The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses
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.
KeywordsChloroplast 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.
- Gifford EM, Foster AS (1989) Morphology and evolution of vascular plants. Freeman, New YorkGoogle Scholar
- Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li YQ, Kanno A, Nishizawa Y, Hirai A, Shinozaki K, Sugiura M (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217:185–194PubMedCrossRefGoogle Scholar
- Maréchal-Drouard L, Weil JH, Dietrich A (1993) Transfer RNAs and transfer RNA genes in plants. Annu Rev Plant Physiol 44:13–32Google Scholar
- Palmer JD (1991) Plastid chromosomes: structure and evolution. In: Hermann RG (ed) The molecular biology of plastids. Cell culture and somatic cell genetics of plants, vol. 7a. Springer, Vienna Berlin Heidelberg, pp 5–53Google Scholar
- Raubeson LA, Jansen RK (2005) Chloroplast genomes of plants. In: Henry RJ (ed) Plant diversity and evolution: genotypic variation in higher plants. CAB International, Wallingford, UK, pp 45–68Google Scholar
- Saltz Y, Beckman J (1981) Chloroplast DNA preparation from Petunia and Nicotiana. Plant Mol Biol Newsl 2:73–74Google Scholar
- Shinozaki K, Ohme M, Tanaka M, Wakasugi T. Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (1986) The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049PubMedGoogle Scholar
- Wakasugi T, Hirose T, Horihata M, Tsudzuki T, Kossel H, Sugiura M (1996) Creation of a novel protein-codong region at the RNA level in black pine chloroplast: the pattern of RNA editing in the gymnosperm chloroplast is different from that in angiosperms. Proc Natl Acad Sci USA 93:8766–8770PubMedCrossRefGoogle Scholar