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

Kenzi Takamura1, Ryuhei Ueno1, Natsuko I. Kondo1, Kako Ohbayashi2, Kumiko Totsu3

1 National Institute for Environmental Studies, 16-2 Onogawa, 305-8506, Tsukuba, Japan; 2 Chubu University, 1200 Matsumoto-cho, 487-8501, Kasugai, Japan; 3 National Institute for Environmental Studies, 16-2 Onogawa, 305-8506, Tsukuba

Corresponding author(s): Kenzi Takamura (takaken@nies.go.jp)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

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

Abstract

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.

Keywords: Occurrence, Specimen, chironomid, DNA barcoding, farm pond, freshwater biodiversity, molecular species delimitation

Project details

Project title: Diversity and habitat preferences of insects of the family Chironomidae investigated with DNA barcoding
Personnel: Kenzi Takamura
Funding: Grant Number 24241078, Grants-in-Aid for Scientific Research (KAKENHI), Japan Society for the Promotion of Science.
Study area descriptions/descriptor: 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.

Data published through GBIF: https://www.gbif.jp/ipt/resource?r=nies_pond_chironomid

Taxonomic coverage

General taxonomic coverage description: 1 family (Chironomidae) including 20 genus of chironomids
Taxonomic ranks
Family: Chironomidae
Genus: Ablabesmyia, Benthalia, Chironomus, Corynoneura, Cricotopus, Dicrotendipes, Endochironomus, Glyptotendipes, Microchironomus, Nilodorum, Parachironomus, Paratanytarsus, Polypedilum, Procladius, Propsilocerus, Psectrocladius, Psectrotanypus, Sergentia, Tanypus, Tanytarsus

Spatial coverage

General spatial coverage: Hyogo, Japan
Coordinates: 34°43'12''N and 34°57'28.8''N Latitude; 134°48'28.8''E and 135°1'37.2''E Longitude 

Temporal coverage: May 23, 2012 - September 15, 2012

Methods

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

Datasets

Dataset description
Object name: Darwin Core Archive DNA barcoding on chironomid specimens collected from ponds in Hyogo, Japan
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: https://www.gbif.jp/ipt/archive.do?r=nies_pond_chironomid
Publication date of data: 2022-06-15
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2022-06-13
Hierarchy level: Dataset

References
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