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Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome

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Abstract

Plants in the family Solanaceae are used as model systems in comparative and evolutionary genomics. The complete chloroplast genomes of seven solanaceous species have been sequenced, including tobacco, potato and tomato, but not peppers. We analyzed the complete chloroplast genome sequence of the hot pepper, Capsicum annuum. The pepper chloroplast genome was 156,781 bp in length, including a pair of inverted repeats (IR) of 25,783 bp. The content and the order of 133 genes in the pepper chloroplast genome were identical to those of other solanaceous plastomes. To characterize pepper plastome sequence, we performed comparative analysis using complete plastome sequences of pepper and seven solanaceous plastomes. Frequency and contents of large indels and tandem repeat sequences and distribution pattern of genome-wide sequence variations were investigated. In addition, a phylogenetic analysis using concatenated alignments of coding sequences was performed to determine evolutionary position of pepper in Solanaceae. Our results revealed two distinct features of pepper plastome compared to other solanaceous plastomes. Firstly, large indels, including insertions on accD and rpl20 gene sequences, were predominantly detected in the pepper plastome compared to other solanaceous plastomes. Secondly, tandem repeat sequences were particularly frequent in the pepper plastome. Taken together, our study represents unique features of evolution of pepper plastome among solanaceous plastomes.

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Acknowledgments

This work was supported by a grant (code20070301034022) from the BioGreen21 program, by the Rural Development Administration and by the ARC program supported by Agriculture and Forestry, Ministry for Food, Agriculture, Forestry and Fisheries, the Republic of Korea. We thank to Kim, Suk-Jun who kindly helped us with drawing a gene map of pepper chloroplast genome.

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Authors and Affiliations

  1. Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro Gwanak-gu, Seoul, 151-921, Republic of Korea

    Yeong Deuk Jo & Byoung-Cheorl Kang

  2. Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea

    Jongsun Park, Wonho Song & Yong-Hwan Lee

  3. Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea

    Jungeun Kim & Cheol-Goo Hur

  4. Bioinformatics, University of science & technology, 113 Gwahangno, Yuseong-gu, Daejeon, 305-333, Republic of Korea

    Jungeun Kim & Cheol-Goo Hur

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  1. Yeong Deuk Jo
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  2. Jongsun Park
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Correspondence to Byoung-Cheorl Kang.

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Communicated by M. Jordan.

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Jo, Y.D., Park, J., Kim, J. et al. Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome. Plant Cell Rep 30, 217–229 (2011). https://doi.org/10.1007/s00299-010-0929-2

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