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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Authors: | Yeong Deuk Jo Jongsun Park Jungeun Kim Wonho Song Cheol-Goo Hur Yong-Hwan Lee Byoung-Cheorl Kang |
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Institution: | (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;(2) Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea;(3) Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon, 305-806, Republic of Korea;(4) Bioinformatics, University of science & technology, 113 Gwahangno, Yuseong-gu, Daejeon, 305-333, Republic of Korea; |
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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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