Evolution of chloroplast matK genes among lower land plants
Date Issued
2004
Date
2004
Author(s)
Chuang, Shu-Lan
DOI
zh-TW
Abstract
The introns of chloroplast trnKUUU belong to Group II introns which contain an open reading frame denoted as matK. The putative gene product MatK is the only one having maturase function in chloroplasts. The trnK5’-matK-trnK3’ structure is consistent in almost all examined higher land plants, and only those chloroplasts of land plants and higher green algae such as Characeae have introns in their trnK genes, but not in other green algae examined. However, chloroplast matK genes are indispensable since in nonphotosynthetic parasitic plant, Epifagus virginiana and fren, Adiantum capillus-veneris which chloroplast genome has rearrangememt, the chloroplast matK is functional even being a free-standing from with dismissed trnK exons.
The chloroplasts of Psilotum, moss and liverworts all have trnK5’-matK-trnK3’ structure, but it is found that matK is a pseudogene in hornwort Anthoceros formosae. Little is known in other lower land plants, it is the purpose of this thesis to examine the presence of chloroplast matK gene is these taxa.
We found a clear trnK5’-matK-trnK3’ structure in Ophioglossum petiolatum, Lycopodiella cernua and Selaginella doederleinii. PCR with degenerate primers failed to amplify any trnK or matK fragments from other ferns or allies. However, dot blot hybridization showed distinct signals in these plant failed to amplify matK fragments. Therefore the matK sequences might be too divergent to use ordinary PCR approach. RT-PCR results showed matK genes are expressed in Ophioglossum petiolatum and Lycopodiella cernua, but no signal detected in Selaginella doederleinii. So the function and expression of matK are not consistent in lower land plants.
Phylogenetic analysis of matK sequence somewhat differ from previous studies, but the incongruence is likely due to the disputable sequence alignment, which causes long branch attraction that will affect phylogeneticinference. Nonetheless, the result showed that Pinus, Ginkgo, Cycas form a monophyletic group, which is sistered to angiosperms. Together, they from a clade that is sistered to Gnetales. Neighbor-joining and Bayesian show Pslosium, Ophioglossum, and Selaginella are monophyletic group. Most parsimony analysis shows Lycopodiella are monophyletic group with Pslosium, Ophioglossum, and Selaginella.
Codon usage analysis showed that the use of codon in matK is in congruent with the average use of chloroplast genomes, showing a bias that can be explained by constraints on GC contents. The result of correspondence analysis suggests the codon usage of chloroplast matK has some properties that is correlated with their evolutionary relationship.
Subjects
葉綠體
trnK
matK
第二類內插子
瓶爾小草
卷柏
密碼子使用
石松
Selaginella
Ophioglossum
chloroplast
codon usage
group II intron
Lycopodium
Type
other
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