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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.
Highlights
The introduction of DNA barcodes by Herbert and co-workers [1,2,3] has brought about large impacts on the advancement of systematic biology; where short, amplified regions of DNA exhibiting large variation among species, yet sufficiently variable within species, are constantly used for species delineation, identification as well as archiving with reference to known, established species [4,5,6]
Results based on the Best Match (BM) and Best Close Match (BCM) criteria are as follows: All four genetic markers were able to correctly identify all 29 species based on the BM criteria
Molecular Marker Assessment The accuracy of a DNA barcode is largely determined by the magnitude of overlap between intraspecific variation and interspecific divergence
Summary
The introduction of DNA barcodes by Herbert and co-workers [1,2,3] has brought about large impacts on the advancement of systematic biology; where short, amplified regions of DNA exhibiting large variation among species, yet sufficiently variable within species, are constantly used for species delineation, identification as well as archiving with reference to known, established species [4,5,6]. The usefulness of DNA barcoding is evident when dealing with taxa displaying phenotypic plasticity throughout diphasic or triphasic life cycles as well as taxa involving cryptic species These phenomena are generally predominant in marine macroalgae, thereby enticing the application of DNA barcoding, as reported in numerous studies encompassing the order Gelidiales [10], Gigartinales, [11,12,13], Graciliariales [14,15], Laminariales [16], and Fucales [17]. The morphologically diverse nature of Kappaphycus and Eucheuma still poses difficulties in species identification [22,23,24,25,26,27,28], even leading to the cultivation of mixed populations that inevitably reduces overall yield [29] These have resulted in the subsequent employment of molecular phylogenetic studies which all share one main objective – to infer and understand the phylogenetic relationships between Kappaphycus and Eucheuma congeners. The suitability of these genetic markers as DNA barcodes are to date, unassessed
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