DNA barcoding on chironomid specimens collected from ponds in Hyogo, Japan

Kenzi Takamura; Ryuhei Ueno; Natsuko I. Kondo; Kako Ohbayashi

doi:10.15468/ez9xzh

DNA barcoding on chironomid specimens collected from ponds in Hyogo, Japan

Citation

Takamura K, Ueno R, I. Kondo N, Ohbayashi K (2024). DNA barcoding on chironomid specimens collected from ponds in Hyogo, Japan. Version 1.3. National Institute of Genetics, ROIS. Occurrence dataset https://doi.org/10.15468/ez9xzh accessed via GBIF.org on 2024-12-11.

Description

This dataset includes 825 chironomid specimen records collected from 20 ponds in Hyogo, Japan in May and September 2012. Specimens were identified to family, genus and species levels through DNA barcoding analysis for approximately 60 % of collected specimen samples, while species of 12 specimens were identified based on morphological identification solely. DNA sequences of COI mitochondrial gene of identified specimens were deposited in DNA Data Bank of Japan (DDBJ) with accession number of LC494722–LC495141.

Sampling Description

Study Extent

Larvae of chironomid species were collected from 20 ponds in Hyogo, Japan in May and September 2012.

Sampling

Samples were collected from sediments using Ekman-Birge grab sampler (15 cm square in the mouth), and from aquatic weed stems (1m) with leaves by hands or aquatic weed sampler. The chironomids were sorted on ice in order to restrain degradation of DNA and preserved individually in 1.5 ml plastic tubes in a freezer for DNA analysis.

Quality Control

Spelling of scientific names were checked against the GBIF Backbone Taxonomy (GBIF Secretariat 2022). Geographical coordinates were validated using GSI maps provided by Geospatial Information Authority of Japan.

Method steps

Morphological identification was performed during the sorting based on the morphological keys (e.g., Andersen et al., 2013; Japan Chironomid Workshop, 2010), and a small number of larvae with unique morphological characters were identified as species.
DNA extraction and sequencing as well as species delimitation based on the sequences, were conducted as described in Takamura et al. (2021) and Takamura et al. (2017).
Specimen data was organized into species occurrence data accompanied with DNA data using a MySQL database. A DDBJ link including accession number was stored in associatedSequences for both DDBJ registered and non-registered specimen records, as far as sharing the same sequences. Specimen records registered to DDBJ can be filtered by occurrenceRemarks. Coordinate uncertainty is represented by a half of the length of the major axis of each pond.

Taxonomic Coverages

1 family (Chironomidae) including 20 genus of chironomids

Ablabesmyia
rank: genus
Benthalia
rank: genus
Chironomus
rank: genus
Corynoneura
rank: genus
Cricotopus
rank: genus
Dicrotendipes
rank: genus
Endochironomus
rank: genus
Glyptotendipes
rank: genus
Microchironomus
rank: genus
Nilodorum
rank: genus
Parachironomus
rank: genus
Paratanytarsus
rank: genus
Polypedilum
rank: genus
Procladius
rank: genus
Propsilocerus
rank: genus
Psectrocladius
rank: genus
Psectrotanypus
rank: genus
Sergentia
rank: genus
Tanypus
rank: genus
Tanytarsus
rank: genus
Chironomidae
rank: family

Geographic Coverages

Hyogo, Japan

Bibliographic Citations

Andersen, T., Ekrem, T., & Cranston, P. S. (2013) 1. The larvae of the Chironomidae (Diptera) of the Holarctic Region –Introduction. In T. P. Andersen, P. S. Cranston, & J. H. Elper (Eds.), Chironomidae of the Holarctic Region: Keys and diagnoses –Larvae (pp. 7–12). Insect Systematics & Evolution, Supplement 66. -
Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294–299. -
GBIF Secretariat (2022). GBIF backbone taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via. GBIF.org on 2022-04-08. -
Japan Chironomid Workshop (Nippon-Yusurika Kenkyukai). (2010) Chironomidae of Japan. Bunichi Sogo Shuppan, Tokyo. -
Takamura K., Ueno R., Kondo N.I., Ohbayashi K. (2021) Pond chironomid communities revealed by molecular species delimitation reflect eutrophication. Ecology and Evolution, 11, 4193–4204. https://doi.org/10.1002/ece3.7315 - 10.1002/ece3.7315
Takamura, K., Ueno, R., Kondo, N.I., Ohbayashi, K. (2017) DNA-sequence-based species delimitation for larval chironomid samples collected from Japanese farm ponds. Japanese Journal of Limnology, 78, 35–43. https://doi.org/10.3739/rikusui.78.35. (in Japanese) - 10.3739/rikusui.78.35

Contacts

Kenzi Takamura
originator
position: Visiting Researcher
National Institute for Environmental Studies
16-2 Onogawa
Tsukuba
305-8506
Ibaraki
JP

Ryuhei Ueno
originator
position: Senior Researcher Associate
National Institute for Environmental Studies
16-2 Onogawa
Tsukuba
305-8506
Ibaraki
JP
email: uenor@nies.go.jp

Natsuko I. Kondo
originator
position: Senior Researcher
National Institute for Environmental Studies
16-2 Onogawa
Tsukuba
305-8506
Ibaraki
JP
email: kondo.natsuko@nies.go.jp

Kako Ohbayashi
originator
position: Assistant
Chubu University
1200 Matsumoto-cho
Kasugai
487-8501
Aichi
JP
email: kakoh@isc.chubu.ac.jp

Kenzi Takamura
metadata author
position: Visiting Researcher
National Institute for Environmental Studies
16-2 Onogawa
Tsukuba
305-8506
Ibaraki
JP

Kenzi Takamura
content provider
position: Visiting Researcher
National Institute for Environmental Studies
16-2 Onogawa
Tsukuba
305-8506
Ibaraki
JP

Ryuhei Ueno
content provider
position: Senior Researcher Associate
National Institute for Environmental Studies
16-2 Onogawa
Tsukuba
305-8506
Ibaraki
JP
email: uenor@nies.go.jp

Natsuko I. Kondo
content provider
position: Senior Researcher
National Institute for Environmental Studies
16-2 Onogawa
Tsukuba
305-8506
Ibaraki
JP
email: kondo.natsuko@nies.go.jp

Kako Ohbayashi
content provider
position: Assistant
Chubu University
1200 Matsumoto-cho
Kasugai
487-8501
Aichi
JP
email: kakoh@isc.chubu.ac.jp

Kumiko Totsu
programmer
position: Specialist (Database engineer)
National Institute for Environmental Studies
16-2 Onogawa
Tsukuba
305-8506
Ibaraki
email: totsu.kumiko@nies.go.jp

Biodiversity Division
administrative point of contact
National Institute for Environmental Studies
email: biodiv.data@nies.go.jp