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Complete sequence of the chloroplast genome from pear (Pyrus pyrifolia): genome structure and comparative analysis

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Abstract

The chloroplast genome of Pyrus was found to be 159,922 bp in length which included a pair of inverted repeats (IRs) of 26,392 bp, separated by a small single-copy region of 19,237 bp and a large single-copy region (LSC) of 87,901 bp. A total of 130 predicted genes (113 unique genes and 17 genes, which were duplicated in the IR) including 79 protein-coding genes, four ribosomal RNA genes and 30 tRNA genes were identified based on similarity to homologs from the chloroplast genome of Nicotiana tabacum. Genome organization was very similar to the inferred ancestral angiosperm chloroplast genome. Comparisons between Pyrus, Malus, and Prunus in Rosaceae revealed 220 indels (≥10 bp). Excluding ycf1 and ycf2, which contained deletions in the coding region, all of these were detected in the spacer or intron regions. Three insertions and 13 deletions were detected in Pyrus compared to the same loci in Malus and Prunus. After comparing 89 noncoding chloroplast DNA regions in Pyrus and Malus, highly variable regions such as ndhC-trnV and trnR-atpA were identified. In Pyrus and Malus, the IR/LSC borders were 62 bp shorter than those of Prunus. In addition, there were length mutations at the IRa/LSC junction and in trnH. A total of 67 simple sequence repeats (more than 10 repeated motifs) were identified in the Pyrus chloroplast genome. The indels and simple sequence repeats will be useful evolutionary tools at both intra- and interspecific levels. Phylogenetic analysis demonstrated a close relationship between Pyrus and Prunus in the Rosaceae.

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Acknowledgments

Sincere appreciation is expressed to Dr. Anne Edwards, John Innes Centre, UK, for her English correction and useful suggestions. This work was partially supported by Grant-in-Aid (no. 17510196 and no. 19580031) for Scientific Research from the Ministry of Education, Science and Culture and by grant-in-aid (Genomics for Agricultural Innovation, DD-4040) for the Ministry of Agriculture, Forestry and Fisheries of Japan.

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Authors and Affiliations

  1. National Institute of Fruit Tree Science, National Agricultural and Food Research Organization Tsukuba, Ibaraki, 305-8605, Japan

    Shingo Terakami & Toshiya Yamamoto

  2. Food Resources Education and Research Center, Kobe University, Hyogo, 675-2103, Japan

    Yuichiro Matsumura & Hironori Katayama

  3. Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Kanako Kurita & Hiroyuki Kanamori

  4. National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Yuichi Katayose

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  1. Shingo Terakami
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Correspondence to Hironori Katayama.

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Communicated by A. Abbott

S. Terakami and Y. Matsumura contributed equally to this work.

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Terakami, S., Matsumura, Y., Kurita, K. et al. Complete sequence of the chloroplast genome from pear (Pyrus pyrifolia): genome structure and comparative analysis. Tree Genetics & Genomes 8, 841–854 (2012). https://doi.org/10.1007/s11295-012-0469-8

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