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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 gene map of Sesamum indicum cp genome.A pair of thick lines at the inside circle represents the inverted repeats (IRa and IRb; 25,141 bp each), which separate the large single copy region (LSC; 85,170 bp) from the small single copy region (SSC; 17,872 bp). Genes drawn inside the circle are transcribed clockwise, while those drawn outside the circle are transcribed counterclockwise. Intron-containing genes are marked by asterisks. The numbers at the outmost circle indicate the locations of 7 repeats including direct (black number), palimdromic (blue number), and dispersed repeats (red numbers), respectively (cf. Table 4).
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pone-0035872-g001: The gene map of Sesamum indicum cp genome.A pair of thick lines at the inside circle represents the inverted repeats (IRa and IRb; 25,141 bp each), which separate the large single copy region (LSC; 85,170 bp) from the small single copy region (SSC; 17,872 bp). Genes drawn inside the circle are transcribed clockwise, while those drawn outside the circle are transcribed counterclockwise. Intron-containing genes are marked by asterisks. The numbers at the outmost circle indicate the locations of 7 repeats including direct (black number), palimdromic (blue number), and dispersed repeats (red numbers), respectively (cf. Table 4).

Mentions: The Sesamum indicum cp genome exhibits the general cp genome structure characteristic of flowering plants. It contains a pair of inverted repeat regions (IRa and IRb) that comprise 25,141 bp each. The two IR regions divide the genome into a large single copy (LSC) region and a small single copy (SSC) region. The LSC region is 85,170 bp, whereas the SSC region is 17,872 bp. The complete cp sequence of S. indicum is 153,324 bp in length (GenBank acc no. JN637766), of which 58% is coding regions and 42% is non-coding regions. A total of 114 genes are contained within the S. indicum cp genome, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes (Figure 1, Table 1). Ten protein-coding and seven tRNA coding genes are duplicated on the IR regions. The LSC region contains 62 protein-coding and 22 tRNA genes, while the SSC region contains 12 protein-coding and one tRNA gene. Similar to the Nicotiana and Panax cp genomes, 18 of the genes in the S. indicum cp genome have one or two introns. Of these, rps12, clpP and ycf3 have two introns. The rps12 gene is a uniquely divided gene with the 5′ end exon located in the LSC region while two copies of 3′ end exon and intron are located in the IR region.


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

Yi DK, Kim KJ - PLoS ONE (2012)

The gene map of Sesamum indicum cp genome.A pair of thick lines at the inside circle represents the inverted repeats (IRa and IRb; 25,141 bp each), which separate the large single copy region (LSC; 85,170 bp) from the small single copy region (SSC; 17,872 bp). Genes drawn inside the circle are transcribed clockwise, while those drawn outside the circle are transcribed counterclockwise. Intron-containing genes are marked by asterisks. The numbers at the outmost circle indicate the locations of 7 repeats including direct (black number), palimdromic (blue number), and dispersed repeats (red numbers), respectively (cf. Table 4).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0035872-g001: The gene map of Sesamum indicum cp genome.A pair of thick lines at the inside circle represents the inverted repeats (IRa and IRb; 25,141 bp each), which separate the large single copy region (LSC; 85,170 bp) from the small single copy region (SSC; 17,872 bp). Genes drawn inside the circle are transcribed clockwise, while those drawn outside the circle are transcribed counterclockwise. Intron-containing genes are marked by asterisks. The numbers at the outmost circle indicate the locations of 7 repeats including direct (black number), palimdromic (blue number), and dispersed repeats (red numbers), respectively (cf. Table 4).
Mentions: The Sesamum indicum cp genome exhibits the general cp genome structure characteristic of flowering plants. It contains a pair of inverted repeat regions (IRa and IRb) that comprise 25,141 bp each. The two IR regions divide the genome into a large single copy (LSC) region and a small single copy (SSC) region. The LSC region is 85,170 bp, whereas the SSC region is 17,872 bp. The complete cp sequence of S. indicum is 153,324 bp in length (GenBank acc no. JN637766), of which 58% is coding regions and 42% is non-coding regions. A total of 114 genes are contained within the S. indicum cp genome, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes (Figure 1, Table 1). Ten protein-coding and seven tRNA coding genes are duplicated on the IR regions. The LSC region contains 62 protein-coding and 22 tRNA genes, while the SSC region contains 12 protein-coding and one tRNA gene. Similar to the Nicotiana and Panax cp genomes, 18 of the genes in the S. indicum cp genome have one or two introns. Of these, rps12, clpP and ycf3 have two introns. The rps12 gene is a uniquely divided gene with the 5′ end exon located in the LSC region while two copies of 3′ end exon and intron are located in the IR region.

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