DNA barcode assessment of Gracilaria salicornia (Gracilariaceae, Rhodophyta) from Southeast Asia

Abstract

BackgroundDNA barcoding is becoming a widely applied tool for the quick and accurate identification of species. The evolution of the mitochondrial cytochrome c oxidase subunit I (COI) gene is sufficiently rapid to allow discrimination between closely related species and biogeographic subgroups within species. Gracilaria salicornia was originally described as being from Manila, the Philippines, and is distributed throughout Asia and the Indian Ocean. To more accurately define this species and its genetic diversity owing to the confusion of identification historically, DNA barcoding using the 5’ end of the COI gene of the mitochondrial genome was applied to specimens collected from the Philippines, Malaysia, Thailand, China, and Japan, and they were compared to other gracilarian species.ResultsWithin species, the COI marker yielded two clusters with nucleotide divergences of 0.0–1.3%. This divergence is slightly higher than the typical intraspecific variation for red algae. A total of eight COI haplotypes were found for G. salicornia, comprising the following groups: H1–H3 from the Philippines; H4 from Okinawa in Japan; H5–H7 from Malaysia, Thailand, and China; and H8 from Thailand.ConclusionAlthough this work concentrated on a limited geographical region of a widespread taxon, the data shows intraspecific molecular divergences in G. salicornia and provides further evidence that DNA barcodes are useful tools for identifying species boundaries and examining biogeographical haplotypes for the genus Gracilaria.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-54-27) contains supplementary material, which is available to authorized users.

Molecular analyses for identification of the Gracilariaceae (Rhodophyta) from the Asia–Pacific region

“…Dixson (Dixson and Saunders 2013). This high value had been considered by geographic sampling (Yang et al 2013a) with high level of variability in COI gene (Kucera and Saunders 2012). Similarly, high variation of intraspecific divergence, 4.4 %, had founded in G. arcuata complex in this study (Table 2), while it had vary with 1.7 % in rbcL gene.…”

“…Unrooted tree of COI were performed using the Neighbor-joining (NJ) algorithm based on the Kimura-2-parameter (K2P) distance method in MEGA 4.0 (Tamura et al 2007). To compare other data, we obtained 13 COI sequences from GenBank and 53 our previous data (Kim et al 2010a;Yang et al 2013a). The rbcL data set was composed of 75 sequences including two outgroups, Curdiea crassa Millar [AY049427] and Melanthalia obtusata (Labillardiere) J. Agardh [AY046431].…”

“…DNA barcoding has become an important tool for the identification of gracilarian species (Kim et al 2010a;Saunders 2005Saunders , 2009). The cytochrome oxidase subunit I (COI) gene, a universal barcode marker in the red algae, has generally revealed greater interspecific sequence divergence relative to the rbcL gene (Kucera and Saunders 2012;Yang et al 2013a). The barcoding gap detected on COI gene reveals the distinct species limit for closely related species in many red algal groups (Saunders 2005;Kucera and Saunders 2012).…”

Small-scale genetic structure of Gracilaria salicornia and its red algal parasite, G. babae (Gracilariaceae, Rhodophyta), in Malaysia

“…Gracilaria salicornia has been documented to have poor long-distance dispersal potential related to the heavy thallus with fragments that tend to sink before establishment (Smith et al 2002). The consistent differentiation of Japanese lineage inferred from the rbcL, cox1, and ITS sequences echoed the findings in a DNA barcoding assessment of G. salicornia, which assigned individuals from Japan and the Philippines into a cluster separated from individuals from other Southeast Asian countries (Yang et al 2013). Maintenance Figure 3: Gracilaria salicornia and G. babae: intraspecific relationships inferred from rbcL haplotypes.…”

Characterization of Herposiphonia pectinata (Decaisne) comb. nov. (Rhodomelaceae, Rhodophyta) from Western Australia, based on morphology and DNA barcoding

“…Molecular techniques can also support species delineation in taxonomy and biodiversity research, by analyzing a short and standardized DNA region, a technique known as "molecular assisted alpha taxonomy" (MAAT), or DNA barcoding (Yang and Kim 2014). One DNA barcoding marker, the 5′ end of mitochondrial-encoded cytochrome c oxidase subunit I gene (COI-5P), has been found useful for species-level identification of red algae (Sherwood et al 2010, Yang et al 2013. Díaz-Tapia and Bárbara (2013) utilized COI-5P sequences in their study of Herposiphonia from the Iberian Peninsula.…”