Distribution of Values of GC-Content of the Fragments in the Spatial Structure of Mitochondrial, Chloroplast and Bacterial Genomes

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

Distribution of values of GC-content of the fragments in spatial structure of chloroplast, mitochondrial, and bacterial genomes were explored. It was found that GC-content in the fragments for most genomes is identically but not independent distributed varaible. Two main types of distribution have been revealed: the gradient distribution and centrally symmetrical distribution. Chloroplast genomes have only a gradient distribution. In bacteria, for the GC-poor genomes, a centrally symmetrical distribution is observed, while there is a gradient distribution in the GC-rich genomes. In mitochondria, both types of distribution are present, the type of distribution depends on the type of an organism.

About the authors

M. Yu Senashova

Institute of Computational Modelling, Siberian Branch of the Russian Academy of Sciences

Email: msen@icm.krasn.ru
Krasnoyarsk, Russia

M. G Sadovsky

Institute of Computational Modelling, Siberian Branch of the Russian Academy of Sciences; Federal Siberian Research Clinical Center, FMBA of Russia; Siberian Federal University

Email: msad@icm.krasn.ru
Krasnoyarsk, Russia; Krasnoyarsk, Russia; Krasnoyarsk, Russia

References

  1. Shimda H. and Sugiuro M. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucl. Acids Res., 19 (5), 983–995 (1991). doi: 10.1093/nar/19.5.983
  2. Young H. A., Lanzatella C. L., Sarath G., and Tobias C. M. Chloroplast genome variation in upland and lowland switchgrass. PLoS One, 6 (8), e23980 (2011). doi: 10.1371/journal.pone.0023980
  3. Lockhart P. J., Penny D., Hendy M. D., Howe C. J., Beanland T. J., and Larkum A. W. D. Controversy on chloroplast origins. FEBS Lett., 301 (2), 127–131 (1992). doi: 10.1016/0014-5793(92)81231-A
  4. Gao L., Yi X., Yang Y. X., Su Y. J., and Wang T. Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol. Biol., 9, 130 (2009). doi: 10.1186/1471-2148-9-130
  5. Wu Z. Q. and Ge S. The phylogeny of the BEP clade in grasses revisited: evidence from the whole-genome sequences of chloroplasts. Mol. Phylogen. Evol., 62 (1), 573–578 (2012). doi: 10.1016/j.ympev.2011.10.019
  6. Qian J., Song J., Gao H., Zhu Y., Xu J., Pang X., Yao H., Sun C., Li X., Li C., Liu J., Xu H., and Chen S. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS One, 8 (2), e57607 (2013). doi: 10.1371/journal.pone.0057607
  7. Zhang T., Fang Y., Wang X., Deng X., Zhang X., Hu S., and Yu J. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes. PLoS One, 7 (1), e30531 (2012). doi: 10.1371/journal.pone.0030531
  8. Yang Y., Zhou T., Duan D., Yang J., Feng L., and Zhao G. Comparative analysis of the complete chloroplast genomes of five Quercus species. Front. Plant Sci., 7, 959 (2016). doi: 10.3389/fpls.2016.00959
  9. Hildebrand F., Meyer A., and Eyre-Walker A. Evidence of selection upon genomic GC-content in bacteria. PLoS Genetics, 6 (9), e1001107 (2010). doi: 10.1371/journal.pgen.1001107
  10. Gorban A. N., Popova T. G., and Zinovyev A. Y. Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences. In silico Biol., 5 (3), 265–282 (2005). doi: 10.48550/arXiv.q-bio/0410033
  11. Gorban A. N., Zinovyev A. Y., and Popova T. G. Seven clusters in genomic triplet distributions. In silico Biol., 3 (4), 471–482 (2003). doi: 10.48550/arXiv.cond-mat/0305681
  12. Lightfield J., Fram N. R., and Ely B. Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage. PLoS One, 6 (3), e17677 (2011). doi: 10.1371/journal.pone.0017677
  13. Peano C., Pietrelli A., Consolandi C., Rossi E., Petiti L., Tagliabue L., De Bellis D., and Landini P. An efficient rRNA removal method for RNA sequencing in GC-rich bacteria. Microb. Informatics Exp., 3, 1 (2013). doi: 10.1186/2042-5783-3-1
  14. Zhou H. Q., Ning L. W., Zhang H. X., and Guo F. B. Analysis of the relationship between genomic GC content and patterns of base usage, codon usage and amino acid usage in prokaryotes: similar GC content adopts similar compositional frequencies regardless of the phylogenetic lineages. PLoS One, 9 (9), e107319 (2014). doi: 10.1371/journal.pone.0107319
  15. Giannoukos G., Ciulla D. M., Huang K., Haas B. J., Izard J., Levin J. Z., Livny J., Earl A. M., Gevers D., Ward D. V., Nusbaum C., Birren B. W., and Gnirke A. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol., 13, r23 (2012). doi: 10.1186/gb-2012-13-3-r23
  16. Behura S. K., Lobo N. F., Haas B., DeBruyn B., Lovin D. D., Shumway M. F., Puiu D., Romero-Severson J., Nene V., and Severson D. W. Complete sequences of mitochondria genomes of Aedes aegypti and Culex quinquefasciatus and comparative analysis of mitochondrial DNA fragments inserted in the nuclear genomes. Insect Biochem. Mol. Biol., 41 (10), 770–777 (2011). doi: 10.1016/j.ibmb.2011.05.006
  17. Johnston I. G. and Williams B. P. Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention. Cell Systems, 2 (2), 101–111 (2016). doi: 10.1101/037960
  18. Ferla M. P. et al. New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS One, 8 (12), e83383 (2013). doi: 10.1371/journal.pone.0083383
  19. Nakamura Y., Sasaki N., Kobayashi M., Ojima N., Yasuike M., Shigenobu Y., Satomi M., Fukuma Y., Shiwaku K., Tsujimoto A., Kobayashi T., Nakayama I., Ito F., Nakajima K., Sano M., Wada T., Kuhara S., Inouye K., Gojobori T., and Ikeo K. The first symbiontfree genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). PLoS One, 8 (3), e57122 (2013). doi: 10.1371/journal.pone.0057122
  20. Godel C., Kumar S., Koutsovoulos G., Ludin P., Nilsson D., Comandatore F., Wrobel N., Thompson M., Schmid C.D., Goto S., BringaudF., Wolstenholme A., Bandi C., Epe C., Kaminsky R., Blaxter M., and Mäser P. The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets. FASEB J., 26 (11), 4650 (2012). doi: 10.1096/fj.12-205096
  21. Imanian B., Pombert J. F., Dorrell R. G., Burki F., and Keeling P. J. Tertiary endosymbiosis in two dinotoms has generated little change in the mitochondrial genomes of their dinof lagellate hosts and diatom endosymbionts. PLoS One, 7 (8), e43763 (2012). doi: 10.1371/journal.pone.0043763
  22. Wei L., He J., Jia X., Qi Q., Liang Z., Zheng H., Ping Y., Liu S, and Sun J. Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution BMC Evol. Biol., 14, 262 (2014). doi: 10.1186/s12862-014-0262-4
  23. Sadovsky M. G., Senashova M. Y., and Malyshev A. V. Amazing symmetrical clustering in chloroplast genomes. BMC Bioinformatics, 21 (Suppl. 2), 83 (2020). doi: 10.1186/s12859-020-3350-z

Copyright (c) 2024 Russian Academy of Sciences

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies