверстов А.В., Любецкий В.А. Прямые повторы в некодирующих областях хлоропластов у семенных растений // Тр. 52-й науч. конф. Моск. физ.-тех. ун-та. 2009. Т. 1. № 1. P. 116—117.
17. Зверков О.А., Русин Л.Ю., Селиверстов А.В., Любецкий В.А. Вставки прямых повторов в микроэволюции пластид и митохондрий семенных растений // Информационные процессы. 2012. Т. 12. № 3. С. 191—197.
Review
For citations:
Zverkov O.A., Rusin L.Y., Seliverstov A.V., Lyubetsky V.A. A STUDY OF DIRECT REPEATS IN MICROEVOLUTION OF PLANT MITOCHONDRIA AND PLASTIDS BASED ON PROTEIN CLUSTERING. Vestnik Moskovskogo universiteta. Seriya 16. Biologiya. 2013;(1):8-13. https://doi.org/10.1234/XXXX-XXXX-2013-1-8-13
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