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Tree Genetics & Genomes

, Volume 8, Issue 2, pp 313–326 | Cite as

Phylogenetic utility of structural alterations found in the chloroplast genome of pear: hypervariable regions in a highly conserved genome

  • Hironori KatayamaEmail author
  • Miho Tachibana
  • Hiroyuki Iketani
  • Shao-Ling Zhang
  • Chiyomi Uematsu
Original Paper

Abstract

The genome structure of pear chloroplast DNA (cpDNA) is extremely highly conserved in comparison with that of other angiosperms, and therefore, relatively few phylogenetic analyses for pear (Pyrus spp.) have been carried out using cpDNA as a marker. In this study, we identified two hypervariable regions in intergenic spacers of cpDNA from 21 species in Pyrus. One of these regions is 857 bp in length and lies between the accD-psaI genes, and the other is a 904-bp region between the rps16-trnQ genes. The mutation rate of gaps for the two regions was 10 and 26 times higher, respectively, than the base change rate. Twenty-five haplotypes were revealed among 21 species in Pyrus by 36 mutations found in the two regions. These included 27 gaps and 9 base changes but excluded cpSSRs. Phylogenetic relationships between the 25 haplotypes were generated by haplotype network analysis. The 25 haplotypes represented three groups (types A–C) with two large deletions, one 228 bp in length between the accD-psaI genes and the other 141 bp between the rps16-trnQ genes. Types A and B consisted mostly of pears native to East and South Asia. Type C contained mainly Pyrus communis and wild relatives native to Europe, West and Central Asia, Russia, and Africa. Type B might have diverged from primitives such as pea pears in type A. Phylogenetic utility of structural alterations (gaps) occurring in the hypervariable regions of Pyrus cpDNA is discussed.

Keywords

Pyrus Pear Chloroplast DNA Hypervariable region Gaps Indels 

Notes

Acknowledgements

Thanks are due to Mr. M. Miyake, Mr. S. Kakehi, Mr. K. Masaki, Mr. T. Takemura, Mr. T. Tanikawa, and Ms. Y. Ohwa in Food Resources Research and Education Center, Kobe University, for maintenance of plant materials. Sincere appreciation is expressed to Dr. Anne Edwards, John Innes Centre, UK, for her English correction and useful suggestions. This work was supported in part by Grant-in-Aid (no. 17510196 and no. 19580031) for Scientific Research from the Ministry of Education, Science and Culture, Japan, and by a General Research Grant from the NIAS Gene Bank.

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Hironori Katayama
    • 1
    Email author
  • Miho Tachibana
    • 2
  • Hiroyuki Iketani
    • 3
  • Shao-Ling Zhang
    • 4
  • Chiyomi Uematsu
    • 5
  1. 1.Food Resources Education and Research CenterKobe UniversityKasaiJapan
  2. 2.Engineering HeadquartersOYO CorporationSaitama-shiJapan
  3. 3.National Institute of Fruit Tree ScienceNational Agricultural and Food Research OrganizationTsukubaJapan
  4. 4.College of HorticultureNanjing Agriculture UniversityNanjingChina
  5. 5.Botanical Gardens, Graduate School of ScienceOsaka City UniversityOsakaJapan

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