title: Assessment of four molecular markers as potential DNA barcodes for red algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta).
abstract: DNA barcoding has been a major advancement in the field of taxonomy, seeing much effort put into the barcoding of wide taxa of organisms, macro and microalgae included. The mitochondrial-encoded cox1 and plastid-encoded rbcL has been proposed as potential DNA barcodes for rhodophytes, but are yet to be tested on the commercially important carrageenophytes Kappaphycus and Eucheuma. This study gauges the effectiveness of four markers, namely the mitochondrial cox1, cox2, cox2-3 spacer and the plastid rbcL in DNA barcoding on selected Kappaphycus and Eucheuma from Southeast Asia. Marker assessments were performed using established distance and tree-based identification criteria from earlier studies. Barcoding patterns on a larger scale were simulated by empirically testing on the commonly used cox2-3 spacer. The phylogeny of these rhodophytes was also briefly described. In this study, the cox2 marker which satisfies the prerequisites of DNA barcodes was found to exhibit moderately high interspecific divergences with no intraspecific variations, thus a promising marker for the DNA barcoding of Kappaphycus and Eucheuma. However, the already extensively used cox2-3 spacer was deemed to be in overall more appropriate as a DNA barcode for these two genera. On a wider scale, cox1 and rbcL were still better DNA barcodes across the rhodophyte taxa when practicality and cost-efficiency were taken into account. The phylogeny of Kappaphycus and Eucheuma were generally similar to those earlier reported. Still, the application of DNA barcoding has demonstrated our relatively poor taxonomic comprehension of these seaweeds, thus suggesting more in-depth efforts in taxonomic restructuring as well as establishment.
authors.affiliation: Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Ji
authors.initials: J
authors.lastname: Tan
authors.forename: Phaik-Eem
authors.initials: PE
authors.lastname: Lim
authors.forename: Siew-Moi
authors.initials: SM
authors.lastname: Phang
authors.forename: Dang Diem
authors.initials: DD
authors.lastname: Hong
authors.forename: H
authors.initials: H
authors.lastname: Sunarpi
authors.forename: Anicia Q
authors.initials: AQ
authors.lastname: Hurtado
mesh_terms: D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D021901:DNA, Intergenic / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D018744:DNA, Plant / Q000032:analysis / Q000235:genetics; D017343:Genes, Plant; D005819:Genetic Markers / Q000502:physiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D000461:Rhodophyta / Q000145:classification* / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic; D004272:DNA, Mitochondrial; D018744:DNA, Plant; D005819:Genetic Markers