The matK gene: sequence variation and application in plant systematics

Abstract

Although the matK gene has been used in addressing systematic questions in four families, its potential application to plant systematics above the family level has not been investigated. This paper examines the rates, patterns, and types of nucleotide substitutions in the gene and addresses its utility in constructing phylogenies above the family level. Eleven complete sequences from the GenBank representing seed plants and liverworts and nine partial sequences generated for genera representing the monocot families Poaceae, Joinvilleaceae, Cyperaceae, and Smilacaceae were analyzed. The study underscored the high rate of substitution in the gene and the presence of mutationally conserved sectors. The use of different sectors of the gene and the cumulative inclusion of informative sites showed that the 3' region was most useful in resolving phylogeny, and that the topology and robustness of the tree reached a plateau after the inclusion of 100 informative sites from that region for the taxa used. The impact of using partial sequencing on sample size is addressed. The presence of a relatively conserved 3' region and the less conserved 5' region provides two sets of characters that can be used at different taxonomic levels from the tribal to the division levels.

Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes

“…Different molecular techniques were employed to measure the genetic diversity among plant species including some gene specific sequences such as matK, rbcL, ITS regions (Hilu and Liang 1997;Ma and Yin 2009;Cao et al 2001;Koch et al 2001;Zhu et al 2003;Yang et al 2004;Zhang et al 2013;Chen et al 2014;Xing 2014). Recently the high-throughput SNP genotyping techniques based on NGS method are used to analyze the genetic diversity (Kumar et al 2012;Shirasawa et al 2016).…”

Using matK sequence data to unravel the phylogeny of Casuarinaceae

“…We amplified approximately 1500 bp of sequence from the 3 0 end of the matK gene (and trnK intron; see Fig. 1) from the chloroplast genome (Hilu and Liang, 1997;Neuhaus and Link, 1987;Olmstead and Palmer, 1994), and used the data to reconstruct a more detailed phylogeny of the Casuarinaceae. This phylogenetic framework was used to to examine the evolution of xeromorphy in Casuarinaceae: did it arise just once before the divergence of Ceuthostoma, Allocasuarina, and Casuarina, or did it arise more than once, with Ceuthostoma acquiring xeromorphic characters in parallel with Casuarina and Allocasuarina?…”

Evaluation of Potential DNA Barcoding Loci from Plastid Genome: Intraspecies Discrimination in Rice (Oryza species)

“…The rbcl based DNA barcoding also seems to be efficient to resolve the issues on taxonomic confusion on the familia and higher levels and also on lower (inter/Intra generic) levels lived in cupressaceae, Cornaceae, Ericaceae, Graniaceae (Gille et al, 1994 Like rbcl, matK is another widely used barcode for plants is another cpDNA gene region which codes for maturase of higher plants while the matK exon being located within the trnk intron (Ems et al, 1999). Among the most preferred choice matK is also included for systemic studies for higher plants as contains greater number of nonsynonymous mutations, indels (insertions and deletions) and nucleotide substation (Olmstead et al, 1994 andHilu et al, 1997). The other ten primer pairs of our panel did not amplified at all in any of the rice genotypes shows no amplification efficiency they are accD ndhF, (Table 3).…”