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Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L.

Yi DK, Kim KJ - PLoS ONE (2012)

Bottom Line: Twenty-eight different simple sequence repeat loci have been detected in the chloroplast genome of S. indicum.Almost all of the SSR loci were composed of A or T, so this may also contribute to the A-T richness of the cp genome of S. indicum.Seven large repeated loci in the chloroplast genome of S. indicum were also identified and these loci are useful to developing S. indicum-specific cp genome vectors.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Korea University, Seoul, Korea.

ABSTRACT
Sesamum indicum is an important crop plant species for yielding oil. The complete chloroplast (cp) genome of S. indicum (GenBank acc no. JN637766) is 153,324 bp in length, and has a pair of inverted repeat (IR) regions consisting of 25,141 bp each. The lengths of the large single copy (LSC) and the small single copy (SSC) regions are 85,170 bp and 17,872 bp, respectively. Comparative cp DNA sequence analyses of S. indicum with other cp genomes reveal that the genome structure, gene order, gene and intron contents, AT contents, codon usage, and transcription units are similar to the typical angiosperm cp genomes. Nucleotide diversity of the IR region between Sesamum and three other cp genomes is much lower than that of the LSC and SSC regions in both the coding region and noncoding region. As a summary, the regional constraints strongly affect the sequence evolution of the cp genomes, while the functional constraints weakly affect the sequence evolution of cp genomes. Five short inversions associated with short palindromic sequences that form step-loop structures were observed in the chloroplast genome of S. indicum. Twenty-eight different simple sequence repeat loci have been detected in the chloroplast genome of S. indicum. Almost all of the SSR loci were composed of A or T, so this may also contribute to the A-T richness of the cp genome of S. indicum. Seven large repeated loci in the chloroplast genome of S. indicum were also identified and these loci are useful to developing S. indicum-specific cp genome vectors. The complete cp DNA sequences of S. indicum reported in this paper are prerequisite to modifying this important oilseed crop by cp genetic engineering techniques.

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The comparison of the LSC, IR and SSC border regions among five cp genomes.
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pone-0035872-g002: The comparison of the LSC, IR and SSC border regions among five cp genomes.

Mentions: The length of angiosperm cp genomes is variable primarily due to expansion and contraction of the inverted repeat IR region and the single copy boundary regions. To elucidate this mechanism, the IR/SC boundary regions of the cp genomes of Sesamum, Nicotiana, Panax, Olea, and Arabidopsis (Figure 2) were compared. Rps19 and ycf1 pseudogenes of various lengths were found at the IR/LSC and IR/SSC boundaries, respectively. The rps19 pseudogene was not found at the LSC region in the Nicotiana and Olea cp genomes. In the Sesamum cp genome, the IR extended into the rps19 gene and created a short rps19 pseudogene of 30 bp at the IR/LSC border. This same pseudogene was 51 bp and 113 bp, respectively, in the Panax and Arabidopsis cp genomes. At the IR/SSC border of the Sesamum cp genome, the IR extended into the ycf1 gene to create a long ycf1 pseudogene of 1,100 bp at the IR/LSC border. This ycf1 pseudogene was 1,164 bp in Olea and 1,649 bp in Panax. In addition, the ycf1 pseudogene and the ndhF gene overlap in both the Olea and Sesamum cp genomes for 97 and 70 bp, respectively.


Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L.

Yi DK, Kim KJ - PLoS ONE (2012)

The comparison of the LSC, IR and SSC border regions among five cp genomes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3351433&req=5

pone-0035872-g002: The comparison of the LSC, IR and SSC border regions among five cp genomes.
Mentions: The length of angiosperm cp genomes is variable primarily due to expansion and contraction of the inverted repeat IR region and the single copy boundary regions. To elucidate this mechanism, the IR/SC boundary regions of the cp genomes of Sesamum, Nicotiana, Panax, Olea, and Arabidopsis (Figure 2) were compared. Rps19 and ycf1 pseudogenes of various lengths were found at the IR/LSC and IR/SSC boundaries, respectively. The rps19 pseudogene was not found at the LSC region in the Nicotiana and Olea cp genomes. In the Sesamum cp genome, the IR extended into the rps19 gene and created a short rps19 pseudogene of 30 bp at the IR/LSC border. This same pseudogene was 51 bp and 113 bp, respectively, in the Panax and Arabidopsis cp genomes. At the IR/SSC border of the Sesamum cp genome, the IR extended into the ycf1 gene to create a long ycf1 pseudogene of 1,100 bp at the IR/LSC border. This ycf1 pseudogene was 1,164 bp in Olea and 1,649 bp in Panax. In addition, the ycf1 pseudogene and the ndhF gene overlap in both the Olea and Sesamum cp genomes for 97 and 70 bp, respectively.

Bottom Line: Twenty-eight different simple sequence repeat loci have been detected in the chloroplast genome of S. indicum.Almost all of the SSR loci were composed of A or T, so this may also contribute to the A-T richness of the cp genome of S. indicum.Seven large repeated loci in the chloroplast genome of S. indicum were also identified and these loci are useful to developing S. indicum-specific cp genome vectors.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Korea University, Seoul, Korea.

ABSTRACT
Sesamum indicum is an important crop plant species for yielding oil. The complete chloroplast (cp) genome of S. indicum (GenBank acc no. JN637766) is 153,324 bp in length, and has a pair of inverted repeat (IR) regions consisting of 25,141 bp each. The lengths of the large single copy (LSC) and the small single copy (SSC) regions are 85,170 bp and 17,872 bp, respectively. Comparative cp DNA sequence analyses of S. indicum with other cp genomes reveal that the genome structure, gene order, gene and intron contents, AT contents, codon usage, and transcription units are similar to the typical angiosperm cp genomes. Nucleotide diversity of the IR region between Sesamum and three other cp genomes is much lower than that of the LSC and SSC regions in both the coding region and noncoding region. As a summary, the regional constraints strongly affect the sequence evolution of the cp genomes, while the functional constraints weakly affect the sequence evolution of cp genomes. Five short inversions associated with short palindromic sequences that form step-loop structures were observed in the chloroplast genome of S. indicum. Twenty-eight different simple sequence repeat loci have been detected in the chloroplast genome of S. indicum. Almost all of the SSR loci were composed of A or T, so this may also contribute to the A-T richness of the cp genome of S. indicum. Seven large repeated loci in the chloroplast genome of S. indicum were also identified and these loci are useful to developing S. indicum-specific cp genome vectors. The complete cp DNA sequences of S. indicum reported in this paper are prerequisite to modifying this important oilseed crop by cp genetic engineering techniques.

Show MeSH
Related in: MedlinePlus