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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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A maximum likelihood tree (-lnL = 428640.9970) of the asterid clade of angiosperm using whole chloroplast genome sequences.The tree was polarized by two outgroup taxa, Spinacea and Arabidopsis. The GTR+G+I base substitution model was adopted based on the Modeltest. Molecular clock was calibrated using two internal splitting points of the members of Araliaceae (70 mya) and Solanaceae (53 mya). The numbers above each node indicate the Bayesian support percentages. Taxon abbreviations are Solanum(bu): Solanum bulbocastanum, Solanum(tu): Solanum tuberosum, Solanum(ly): Solanum lycopersicum, Nicotiana(sy): Nicotiana sylvestris, Nicotiana(ta): Nicotiana tabacum, Nicotiana(to): Nicotiana tomentosiformis, Olea(eb): Olea europaea cv. bianchera, Olea(ee): Olea europaea subsp. europaea, Olea(em): Olea europaea subsp. maroccana, Olea(ec): Olea europaea subsp. Cuspidate and Olea(ew): Olea europaea subsp. Woodiana, respectively.
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pone-0035872-g005: A maximum likelihood tree (-lnL = 428640.9970) of the asterid clade of angiosperm using whole chloroplast genome sequences.The tree was polarized by two outgroup taxa, Spinacea and Arabidopsis. The GTR+G+I base substitution model was adopted based on the Modeltest. Molecular clock was calibrated using two internal splitting points of the members of Araliaceae (70 mya) and Solanaceae (53 mya). The numbers above each node indicate the Bayesian support percentages. Taxon abbreviations are Solanum(bu): Solanum bulbocastanum, Solanum(tu): Solanum tuberosum, Solanum(ly): Solanum lycopersicum, Nicotiana(sy): Nicotiana sylvestris, Nicotiana(ta): Nicotiana tabacum, Nicotiana(to): Nicotiana tomentosiformis, Olea(eb): Olea europaea cv. bianchera, Olea(ee): Olea europaea subsp. europaea, Olea(em): Olea europaea subsp. maroccana, Olea(ec): Olea europaea subsp. Cuspidate and Olea(ew): Olea europaea subsp. Woodiana, respectively.

Mentions: A maximum likelihood tree was obtained with the likelihood value of -lnL = 428640.9970 with the GTR+G+I base substitution model (Figure 5). The majority of clades are supported by the high levels of Bayesian percentages. We also estimated the splitting times of major clades of asterids using molecular clocks. Two internal fossil data (Araliaceae 70 million years ago (mya) and Solanaceae 53 mya) were used to calibration the clock [35], [36]. The resulting tree indicate that Sesamum (Pedaliaceae) form a sister group to the Oleaeaeae (represented by Jsaminum and Olea) and the two lineages diverged at the Cretaceous-Tertiary (K-T) boundary in geological time (Figure 5).


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

Yi DK, Kim KJ - PLoS ONE (2012)

A maximum likelihood tree (-lnL = 428640.9970) of the asterid clade of angiosperm using whole chloroplast genome sequences.The tree was polarized by two outgroup taxa, Spinacea and Arabidopsis. The GTR+G+I base substitution model was adopted based on the Modeltest. Molecular clock was calibrated using two internal splitting points of the members of Araliaceae (70 mya) and Solanaceae (53 mya). The numbers above each node indicate the Bayesian support percentages. Taxon abbreviations are Solanum(bu): Solanum bulbocastanum, Solanum(tu): Solanum tuberosum, Solanum(ly): Solanum lycopersicum, Nicotiana(sy): Nicotiana sylvestris, Nicotiana(ta): Nicotiana tabacum, Nicotiana(to): Nicotiana tomentosiformis, Olea(eb): Olea europaea cv. bianchera, Olea(ee): Olea europaea subsp. europaea, Olea(em): Olea europaea subsp. maroccana, Olea(ec): Olea europaea subsp. Cuspidate and Olea(ew): Olea europaea subsp. Woodiana, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0035872-g005: A maximum likelihood tree (-lnL = 428640.9970) of the asterid clade of angiosperm using whole chloroplast genome sequences.The tree was polarized by two outgroup taxa, Spinacea and Arabidopsis. The GTR+G+I base substitution model was adopted based on the Modeltest. Molecular clock was calibrated using two internal splitting points of the members of Araliaceae (70 mya) and Solanaceae (53 mya). The numbers above each node indicate the Bayesian support percentages. Taxon abbreviations are Solanum(bu): Solanum bulbocastanum, Solanum(tu): Solanum tuberosum, Solanum(ly): Solanum lycopersicum, Nicotiana(sy): Nicotiana sylvestris, Nicotiana(ta): Nicotiana tabacum, Nicotiana(to): Nicotiana tomentosiformis, Olea(eb): Olea europaea cv. bianchera, Olea(ee): Olea europaea subsp. europaea, Olea(em): Olea europaea subsp. maroccana, Olea(ec): Olea europaea subsp. Cuspidate and Olea(ew): Olea europaea subsp. Woodiana, respectively.
Mentions: A maximum likelihood tree was obtained with the likelihood value of -lnL = 428640.9970 with the GTR+G+I base substitution model (Figure 5). The majority of clades are supported by the high levels of Bayesian percentages. We also estimated the splitting times of major clades of asterids using molecular clocks. Two internal fossil data (Araliaceae 70 million years ago (mya) and Solanaceae 53 mya) were used to calibration the clock [35], [36]. The resulting tree indicate that Sesamum (Pedaliaceae) form a sister group to the Oleaeaeae (represented by Jsaminum and Olea) and the two lineages diverged at the Cretaceous-Tertiary (K-T) boundary in geological time (Figure 5).

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