Report of Systematic Zoology Lab Practicum, July, 2012

Partial sequence of cytochrome c oxidase subunit I gene from Paradorippe granulata (Crustacea: Decapoda)

Kentaro Yamada and Kousuke Watanabe

Division of Biology, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo 060-0810, Japan

Material and Methods
A crab was obtained subtidally by an Ekman-Birge grab sampler from sandy bottom, about 7 m in depth, in Oshoro Bay, Hokkaido, Japan, about 43°12′N, 140°51′E, on 25 June 2012 by Kentaro Yamada and Kousuke Watanabe. It was photographed and identified by Hiroshi Kajihara as Paradorippe granulata (De Haan, 1841), and fixed in 99% EtOH. DNA was extracted from one of the legs using the silica method (Boom et al. 1990) with some modifications. Extracted DNA was dissolved in 30 µl of deionized water and has been preserved at –20°C. Remaining morphological voucher specimen has been deposited at the Hokkaido University Museum under the catalogue number ICHU22100245 (contact: Dr. Hiroshi Kajihara, kazi@mail.sci.hokudai.ac.jp).
      An about 600-bp fragment of mitochondrial cytochrome c oxidase subunit I gene (COI) was amplified by polymerase chain reaction (PCR) using LCO1490 (5′-GGTCAACAAATCATAAAGATATTGG-3′) and HCO2198 (5′-TAAACTTCAGGGTGACCAAAAAATCA-3′) (Folmer et al. 1994). A hot start PCR was performed by a thermal cycler, iCycler (Bio-Rad), in a 20-µl reaction volume containing 1 µl of template total DNA (approximately 10–100 ng) and 19 µl of premix made with 632-µl deionized water, 80-µl Ex Taq Buffer (TaKara Bio), 64-µl dNTP (each 25 mM), 8-µl each primer (each 10 µM), and 0.1-µl TaKara Ex Taq (5 U/µl,TaKara Bio). Thermal cycling condition comprised an initial denaturation at 95°C for 30 sec; 30 cycles of denaturation at 95°C for 30 sec, annealing at 45°C for 30 sec, and elongation at 72°C for 45°C and a final elongation at 72°C for 7 min.
      The PCR product was purified with the silica method (Boom et al. 1990). Both strands were sequenced with a BigDye® Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) following the manufacturer's protocol, using the same primer set as the initial PCR amplification. Sequencing was performed with ABI Prism 3730 DNA Analyzer (Applied Biosystems). Chromatogram and sequence data were operated with MEGA v.5 software (Tamura et al. 2011).


Results
A total of 634 bp of COI sequence was determined from ICHU22100245, identified as Paradorippe granulata (De Haan, 1841) (see Appendix).


Taxonomy
Phylum Arthropoda
Subphylum Crustacea
Class Malacostraca
OrderDecapoda
Family Dorippidae
Genus Paradorippe Serène & Romimohtarto, 1969
Paradorippe granulata (De Haan, 1841)
(Figs 1, 2)

Japanese name: Samehada-heike-gani



Fig. 1. Paradorippe granulata (De Haan, 1841), ICHU22100245, dorsal view.


Fig. 2. Paradorippe granulata (De Haan, 1841), ICHU22100245, ventral view.



References

Boom, R., Sol, C. J. A., Salimans, M. M. M., Jansen, C. L., Wertheim-van Dillen, P. M. E., and van der Noordaa, J. 1990. Rapid and simple method for purification of nucleic acids. Journal of Clinical Microbiology 28: 495–503.