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

Mi Yeon Yang,Myung Sook Kim,Paul John L Geraldino

doi:10.1186/1999-3110-54-27

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.

Highlights

DNA barcoding is becoming a widely applied tool for the quick and accurate identification of species
A 650 base pair segment of the 5’ region of the mitochondrial c oxidase subunit I (COI) gene is currently used in DNA barcoding for cataloguing
DNA barcoding A fragment of 616 bp at the 5’-end of the COI gene was analyzed in each of 49 specimens of Gracilaria salicornia from Southeast Asia and 15 sequences of Gracilariaceae from GenBank (Table 1)

Summary

Introduction

DNA barcoding is becoming a widely applied tool for the quick and accurate identification of species. 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. Gracilaria salicornia has long been considered morphologically variable and wideranging habitat from the intertidal to the near-subtidal zones. Since this species has simple morphological features and phenotypic plasticity, its identification has often been confused with similar related species (Xia, 1986). In G. salicornia, the sequencing of standard region for DNA barcoding has not been investigated to compare genetic diversity among populations

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