DNA barcoding has been widely used in species identification and biodiversity research. A short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence serves as a DNA bio-barcode. We collected DNA barcodes, based on COI sequences from 156 species (529 sequences) of fish, insects...
DNA barcoding has been widely used in species identification and biodiversity research. A short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence serves as a DNA bio-barcode. We collected DNA barcodes, based on COI sequences from 156 species (529 sequences) of fish, insects, and shellfish. We present results on phylogenetic relationships to assess biodiversity the in the Korean peninsula. Average GC% contents of the 68 fish species (46.9%), the 59 shellfish species (38.0%), and the 29 insect species (33.2%) are reported. Using the Kimura 2 parameter in all possible pairwise comparisons, the average interspecific distances were compared with the average intraspecific distances in fish (3.22 vs. 0.41), insects (2.06 vs. 0.25), and shellfish (3.58 vs. 0.14). Our results confirm that distance-based DNA barcoding provides sufficient information to identify and delineate fish, insect, and shellfish species by means of all possible pairwise comparisons. These results also confirm that the development of an effective molecular barcode identification system is possible. All DNA barcode sequences collected from our study will be useful for the interpretation of species-level identification and community-level patterns in fish, insects, and shellfish in Korea, although at the species level, the rate of correct identification in a diversified environment might be low.
DNA barcoding has been widely used in species identification and biodiversity research. A short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence serves as a DNA bio-barcode. We collected DNA barcodes, based on COI sequences from 156 species (529 sequences) of fish, insects, and shellfish. We present results on phylogenetic relationships to assess biodiversity the in the Korean peninsula. Average GC% contents of the 68 fish species (46.9%), the 59 shellfish species (38.0%), and the 29 insect species (33.2%) are reported. Using the Kimura 2 parameter in all possible pairwise comparisons, the average interspecific distances were compared with the average intraspecific distances in fish (3.22 vs. 0.41), insects (2.06 vs. 0.25), and shellfish (3.58 vs. 0.14). Our results confirm that distance-based DNA barcoding provides sufficient information to identify and delineate fish, insect, and shellfish species by means of all possible pairwise comparisons. These results also confirm that the development of an effective molecular barcode identification system is possible. All DNA barcode sequences collected from our study will be useful for the interpretation of species-level identification and community-level patterns in fish, insects, and shellfish in Korea, although at the species level, the rate of correct identification in a diversified environment might be low.
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문제 정의
In conclusion, we obtained DNA barcodes using COI sequences from fish, insects, and shellfish. The aims of this research were species identification and contribution to biodiversity research. At the species level, the rate of correct identifications might be low in a diversified environment.
이론/모형
A cutoff value for the BLAST result was established as follows: query coverage ＞ 90% and identity ＞ 75% for COI. The levels of sequence divergence within and between the selected species were investigated using the pairwise Kimura 2 parameter (K2P) distance model [12]. The neighbor-joining tree, with gap positions ignored on a pairwise basis, was constructed using the neighbor-joining (NJ) method with K2P distances in MEGA4 [13].
The levels of sequence divergence within and between the selected species were investigated using the pairwise Kimura 2 parameter (K2P) distance model [12]. The neighbor-joining tree, with gap positions ignored on a pairwise basis, was constructed using the neighbor-joining (NJ) method with K2P distances in MEGA4 [13]. These distances were hierarchically arranged in accordance with intraspecific and interspecific species differences within each genus.
성능/효과
In our polytypic species analysis with more than 3 individuals in each species, the average intraspecific difference was approximately 0.5%, and the maximum intraspecific divergence was only 1.86% (Table 2). The highest overall GC% content was found in the 18 species of fish.
Sixteen of the 21 species with GC% content ≥45% were fish, whereas only 1 shellfish species exhibited GC% content ≥45%.
With respect to the COI sequences of the 156 species represented, the interspecific K2P distances for the COI sequences from the 68 fish species, the 59 shellfish species, and the 29 insect species ranged from 0% to 45.25% (fish, 0% to 40.99%; insects, 0% to 10.34%; shellfish, 0% to 45.25%) (Fig. 2A), whereas the intraspecific K2P distances with ≥3 sequences ranged from 0% to 0.985% (fish, 0% to 0.985%; insects, 0.005% to 0.635%; shellfish, 0% to 0.817%) (Fig. 2B).
참고문헌 (14)
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