The cpDNA genes rbcL, matK
, ndhF, the pseudogene rps 16, and the intergenic spacer trnL-Y are the five best sampled regions for the family and most of them are easily alignable across Cyperaceae.
Nuclear expression of MATK
is a novel marker of type II enteropathy-associate T-cell lymphoma.
Molecular phylogenetics of Acacia subgenera Acacia and Aculeiferum (Fabaceae: Mimosoideae) based on the chlotoplast matK
coding sequence and fanking trnK intron spacer regions.
Identification to species was achieved for 18% (trnH-psbA), 15% (rbcL), 5% (matK
) and 0% (ITS2) across all samples.
The chloroplastic matK
region is one of the most rapidly evolving genes with suitable length and high level of discrimination among angiosperm .
Abbreviations ITS2: Internal transcribed spacer 2 rDNA: Ribosomal DNA IS-GD: Intraspecific genetic distances ITS: Internal transcribed spacer IG-GD: Intragenomic genetic distance SNP: Single nucleotide polymorphisms HMM: Hidden Markov model NJ tree: Neighbor-joining tree PCR: Polymerase chain reaction bp: Base pair INDELS: Insertions and deletions RAPD: Random amplified polymorphic DNA AP-PCR: Arbitrarily primed PCR AFLP: Amplified fragment length polymorphism matK
: Maturase K rbcL: Ribulose-bisphosphate carboxylase gene trnH-psbA: Intergenic spacer ISSR: Inter-simple sequence repeat SRAP: Sequence-related amplified polymorphism.
For plants, the DNA barcodes (rpoC1+rpoB + matK
or rpoC1 + matK+trnH-psbA) (Kress & Erickson, 2009, Hollingsworth, Graham, & Little, 2011), and an internal transcribed spacer (ITS1+ITS2) (Chen et al., 2010; Selvaraj et al., 2012), have been suggested by different researches for plant species identification.
To reconstruct the phylogeny of the cosmopolitan aquatic plant family Hydrocharitaceae, DNA sequences from 17 genera were sampled, including eight genes: 18S from the nucleus; rbcL, matK
, trnK5' intron, rpoB, and rpoC1 from chloroplasts; and cob and atp1 from mitochondria.
For the first time, the polymerase chain reaction was performed for matK
and rbcL genes of Atriplex pratovii.
Methods: HRM analysis was performed in triplicate on each of the 26 taxa to establish the [T.sub.m] for each primer set (matK
, rbcLA, rbcLB, rbcLC, rpoC 1, and trnL).
In plants, however, CO1 had limited use for differentiating species across a wide range of taxa and the a combination of rbcL + matK
was adopted for a two locus barcode system (8).This sets precedence for reconsideration of the default fungal barcode locus.