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Contents : Taiwania 49(4): 273-287 2004 The Evolution of Chloroplast matK Genes Including Identification of New Homologues from Ophioglossum petiolatum and Two Lycophytes (1) Shu-Lan Chuang and Jer-Ming Hu (1 2) (Manuscript received 27 October 2004 accepted 24 November 2004) ABSTRACT: The introns of chloroplast trnKUUU belong to Group II introns and contain an open reading frame denoted as matK. The trnK5 -matK-trnK3 structure is consistent in almost all examined higher land plants and in Characeae but not in other green algae examined. The putative gene product MatK is the only maturase in chloroplasts. Functional chloroplast matK genes are retained even in the nonphotosynthetic parasite Epifagus virginiana and the fern Adiantum capillus-veneris in which chloroplast genome rearrangement has left matK free-standing apart from trnK exons. Among lower land plants the chloroplasts of Psilotum mosses and liverworts all have trnK5 -matK-trnK3 structure but matK is a pseudogene in hornwort Anthoceros formosae. In this study we found a clear trnK5 -matK-trnK3 structure in Ophioglossum petiolatum Lycopodiella cernua and Selaginella doederleinii but PCR with degenerate primers failed to amplify any trnK or matK fragments from other ferns and fern allies. However dot blot hybridization showed distinct signals in these plants that failed to amplify matK fragments by PCR indicating that the matK sequences in those taxa may be too divergent to amplify by an ordinary PCR approach. RT-PCR results showed matK genes are expressed in Ophioglossum petiolatum and Lycopodiella cernua but no signal was detected in Selaginella doederleinii. Overall the expression patterns of matK are not consistent in lower land plants. Phylogenetic analysis of matK sequence showed that Pinus Ginkgo and Cycas form a monophyletic group which is sister to angiosperms. Together they form a clade that is sister to Gnetales. This ad hoc reconstruction is likely due to the high evolutionary rate in matK. KEY WORDS: Chloroplast matK Lycopodiella cernua Selaginella doederleinii Ophioglossum petiolatum Evolution. INTRODUCTION Over forty plastid genomes including more than twenty land plants have been completely sequenced and are available in GenBank thus providing fruitful information on gene structures of plastid genomes. Although introns are not common in organelle genomes of land plants at least 18 plastid genes have been found to harbor introns (Odintsova and Yurina 2003). All but one of the chloroplast introns belong to Group II or III subclass introns with specific RNA secondary structure (Michel et al. 1989 Sugiura 1992). The only exception is the intron of tRNALeu gene a group I intron that seems to have an ancient origin dated back to cyanobacteria (Kuhsel et al. 1990 Besendahl et al. 2002). Chloroplast matK which is encoded by the trnK intron is commonly present in land plants and is the only maturase-like gene in plant plastids. The gene was first characterized in tobacco (Sugita et al. 1985) and further designated as matK in mustard (Sinapis alba) based on its similar structure and composition to mitochondrial Group II intron-encoded maturases in yeast (Neuhaus and Link 1987). 1. Institute of Ecology and Evolutionary Biology National Taiwan University No.1 Sec. 4 Roosevelt Road Taipei 106 Taiwan. 2. Corresponding author. Email: jmhu@ntu.edu.tw 274 TAIWANIA Vol. 49 No. 4 Group II introns are known for their self-splicing ability under certain conditions (Henke et al. 1995) however the splicing is usually facilitated by other nuclear-encoded proteins (Schmelzer et al. 1983) or by their own intron-encoded ORF (Guo et al. 1997) which shows a reverse transcriptase activity. The putative protein encoded by this ORF contains a highly conserved maturase domain (X-domain) near the C-terminal region. This domain is about 500 amino acids in length and exists in all the Group II intron genes with ORF responsible for the maturase activity of chloroplasts and mitochondria or in a freestanding form (Mohr et al. 1993). This X-domain has a strongly conserved sequence SX3-6TLAXKXK and most of the sequences have a large excess of basic over acidic amino acids (Mohr et al. 1993) and are mostly hydrophilic (Sugita et al. 1985). The putative maturase function of chloroplast MatK protein is mostly based on sequence comparisons and sparse data for the presence of a spliced form RNA in rice (Chiba et al. 1996) the detection of proteins in Solanum (du Jardin et al. 1994) and RNA-binding activity in Sinapis (Liere and Link 1995). Nonetheless matK gene is indispensable since it is intact and free-standing in the highly reduced plastid genome of the parasitic Epifagus virginiana (Wolfe et al. 1992 Mohr et al. 1993 Ems et al. 1995). Interestingly six Group II introns are left in the remaining 2

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