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

Latest version published by National Institute of Genetics, ROIS on 15 June 2022 National Institute of Genetics, ROIS
Publication date:
15 June 2022
CC-BY 4.0

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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.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 825 records.

1 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

Occurrence (core)

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How to cite

Researchers should cite this work as follows:

National Institute for Environmental Studies (2022) DNA barcoding on chironomid specimens collected from ponds in Hyogo, Japan. Version 1.2. National Institute for Environmental Studies. Dataset/Species occurrences. https://doi.org/10.15468/ez9xzh


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The publisher and rights holder of this work is National Institute of Genetics, ROIS. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 12bcc17a-9eb7-4377-96df-1a2135900550.  National Institute of Genetics, ROIS publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF Japan.


Occurrence; Specimen; chironomid; DNA barcoding; farm pond; freshwater biodiversity; molecular species delimitation


Natsuko I. Kondo
  • Content Provider
Senior Researcher
National Institute for Environmental Studies
16-2 Onogawa
305-8506 Tsukuba
Kako Ohbayashi
  • Content Provider
Chubu University
1200 Matsumoto-cho
487-8501 Kasugai
Kumiko Totsu
  • Programmer
Specialist (Database engineer)
National Institute for Environmental Studies
16-2 Onogawa
305-8506 Tsukuba
Kenzi Takamura
  • Content Provider
  • Metadata Provider
  • Originator
  • Point Of Contact
Visiting Researcher
National Institute for Environmental Studies
16-2 Onogawa
305-8506 Tsukuba
Biodiversity Division
  • Point Of Contact
National Institute for Environmental Studies
Ryuhei Ueno
  • Content Provider
Senior Researcher Associate
National Institute for Environmental Studies
16-2 Onogawa
305-8506 Tsukuba

Geographic Coverage

Hyogo, Japan

Bounding Coordinates South West [34.72, 134.808], North East [34.958, 135.027]

Taxonomic Coverage

1 family (Chironomidae) including 20 genus of chironomids

Family Chironomidae
Genus Ablabesmyia, Benthalia, Chironomus, Corynoneura, Cricotopus, Dicrotendipes, Endochironomus, Glyptotendipes, Microchironomus, Nilodorum, Parachironomus, Paratanytarsus, Polypedilum, Procladius, Propsilocerus, Psectrocladius, Psectrotanypus, Sergentia, Tanypus, Tanytarsus

Temporal Coverage

Start Date / End Date 2012-05-23 / 2012-09-15

Project Data

No Description available

Title Diversity and habitat preferences of insects of the family Chironomidae investigated with DNA barcoding
Funding Grant Number 24241078, Grants-in-Aid for Scientific Research (KAKENHI), Japan Society for the Promotion of Science.
Study Area Description The farm ponds studied are located in the Banshu Plain of the Setonaikai Coast, Western Japan. They roughly range in the latitude of 34°43' to 34°58' and the longitude of 134°48' to 135°2'. In the Hyogo Prefecture where the ponds are located, there were over 55,000 farm ponds in 1950s, but over 4,500 ponds were lost mainly due to urban development by 1997. Recently, a rapid loss of farm ponds as a biodiversity habitat is continuing in this area.
Design Description This project is a part of the freshwater biodiversity research among farm ponds in the Banshu Plain of the Setonaikai Coast, Western Japan. These ponds have been built for agricultural irrigation, but now they are habitats for a wide variety of taxa originated from freshwater and its surrounding landscapes. This unique biodiversity has been threatened with recent urban development, so that the biodiversity research has been undertaken to reveal the present status as well as causes of dynamics (decline or increase) for a wide variety of freshwater taxa since the 1990s. The faunal and floral surveys of the research have been based on species identification of organisms by taxonomical specialists who were proficient in morphological characteristics of the species. Hence, the work has a fair amount of difficulties in delimitation of species which share common characteristics in key morphological features. This project adopts the methodology of molecular species delimitation, so that it enables to deepen the biodiversity analysis further, and is expected to promote the understanding and conservation of the biodiversity in the area.

The personnel involved in the project:

Kenzi Takamura

Sampling Methods

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.

Study Extent Larvae of chironomid species were collected from 20 ponds in Hyogo, Japan in May and September 2012.
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 step description:

  1. 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.
  2. 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).
  3. 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.

Bibliographic Citations

  1. 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.
  2. 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.
  3. GBIF Secretariat (2022). GBIF backbone taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via. GBIF.org on 2022-04-08.
  4. Japan Chironomid Workshop (Nippon-Yusurika Kenkyukai). (2010) Chironomidae of Japan. Bunichi Sogo Shuppan, Tokyo.
  5. 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
  6. 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

Additional Metadata

Alternative Identifiers 12bcc17a-9eb7-4377-96df-1a2135900550