The chloroplast genome from a lycophyte (microphyllophyte), <Emphasis Type="Italic">Selaginella uncinata</Emphasis>, has a unique inversion,transpositions and many gene losses |
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Authors: | Sumika Tsuji Kunihiko Ueda Tomoaki Nishiyama Mitsuyasu Hasebe Sumi Yoshikawa Akihiko Konagaya Takumi Nishiuchi Kazuo Yamaguchi |
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Institution: | (1) Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan;(2) Division of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa 920-1192, Japan;(3) Division of Evolutionary Biology, National Institute of Basic Biology, Okazaki 444-8585, Japan;(4) Department of Basic Biology, The Graduate University of Advanced Studies SOKENDAI, Okazaki 444-8585, Japan;(5) Advanced Genome Information Technology Research Group, RIKEN GSC, Tsurumi, Yokohama 230-0045, Japan;(6) Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan |
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Abstract: | 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.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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Keywords: | Chloroplast Lycophyte Pseudogene Selaginella uncinata Selaginellaceae tRNA genes |
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