Journal of Plant Research

, Volume 120, Issue 2, pp 281–290 | Cite as

The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses

  • Sumika Tsuji
  • Kunihiko Ueda
  • Tomoaki Nishiyama
  • Mitsuyasu Hasebe
  • Sumi Yoshikawa
  • Akihiko Konagaya
  • Takumi Nishiuchi
  • Kazuo Yamaguchi
Regular Paper


We determined the complete nucleotide sequence of the chloroplast genome of Selaginella uncinata, a lycophyte belonging to the basal lineage of the vascular plants. The circular double-stranded DNA is 144,170 bp, with an inverted repeat of 25,578 bp separated by a large single copy region (LSC) of 77,706 bp and a small single copy region (SSC) of 40,886 bp. We assigned 81 protein-coding genes including four pseudogenes, four rRNA genes and only 12 tRNA genes. Four genes, rps15, rps16, rpl32 and ycf10, found in most chloroplast genomes in land plants were not present in S. uncinata. While gene order and arrangement of the chloroplast genome of another lycophyte, Hupertzia lucidula, are almost the same as those of bryophytes, those of S. uncinata differ considerably from the typical structure of bryophytes with respect to the presence of a unique 20 kb inversion within the LSC, transposition of two segments from the LSC to the SSC and many gene losses. Thus, the organization of the S. uncinata chloroplast genome provides a new insight into the evolution of lycophytes, which were separated from euphyllophytes approximately 400 million years ago.


Chloroplast Lycophyte Pseudogene Selaginella uncinata Selaginellaceae tRNA genes 



We are very grateful to Prof. M. Takamiya for cytogenetical observations of S. uncinata. We also thank T. Hoshino for drawing the chromosome map and H. Mizuno for technical assistance with DNA sequencing.

Supplementary material


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Copyright information

© The Botanical Society of Japan and Springer 2007

Authors and Affiliations

  • Sumika Tsuji
    • 1
  • Kunihiko Ueda
    • 2
  • Tomoaki Nishiyama
    • 1
  • Mitsuyasu Hasebe
    • 3
    • 4
  • Sumi Yoshikawa
    • 5
    • 6
  • Akihiko Konagaya
    • 5
    • 6
  • Takumi Nishiuchi
    • 1
    • 2
  • Kazuo Yamaguchi
    • 1
    • 2
  1. 1.Division of Functional Genomics, Advanced Science Research CenterKanazawa UniversityKanazawaJapan
  2. 2.Division of Life Science, Graduate School of Natural Science and TechnologyKanazawa UniversityKanazawaJapan
  3. 3.Division of Evolutionary BiologyNational Institute of Basic BiologyOkazakiJapan
  4. 4.Department of Basic BiologyThe Graduate University of Advanced Studies SOKENDAIOkazakiJapan
  5. 5.Advanced Genome Information Technology Research GroupRIKEN GSCYokohamaJapan
  6. 6.Department of Computer Science, Graduate School of Information Science and EngineeringTokyo Institute of TechnologyTokyoJapan

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