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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 levels of evolutionary divergences among the SSC, LSC, and IR regions of cp genomes. Y-axis represents the sequence divergences. The IR region evolves slower than the SSC or the LSC regions regardless the CDS, intron and IGS.
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pone-0035872-g006: The levels of evolutionary divergences among the SSC, LSC, and IR regions of cp genomes. Y-axis represents the sequence divergences. The IR region evolves slower than the SSC or the LSC regions regardless the CDS, intron and IGS.

Mentions: To address the evolutionary constraint issue in the Sesamum cp genome, a series of comparative sequence analyses were conducted using Sesamum cp DNA sequences along with the published cp genome sequences of Olea, Nicotiana and Panax (Table S1, S2, and S3). These three sequences were selected because they belong to the same or closely related taxonomic orders, Lamiales and Solanales. The gene order of the cp genomes was co-linear among these four genera. An alignment of the protein-coding genes, introns, and intergenic spacer regions, along with positional information of the cp genomes for Sesamum and three other genera was performed. Of 114 genes, 84 CDS were analyzed. The 30 tRNA genes were excluded in this comparative analysis due to their short length. A total of 110 IGS and 19 intron sequences were also analyzed. First, the sequence comparison data was partitioned into CDS, intron, and IGS regions. The sequence divergence ratios among the three regions (CDS:intron:IGS) were 1∶1.3∶2.2 between Sesamum and Olea, 1∶1.3∶2.3 between Sesamum and Nicotiana, and 1∶1.3∶2.1 between Sesamum and Panax (Table 5). The ratios in these three comparisons are similar. This clearly suggests that the intron sequences have evolved more rapidly than the CDS but slower than the IGS sequences. Second, the sequence comparison data was partitioned into IR, LSC and SSC regions. The sequence divergence ratios among the three regions (IR:LSC:SSC) were 1∶4.7∶6.9 between Sesamum and Olea, 1∶5.3∶6.8 between Sesamum and Nicotiana, and 1∶5.2∶6.2 between Sesamum and Panax. That the ratios are relatively consistent between three different comparisons clearly suggests that the IR regions have evolved much slower than the LSC and SSC regions (Figure 6). The same tendencies are prominent even when comparing the CDS or noncoding sequences for each of the three regions separately. As an example, 19 intron sequences show markedly slow down patterns of base substitutions in IR regions (Figure 3). Furthermore, the Ka/Ks ratio data for the CDS also indicate that the IR region has stronger selection pressures than either the LSC or SSC regions; therefore, these data confirm that positional effects are stronger constraints for sequence evolution than the functional groups of chloroplast genes.


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

Yi DK, Kim KJ - PLoS ONE (2012)

The levels of evolutionary divergences among the SSC, LSC, and IR regions of cp genomes. Y-axis represents the sequence divergences. The IR region evolves slower than the SSC or the LSC regions regardless the CDS, intron and IGS.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0035872-g006: The levels of evolutionary divergences among the SSC, LSC, and IR regions of cp genomes. Y-axis represents the sequence divergences. The IR region evolves slower than the SSC or the LSC regions regardless the CDS, intron and IGS.
Mentions: To address the evolutionary constraint issue in the Sesamum cp genome, a series of comparative sequence analyses were conducted using Sesamum cp DNA sequences along with the published cp genome sequences of Olea, Nicotiana and Panax (Table S1, S2, and S3). These three sequences were selected because they belong to the same or closely related taxonomic orders, Lamiales and Solanales. The gene order of the cp genomes was co-linear among these four genera. An alignment of the protein-coding genes, introns, and intergenic spacer regions, along with positional information of the cp genomes for Sesamum and three other genera was performed. Of 114 genes, 84 CDS were analyzed. The 30 tRNA genes were excluded in this comparative analysis due to their short length. A total of 110 IGS and 19 intron sequences were also analyzed. First, the sequence comparison data was partitioned into CDS, intron, and IGS regions. The sequence divergence ratios among the three regions (CDS:intron:IGS) were 1∶1.3∶2.2 between Sesamum and Olea, 1∶1.3∶2.3 between Sesamum and Nicotiana, and 1∶1.3∶2.1 between Sesamum and Panax (Table 5). The ratios in these three comparisons are similar. This clearly suggests that the intron sequences have evolved more rapidly than the CDS but slower than the IGS sequences. Second, the sequence comparison data was partitioned into IR, LSC and SSC regions. The sequence divergence ratios among the three regions (IR:LSC:SSC) were 1∶4.7∶6.9 between Sesamum and Olea, 1∶5.3∶6.8 between Sesamum and Nicotiana, and 1∶5.2∶6.2 between Sesamum and Panax. That the ratios are relatively consistent between three different comparisons clearly suggests that the IR regions have evolved much slower than the LSC and SSC regions (Figure 6). The same tendencies are prominent even when comparing the CDS or noncoding sequences for each of the three regions separately. As an example, 19 intron sequences show markedly slow down patterns of base substitutions in IR regions (Figure 3). Furthermore, the Ka/Ks ratio data for the CDS also indicate that the IR region has stronger selection pressures than either the LSC or SSC regions; therefore, these data confirm that positional effects are stronger constraints for sequence evolution than the functional groups of chloroplast genes.

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