Research Article | Volume: 2, Issue: 3, May-June, 2014
Comparative and Bioinformatics Analyses of the Solanaceae Chloroplast Genomes: Plastome Organization is more or Less Conserved at Family Level
Chloroplast genome of the seven members of the family solanaceae – Nicotiana tabacum, N. sylvestris, N. tomentosiformis, N. undulate, Solanum tuberosum, S. lycopersicum, and S. bulbocastanum were extracted from NCBI Gene Bank and were subjected to the bioinformatics study. In this study we found that the genes and amino acid sequences in the proteins were almost identical and conserved. Even the structure and sequences of introns were more or less conserved. Certain variations were observed in the nature and occurrence of open reading frames, which may be due to species specific genome. Some variations were also observed when compared these dicot genomes with the monocot genome of rice. But in contrast to some primitive species such as members of cryptophyta, there were fewer numbers of genes which may be due to the transfer of some chloroplast genes into the nuclear genome.
Dipen Ghimiray and Binod Chandra Sharma. Comparative and Bioinformatics Analyses of the Solanaceae Chloroplast Genomes: Plastome Organization is more or Less Conserved At Family Level. J App Biol Biotech. 2014; 2 (03): 021-026. DOI: 10.7324/JABB.2014.2305
1. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matshubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H and Sugiura M. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO Journal. 1986; 5: 2043-2049.
2 Yukawa M, Tsudzuki T and Sugiura M. The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum. Molecular Genetics and Genomics. 2006; 275 (4):367-373.
3 Thyssen G, Svab Z and Maliga P. NCBI Genome Project, NIH, Bethesda, USA, 2011.
4 Daniell H, Lee SB, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J and Jansen RK. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theoretical and Applied Genetics. 2006; 112 (8): 1503-1518.
5 Shimada H and Sugiura M. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucleic Acids Research. 1991; 19 (5): 983-995.
6 Sato S, Nakamura Y, Kaneko T, Asamizu E and Tabata S. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Research. 1999; 6 (5): 283-290.
7 Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H & Deeper YV. The Complete Chloroplast and Mitochondrial DNA Sequence of Ostreococcus tauri: Organelle Genomes of the Smallest Eukaryote are Example of Compaction. Molecular Biology and Evolution. 2007; 24(4): 956-968.
8 Sharma BC and Ghimiray D. Analysis of the Cryptophyta chloroplast genome reveals presence of additional genes and absence of introns in their genome. Biological Forum 2012; 4(2): 1-7.
9 Tang J, Xia H, Cao M, Zhang X, Zeng W, Hu S, Tong W, Wang J, Wang J, Yu J, Yang H and Zhu L. A comparison of rice chloroplast genomes. Plant Physiology. 2004; 135 (1):412-420.
10 Shanker A. Chloroplast genomes of bryophytes: A review. Archive for Bryology. 2012; 143:1-5.
11 Turmel M, Otis C and Lemieux C. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proc. Natl. Acad. Sci. U.S.A. 1999; 96 (18): 10248-10253.
12 Turmel M, Otis C and Lemieux C. The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc. Natl. Acad. Sci. U.S.A. 2002; 99 (17): 11275-11280.
13 Turmel M, Otis C and Lemieux C. The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales. BMC Biology. 2005, 3:22 doi:10.1186/1741-7007-3-22.
14 Turmel M, Otis C and Lemieux C. The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants. Molecular Biology and Evolution. 2006; 23 (6):1324-1338.
15 Turmel M, Gagnon MC, O'Kelly CJ, Otis C and Lemieux C. The chloroplast genomes of the green algae Pyramimonas, Monomastix and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of euglenids. Molecular Biology and Evolution. 2009; 26 (3): 631-648.
16 Turmel M, Otis C and Lemieux C. The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales. Molecular Biology and Evolution. 2009; 26 (10): 2317-2331.
17 Lyubetsky VA, Rubanov LI and Seliverstov AV. Lack of conservation of bacterial type promoters in plastids of Streptophyta. Biology Direct. 2010; 5:34 doi:10.1186/1745-6150-5-34.
18 Gargano D, Vezzi A, Scotti N, Gray JC, Valle G, Grillo S and Cardi T. The complete nucleotide sequence of potato (Solanum tuberosum cv. Desiree) chloroplast DNA. In Abstracts: 2nd Solanaceae Genome Workshop 2005: 107
19 NCBI GenBank, USA. http://www.ncbi.nlm.nih.gov/genomes
20 Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li YQ, Kanno A, Nishizawa Y, Hirai A, Shinozaki K & Sugiura M. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Molecular and General Genetics. 1989; 217 (2-3): 185-194.
21 Douglas SE and Penny SL. The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae. Journal of Molecular Evolution. 1999; 48 (2) :236-244.
22 Khan H, Parks N, Kozera C, Curtis BA, Parsons BJ, Bowman S and Archibald JM. Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny. Molecular Biology and Evolution. 2007; 24 (8): 1832- 1842.
23 Donaher N, Tanifuji G, Onodera NT, Malfatti SA, Chain PS, Hara Y and Archibald JM. The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biology and Evolution. 2009; 1: 439-448.
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