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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 correlation pattern of indel numbers and indel sizes among three cp genomes.The X-axis and Y-axis represent the indel sizes in base pair and indel numbers, respectively.
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pone-0035872-g007: The correlation pattern of indel numbers and indel sizes among three cp genomes.The X-axis and Y-axis represent the indel sizes in base pair and indel numbers, respectively.

Mentions: The indel patterns of chloroplast genomes from the three different hierarchical comparisons are summarized in Figure 7. The data suggest that similar indel patterns are observed, regardless of the taxonomic hierarchies. The data also indicate that large indels are relatively rare and that the majority of indels are less than 10 bp in length (Figure 7, Table S4).


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

Yi DK, Kim KJ - PLoS ONE (2012)

The correlation pattern of indel numbers and indel sizes among three cp genomes.The X-axis and Y-axis represent the indel sizes in base pair and indel numbers, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0035872-g007: The correlation pattern of indel numbers and indel sizes among three cp genomes.The X-axis and Y-axis represent the indel sizes in base pair and indel numbers, respectively.
Mentions: The indel patterns of chloroplast genomes from the three different hierarchical comparisons are summarized in Figure 7. The data suggest that similar indel patterns are observed, regardless of the taxonomic hierarchies. The data also indicate that large indels are relatively rare and that the majority of indels are less than 10 bp in length (Figure 7, Table S4).

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