Application of the matK gene sequences to grass systematics

Abstract

The 3′ region of the matK gene from 17 species, representing 13 tribes and six subfamilies of the Poaceae, is used to investigate the potential of the gene in addressing systematic questions in the family. The aligned sequences were analyzed by the Wagner parsimony methods using PAUP and PHYLIP and by the neighbor-joining method. Out of the 583 bp sequenced, 30% were variable and 14.9% were informative. The strict consensus tree, rooted by Joinvillea (Joinvilleaceae), showed well-resolved major clades that represent the grass subfamilies. The bambusoid Phyllostachys appeared as a basal clade in the family. Oryza diverged either before or after the Pooideae in the parsimony and neighbor-joining methods, respectively. The three members of the Pooideae grouped in a monophyletic lineage in both analyses. Arundo (Arundinoideae) was basal to the subfamilies Panicoideae and Chloridoideae. Analysis of the various types of DNA mutations underscores the potential of the matK gene in providing insight into grass systematic and evolution. Keywords: matK, Poaceae, grasses, phylogeny, chloroplast, DNA sequence.

Molecular phylogeny and evolution of tropical vegetal genus Coccinia (Cucurbitaceae) using chloroplast barcode markers and its implications for speciation patterns

“…accessions and other member of Cucurbitaceae, while land races CgVM4 and CgVM6 were observed to be placed in another clade, as compared to out-grouped Echinopepon insularis (Figure 4). The transmutation detected in this locus appears to be a reflection of differential rates of transition/ transversion mutations in different sectors of the matK gene (Liang & Hilu 1996).…”

Sequence analysis of Maturase K (matK): A chloroplast-encoding gene in some selected pulses

“…Before now, among the genes, sequences for the rbcl gene was frequently used and analysed by researchers in the bid to understanding plant systematics beyond the family level (Donoghue et al, 1992;Chase et al, 1993;Duval et al, 1993). However, maturase K (matk) gene, formally known as orfk has emerged as a gene of interest with potential in plant molecular systematics and evolution because of the genes' rapid evolution at nucleotide and corresponding amino acid levels (Johnson and Soltis, 1995;Liang and Hilu, 1996;Miller et al, 2006).…”

Universal primers for the amplification of the plastid <i>trnK/matK</i> region in land plants

“…However, once the rather time consuming alignment has been performed, fast evolving regions -especially matK -not only tend to provide the highest phylogenetic structure, they also offer the desired phylogenetic information even at deeper nodes (Borsch & al., 2003;Müller & al., 2006;Borsch & Quandt, 2009). For flowering plants, this marker is already well established and easily accessible with standard PCR primers published by Liang & Hilu (1996) and Hilu & Liang (1997) and by Johnson & Soltis (1995). The use of these primers for early diverging land plant lineages, however, has been problematic.…”

“…1. The forward MG15 primer (Liang & Hilu, 1996) spans the spacer-exon junction of the 5' trnK-exon. The short spacer sequence shows a large variability among land plant lineages and reveals numerous mismatches.…”

“…However, the conserved structure at the hydroxyl end in combination with a lower annealing temperature still allows proper PCR amplification. The available reverse primers (Johnson & Soltis, 1995;Liang & Hilu, 1996) are located at the intron-exon junction of the 3' trnK-exon. Mosses, hornworts and ferns share a thymidin residue at position -4 that is lacking in the remaining land plant lineages.…”