Theoretical and Applied Genetics

, Volume 115, Issue 4, pp 571–590 | Cite as

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

  • Christopher Saski
  • Seung-Bum Lee
  • Siri Fjellheim
  • Chittibabu Guda
  • Robert K. Jansen
  • Hong Luo
  • Jeffrey Tomkins
  • Odd Arne Rognli
  • Henry DaniellEmail author
  • Jihong Liu Clarke
Original Paper


Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19-37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae.


Sorghum Bacterial Artificial Chromosome Inverted Repeat Chloroplast Genome Rolling Circle Amplification 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Investigations reported in this article were supported in part by grants from USDA 3611-21000-017-00D and NIH 2 R01 GM 063879 to Henry Daniell, from NSF DEB 0120709 to Robert K. Jansen, from USDA USDA-BRAG 2005-39454-16511, CREES SC-1700315 to Hong Luo and from the Research Council of Norway BILAT-174998/D15 to Jihong Liu Clarke.

Supplementary material


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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Christopher Saski
    • 1
  • Seung-Bum Lee
    • 2
  • Siri Fjellheim
    • 3
  • Chittibabu Guda
    • 4
  • Robert K. Jansen
    • 5
  • Hong Luo
    • 6
  • Jeffrey Tomkins
    • 1
  • Odd Arne Rognli
    • 3
  • Henry Daniell
    • 2
    Email author
  • Jihong Liu Clarke
    • 7
  1. 1.Clemson University Genomics InstituteClemson UniversityClemsonUSA
  2. 2.4000 Central Florida Blvd, Department of Molecular Biology and Microbiology, Biomolecular ScienceUniversity of Central FloridaOrlandoUSA
  3. 3.Department of Plant and Environmental SciencesNorwegian University of Life SciencesAasNorway
  4. 4.Gen*NY*Sis Center for Excellence in Cancer Genomics and Department of Epidemiology and BiostatisticsState University of New York at AlbanyNew YorkUSA
  5. 5.Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404University of TexasAustinUSA
  6. 6.Department of Genetics and BiochemistryClemson UniversityClemsonUSA
  7. 7.Department of Genetics and BiotechnologyNorwegian Institute for Agricultural and Environmental SciencesAasNorway

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