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Complete Chloroplast Genome of Chionographis japonica (Willd.) Maxim. (Melanthiaceae): Comparative Genomics and Evaluation of Universal Primers for Liliales

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Abstract

The complete chloroplast genome of Chionographis japonica (Willd.) Maxim. (Melanthiaceae, Liliales) was mapped using polymerase chain reaction and the Sanger method. The circular double-stranded DNA was a typical quadripartite structure consisting of two inverted repeated regions (27,397 bp), a small single copy region (18,205 bp), and a large single-copy region (81,646 bp), with a total length of 154,645 bp. The genome consisted of 137 coding genes, including 91 protein-coding genes, 38 distinct tRNA, and 8 rRNA genes. The ycf15 and ycf68 genes had several internal stop codons interpreted as pseudogenes. The inverted repeat (IR) region expanded to part of the rps3 gene in the junction between large single-copy and IRA regions in C. japonica. We designed 785 primers, of which 481 were used to map the entire chloroplast genome of C. japonica. Primers were compared with the complete chloroplast sequence of Smilax china (Smilacaceae) to identify primers that could be used for other Liliales members and whole chloroplast genome sequencing. Of the primers used for C. japonica, 398 could be used with other smaller species within the order.

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Acknowledgments

We would like to thank Do Hoang Dang Khoa and Sang-Chul Kim of Gachon University for assistance with the analysis and in collection of Chionographis. This study was supported by the National Research Foundation of Korea (NRF) grant fund (MEST 2010–0029131).

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  1. Department of Life Science, Gachon University, Seongnam, 461-701, South Korea

    Sarah S. Bodin, Jung Sung Kim & Joo-Hwan Kim

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Correspondence to Joo-Hwan Kim.

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Supplementary Table 1

Primers used for the sequence mapping of C. japonica, separated by region (LSC, SSC, IR) and named according to the appropriate location within the Chionographis sequence. Primers compared with S. china and those with greater than 80 % similarity are listed along with nucleotide position compared with Chionographis (PDF 167 kb)

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Bodin, S.S., Kim, J.S. & Kim, JH. Complete Chloroplast Genome of Chionographis japonica (Willd.) Maxim. (Melanthiaceae): Comparative Genomics and Evaluation of Universal Primers for Liliales. Plant Mol Biol Rep 31, 1407–1421 (2013). https://doi.org/10.1007/s11105-013-0616-x

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