Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

Complete chloroplast genome sequences of Solanum bulbocastanum , Solanum lycopersicum and comparative analyses with other Solanaceae genomes

Complete chloroplast genome sequences of Solanum bulbocastanum , Solanum lycopersicum and... Despite the agricultural importance of both potato and tomato, very little is known about their chloroplast genomes. Analysis of the complete sequences of tomato, potato, tobacco, and Atropa chloroplast genomes reveals significant insertions and deletions within certain coding regions or regulatory sequences (e.g., deletion of repeated sequences within 16S rRNA, ycf 2 or ribosomal binding sites in ycf 2). RNA, photosynthesis, and atp synthase genes are the least divergent and the most divergent genes are clpP , cemA , ccsA , and matK . Repeat analyses identified 33–45 direct and inverted repeats ≥30 bp with a sequence identity of at least 90%; all but five of the repeats shared by all four Solanaceae genomes are located in the same genes or intergenic regions, suggesting a functional role. A comprehensive genome-wide analysis of all coding sequences and intergenic spacer regions was done for the first time in chloroplast genomes. Only four spacer regions are fully conserved (100% sequence identity) among all genomes; deletions or insertions within some intergenic spacer regions result in less than 25% sequence identity, underscoring the importance of choosing appropriate intergenic spacers for plastid transformation and providing valuable new information for phylogenetic utility of the chloroplast intergenic spacer regions. Comparison of coding sequences with expressed sequence tags showed considerable amount of variation, resulting in amino acid changes; none of the C-to-U conversions observed in potato and tomato were conserved in tobacco and Atropa . It is possible that there has been a loss of conserved editing sites in potato and tomato. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png TAG Theoretical and Applied Genetics Springer Journals

Complete chloroplast genome sequences of Solanum bulbocastanum , Solanum lycopersicum and comparative analyses with other Solanaceae genomes

Download PDF
16 pages

Loading next page...
 
/lp/springer-journals/complete-chloroplast-genome-sequences-of-solanum-bulbocastanum-solanum-XeloVd8FhM

References (109)

Publisher
Springer Journals
Copyright
Copyright © 2006 by Springer-Verlag
Subject
Life Sciences; Biotechnology; Biochemistry, general; Plant Biochemistry; Agriculture; Plant Genetics & Genomics; Plant Breeding/Biotechnology
ISSN
0040-5752
eISSN
1432-2242
DOI
10.1007/s00122-006-0254-x
pmid
16575560
Publisher site
See Article on Publisher Site

Abstract

Despite the agricultural importance of both potato and tomato, very little is known about their chloroplast genomes. Analysis of the complete sequences of tomato, potato, tobacco, and Atropa chloroplast genomes reveals significant insertions and deletions within certain coding regions or regulatory sequences (e.g., deletion of repeated sequences within 16S rRNA, ycf 2 or ribosomal binding sites in ycf 2). RNA, photosynthesis, and atp synthase genes are the least divergent and the most divergent genes are clpP , cemA , ccsA , and matK . Repeat analyses identified 33–45 direct and inverted repeats ≥30 bp with a sequence identity of at least 90%; all but five of the repeats shared by all four Solanaceae genomes are located in the same genes or intergenic regions, suggesting a functional role. A comprehensive genome-wide analysis of all coding sequences and intergenic spacer regions was done for the first time in chloroplast genomes. Only four spacer regions are fully conserved (100% sequence identity) among all genomes; deletions or insertions within some intergenic spacer regions result in less than 25% sequence identity, underscoring the importance of choosing appropriate intergenic spacers for plastid transformation and providing valuable new information for phylogenetic utility of the chloroplast intergenic spacer regions. Comparison of coding sequences with expressed sequence tags showed considerable amount of variation, resulting in amino acid changes; none of the C-to-U conversions observed in potato and tomato were conserved in tobacco and Atropa . It is possible that there has been a loss of conserved editing sites in potato and tomato.

Journal

TAG Theoretical and Applied Genetics – Springer Journals

Published: May 1, 2006

There are no references for this article.