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Photo images, 3D/CT data and mtDNA of the freshwater mussels (Bivalvia: Unionidae) in the Kyushu and Ryukyu Islands, Japan, with SEM/EDS analysis of the shell

Latest version published by Biodiversity Data Journal on Nov 30, 2018 Biodiversity Data Journal

Photo images, 3D/CT data, mtDNA data, SEM images, and EDS elemental analysis of freshwater mussels that inhabit the Kyushu and Ryukyu Islands (61 individuals, nine species/subspecies) were published online in a local database (http://ffish.asia/Unionidae3D), GBIF (http://ipt.pensoft.net/resource?r=unionidae3d) and DDBJ/EMBL/Genbank (LC431810–LC431840).

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 61 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)
    61
  • Multimedia 
    183

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 61 records in English (9 KB) - Update frequency: unknown
Metadata as an EML file download in English (16 KB)
Metadata as an RTF file download in English (12 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Photo images, 3D/CT data and mtDNA of the freshwater mussels (Bivalvia: Unionidae) in the Kyushu and Ryukyu Islands, Japan, with SEM/EDS analysis of the shell

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Biodiversity Data Journal. This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0 License.

GBIF Registration

This resource has not been registered with GBIF

Keywords

3D model; Anatomy; CT scan; Digital archiving; Elemental composition; Energy dispersive X-ray spectrometry (EDS); Freshwater mussels; Morphology; Open science; Scanning electron microscope (SEM); Shell exoskeleton;; Specimen

Contacts

Who created the resource:

Yuichi Kano
Associate Professor
Kyushu University WEST2-1008, Kyushu University 8190395 Fukuoka-shi Fukuoka JP
http://ffish.asia

Who can answer questions about the resource:

Yuichi Kano
Associate Professor
Kyushu University WEST2-1008, Kyushu University 8190395 Fukuoka-shi Fukuoka JP
http://ffish.asia

Who filled in the metadata:

Yuichi Kano
Associate Professor
Kyushu University WEST2-1008, Kyushu University 8190395 Fukuoka-shi Fukuoka JP
http://ffish.asia

Who else was associated with the resource:

Author
Yuichi Kano
Associate professor
Kyushu University WEST2-1008, Kyushu University 8190395 Fukuoka-shi Fukuoka JP
http://ffish.asia
Author
Yoshihisa Kurita
Assistant professor
Kyushu University Fukuoka JP
Author
Kazuki Kanno
Doctoral course
Kyushu University Fukuoka JP
Author
Kengo Saito
Doctoral course
Kyushu University Fukuoka JP
Author
Hironori Hayashi
Assistant professor
Kyushu University Fukuoka JP
Author
Norio Onikura
Associate professor
Kyushu University Fukuoka JP
Author
Takeshi Yamasaki
General manager
Yamashina Institute for Ornithology, Japan Chiba JP

Geographic Coverage

Freshwater habitats of Kyushu and Ryukyu Islands, Japan.

Bounding Coordinates South West [24.4, 124.2], North East [33.8, 131.2]

Taxonomic Coverage

All freshwater mussels (family Unionidae) distributed in the Kyushu and Ryukyu Islands were studied except Anemina arcaeformis, Hyriopsis schlegelii, and Sinanodonta sp. A shell exoskeleton that was photographically identified as A. arcaeformis was reported from Miyazaki Prefecture, Kyushu Island (Toayama and Nishi 2016), although all other details remain unclear. Hyriopsis schlegelii individuals were artificially introduced to Isahaya Bay for water purification (Ishizaki et al. 2007), even though H. schlegelii is non-native to Kyushu Island. Sinanodonta sp. (or spp.) populations were informally reported from the Ryukyu Islands, but some of the populations were likely introduced from Taiwan (Shokita 1984, Kurozumi 2003, Imai 2008).

Kingdom  Animalia (Animals)
Phylum  Mollusca (Molluscs)
Class  Bivalvia (Bivalves)
Order  Unionoida (Freshwater mussels and pearl mussels)
Family  Unionidae (Freshwater mussels)
Species  Cristaria tenuis ("Dobu-gai-modoki"),  Inversidens brandti ("Obaeboshi-gai"),  Inversiunio yanagawensis ("Nise-matsukasa-gai"),  Lanceolaria grayana ("Tongari-sasanoha-gai"),  Obovalis omiensis ("Kataha-gai"),  Pronodularia japanensis ("Matsukasa-gai"),  Sinanodonta lauta ("Numa-gai"),  Sinanodonta japonica ("Ta-gai")
Subspecies  Nodularia douglasiae nipponensis ("Ishi-gai")

Temporal Coverage

Start Date / End Date 2013-12-21 / 2018-06-29

Sampling Methods

Sampling sites of the nine freshwater mussel species in the Kyushu and Ryukyu Islands. The number attached to each circle indicates the number of individuals.

Study Extent Freshwater mussels were collected in the wild of the Kyushu and Ryukyu Islands, Japan.
Quality Control Identification followed Masuda and Uchiyama (2004), Kondo (2008) and Sano et al. (2017).

Method step description:

  1. Individual photo images were taken in the field (Kano and Nakajima 2014). The specimens were fixed in 10% formalin followed by preservation in 70% ethanol. A small segment of the soft body was cut off and separately preserved in 99% ethanol for mtDNA analysis. All specimens were CT scanned (Aloka Latheta LCT-200, Hitachi Ltd., Japan), and 3D surface models (CT value: −450 to 600) were extracted from the CT data. mtDNA analysis of 16S-rRNA was conducted for 31 individuals. For PCR amplification, we used the primer pair Unio16SFwd (forward: 5′-TGCCTGTTTACCAAAAACATCG-3′) and Unio16SRev (reverse: 5′-CTTGGGGTCCTTTCGTACA-3′). PCR amplification was performed in 10-µL reaction mixtures that contained 5 µL KAPA 2G™ Robust HotStart ReadyMix (Kapa Biosystems, USA), 1 µM of each primer, 1 µL DNA template, and 2 µL sterile deionised water. The reaction mixtures were preheated at 95°C for 3 min, followed by 30 amplification cycles (95°C for 15 s, 50°C for 15 s, and 72°C for 40 s) with a final 5-min extension at 72°C. Direct sequencing of the PCR products was conducted externally (FASMAC, Japan). The nucleotide sequences were deposited in DDBJ/EMBL/GenBank (accession numbers: LC431810–LC431840). The SEM/EDS analysis was conducted for 29 individuals. A shell fragment was cut off from each specimen (from the posterior part of the shell), and the inner side of the shell was analysed by SEM (JCM-6000, JEOL Ltd., Japan) to observe the microscopic images of the pearled surface. Furthermore, EDS analysis (JED-2300, JEOL Ltd.) was conducted to determine the elemental composition of the shell fragment by targeting B, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, K and Ca.

Additional Metadata

Alternative Identifiers http://ipt.pensoft.net/resource?r=unionidae3d