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. 2020 Apr 29;30:105651. doi: 10.1016/j.dib.2020.105651

Dataset supporting description of the new mussel species of genus Gigantidas (Bivalvia: Mytilidae) and metagenomic data of bacterial community in the host mussel gill tissue

Sook-Jin Jang a, Phuong-Thao Ho b, Si-Yeong Jun c, Dongsung Kim d, Yong-Jin Won a,c,⁎
PMCID: PMC7206200  PMID: 32395595

Abstract

This article contains supplementary data from the research paper entitled “A newly discovered Gigantidas bivalve mussel from the Onnuri Vent Field on the northern Central Indian Ridge” [1], describes a new mussel species within the subfamily Bathymodiolinae named Gigantidas vrijenhoeki. Data are comprised of two parts: 1) shell image and molecular analyses of G. vrijenhoeki and 2) metagenomic community analyses of gill-associated symbiotic bacteria on G. vrijenhoeki. G. vrijenhoeki data were obtained from type specimens described in Jang et al. 2020 [1]. The molecular analysis was conducted by calculating genetic distance at intra- and inter-specific level within genus Gigantidas based on the sequence data of two mitochondrial genes (COI and ND4). The metagenomic dataset of gill-associated symbionts were generated by Illumina Miseq sequencing of the V3-V4 region of 16S rRNA from 12 specimens of G. vrijenhoeki collected from the same vent site, Onnuri Vent Field.

Keywords: Gigantidas vrijenhoeki, Gill associated symbionts, Mitochondrial gene, Genetic distance, Metagenome, Microbial diversity

Specifications Table

Subject Ecology, Evolution, Behavior and Systematics
Specific subject area Morphology, molecular evolution, metagenomics, bacterial community analysis
Type of data Table
Image
Raw DNA sequences
How data were acquired Applied Biosystems 3730xl DNA Analyzer (Applied Biosystems Inc, South Korea) for sequencing five gene fragments of the mytilid mussel, Gigantidas vrijenhoeki, and MEGA X software for calculating genetic distances at intra- and inter specific level. Illumina Miseq platform with 2 × 300 bp paired-end protocol and microbiome taxonomic profiling pipeline in EzBioCloud (ChunLab, Inc., Seoul, Korea) for bacterial community analysis of the gill-associated symbionts.
Data format Raw and Analyzed
Parameters for data collection The morphological image and genomic DNA of G. vrijenhoeki were obtained from samples preserved in 95% ethanol. Bacterial community analyses were conducted using gill tissue from samples stored at −80°C.
Description of data collection Mussel samples (Gigantidas vrijenhoeki) were collected by a video-guided hydraulic grab (Oktopu, Germany). The genomic DNA of mussel specimens was amplified using two mitochondrial genetic markers for COI and ND4 genes, and the microbial 16S rRNA sequences were amplified using V3-V4 primers.
Data source location Onnuri Vent Field, Indian Ocean (11°24.88’S, 66°25.42’E)
Data accessibility Data is available with the article.
Metagenomic data of microbial 16S rRNA were deposited to NCBI under the following accession numbers.
SRR11358622 to SRR11358634 are available in the NCBI BioSample Submission Portal as Bioproject PRJNA613556.
Repository name: [NCBI]
Data identification number:
[SRR11358622–11358634] (for metagenomic data of microbial 16S rRNA gene)
Direct URL to data: [https://www.ncbi.nlm.nih.gov/sra/PRJNA613556]
Related research article Jang, S.-J., Ho, P.-T., Jun, S.-Y., Kim, D., Won, Y.-J., 2020. A newly discovered Gigantidas bivalve mussel from the Onnuri Vent Field in the northern Central Indian Ridge. Deep Sea Research Part I: Oceanographic Research Papers. http://doi.org/10.1016/j.dsr.2020.103299.
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Value of the Data

  • •

    These data present comprehensive information on both Gigantidas vrijenhoeki and its bacterial symbionts, which is a new species of genus Gigantidas first discovered at the Central Indian Ridge.

  • •

    These data could be utilized to research the biodiversity and genetic diversity of vent fauna, and the phylogenetic history of bathymodioline mussels and gill associated symbiotic bacteria.

  • •

    These data would provide useful information to understand the evolutionary and ecological process of host mussel species and symbiotic bacteria system under the effect of environment.

1. Data Description

The data in this article were produced using the newly discovered hydrothermal vent mussel, Gigantidas vrijenhoeki, at the Onnuri Vent Field on the northern Central Indian Ridge. Figure 1 represents shell images of three type specimens of G. vrijenhoeki reported in Jang et al., 2020 (paratype #1, #7, and # 10), which highlight the shell variation with growth. We estimated the genetic distance of G. vrijenhoeki at intraspecific and interspecific levels within genus Gigantidas based on mitochondrial COI and ND4 genes using 11 specimens. The mitochondrial DNA sequences of taxa within Gigantidas were downloaded from GenBank of NCBI. Table 1 provides the accession number of each sequence used in this article. Tables 2 and 3 present the genetic distance at the intraspecific and interspecific levels, respectively. Table 4 presents the microbial community composition in the gill tissue of G. vrijenhoeki at order and species levels. The community analyses were based on the V3-V4 region of the 16S rRNA gene. Raw data were deposited in NCBI.

Fig. 1.

Fig 1

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Shell variation in Gigantidas vrijenhoeki n. sp. A, paratype #1; B, paratype #7; and C, paratype #10.

Table 1.

GenBank accession number of sequences used to calculate genetic distance.

Species1 Locality2 COI ND4 References (COI, ND4)
G. vrijenhoeki (H) CIR (I) MN136491 MN136502 [1]
G. vrijenhoeki (P1) CIR (I) MN136492 MN136503
G. vrijenhoeki (P2) CIR (I) MN136493 MN136504
G. vrijenhoeki (P3) CIR (I) MN136494 MN136505
G. vrijenhoeki (P4) CIR (I) MN136495 MN727845
G. vrijenhoeki (P5) CIR (I) MN136496 MN727846
G. vrijenhoeki (P6) CIR (I) MN136497 MN727847
G. vrijenhoeki (P7) CIR (I) MN136498 MN727848
G. vrijenhoeki (P8) CIR (I) MN136499 MN727849
G. vrijenhoeki (P9) CIR (I) MN136500 MN727850
G. vrijenhoeki (P10) CIR (I) MN136501 MN727851
G. sp. Kikaijima NW (WP) HF545112 HF545188 [10]
G. securiformis NW (WP) HF545109 HF545186
G. hirtus NW (WP) AB170047 AB175299 [11]
G. haimaensis NW (WP) MK534977 MK534972 [12]
G. platifrons NW (WP) HF545106 HF545183 [10]
G. taiwanensis NW (WP) GU966638 HF545215 [10,13]
G. japonicus NW (WP) HF545108 HF545185 [10]
G. horikoshii NW (WP) HF545113 HF545190
G. tangaroa SW (WP) AY608439 AY649811 [2,14]
G. sp. Sissano 1 SW (WP) HF545125 HF545217 [10]
G. gladius SW (WP) AY649802 AY649813 [2]
G. crypta WP HF545105 HF545185 [10]
G. mauritanicus NA AY649801 AY649810 [2]
G. childressi GoM (NA) KU597636 AY130248 [2,15]
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1

For G. vrijenhoeki: H = Holotype; P = Paratype

2

known locality (Ocean Basin): CIR = Central Indian Ridge; I = Indian Ocean; GoM = Gulf of Mexico; NA = Northern Atlantic; NW = Northwest Pacific; SW = Southwest Pacific; WP = Western Pacific.

Table 2.

K2P pairwise genetic distance (%) matrix at intraspecific level in Gigantidas vrijenhoeki based on fragments of 532 bp COI gene (below diagonal) and 511 bp ND4 gene (above diagonal).

Specimen 1 2 3 4 5 6 7 8 9 10 11
1. Holotype 0.59 0.20 0.59 0.20 0.79 0.20 0.20 0.59 0.59 0.20
2. Paratype 1 0.19 0.39 0.79 0.39 0.99 0.39 0.39 0.79 0.79 0.39
3. Paratype 2 0.19 0.00 0.39 0.00 0.59 0.00 0.00 0.39 0.39 0.00
4. Paratype 3 0.19 0.00 0.00 0.39 0.59 0.39 0.39 0.39 0.79 0.39
5. Paratype 4 0.19 0.00 0.00 0.00 0.59 0.00 0.00 0.39 0.39 0.00
6. Paratype 5 0.19 0.00 0.00 0.00 0.00 0.59 0.59 0.20 0.99 0.59
7. Paratype 6 0.38 0.19 0.19 0.19 0.19 0.19 0.00 0.39 0.39 0.00
8. Paratype 7 0.57 0.38 0.38 0.38 0.38 0.38 0.57 0.39 0.39 0.00
9. Paratype 8 0.38 0.19 0.19 0.19 0.19 0.19 0.38 0.57 0.79 0.39
10. Paratype 9 0.57 0.38 0.38 0.38 0.38 0.38 0.57 0.76 0.57 0.39
11. Paratype 10 0.38 0.19 0.19 0.19 0.19 0.19 0.38 0.57 0.00 0.57
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Table 3.

K2P pairwise genetic distance (%) matrix at interspecific level in genus Gigantidas based on 401 bp COI (below diagonal) and 423 bp ND4 (above diagonal). The genetic distance between Gigantidas vrijenhoeki and other species is indicated in bold.

Species 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
1. G. vrijenhoeki 13.37 16.20 15.25 16.17 16.47 24.47 15.90 24.26 25.94 10.72 13.92 23.46 14.52 14.82
2. G. sp. Kikaijima 7.49 19.82 15.97 19.60 18.15 25.33 21.32 29.27 26.88 17.20 16.17 26.26 17.81 18.05
3. G. securiformis 9.81 10.37 18.46 15.13 14.12 24.94 14.80 28.28 26.75 17.47 7.10 25.67 12.60 14.66
4. G. hirtus 9.89 11.75 13.93 20.01 18.89 20.34 16.80 24.26 26.40 16.23 16.53 26.12 19.24 20.18
5. G. haimaensis 11.78 10.75 9.03 12.40 5.79 27.39 13.30 25.72 29.07 18.89 9.93 26.92 4.75 4.71
6. G. platifrons 12.67 11.00 7.26 12.64 4.70 26.12 13.83 28.72 26.61 18.15 11.65 29.06 6.59 7.93
7. G. taiwanensis 12.67 11.99 14.18 12.70 14.24 13.27 25.77 29.99 27.86 24.20 23.93 30.36 25.72 26.46
8. G. japonicus 13.06 10.42 10.56 14.03 10.56 10.22 12.29 26.29 26.54 17.17 11.79 25.43 13.33 13.23
9. G. horikoshii 14.18 14.88 15.22 16.19 16.78 17.29 17.21 17.57 17.06 25.15 23.27 21.59 24.87 24.70
10. G. tangaroa 8.65 7.73 3.09 11.67 7.26 6.40 11.65 8.73 13.90 24.09 24.26 25.05 26.88 26.29
11. G. sp. Sissano 1 9.29 9.27 13.57 11.14 13.36 14.27 11.65 13.66 13.15 11.65 15.19 28.80 18.50 18.73
12. G. gladius 14.85 11.97 14.21 14.48 13.60 15.60 15.81 15.81 10.33 11.95 13.47 23.88 9.36 10.43
13. G. crypta 15.64 16.03 16.93 17.46 18.10 19.17 18.89 19.17 17.10 15.99 16.97 14.71 26.86 26.01
14. G. mauritanicus 11.09 9.83 7.53 11.70 4.98 4.15 13.24 10.25 16.61 6.67 13.03 15.22 18.84 3.93
15. G. childressi 14.33 12.64 9.62 13.36 6.39 6.09 15.99 11.17 19.12 8.73 15.37 16.58 16.26 3.37
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Table 4.

Relative abundance (%) among 16S rRNA reads obtained mussel gill at order level and at species level.

G011 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12 B01
Taxon name at order level (%)
uncultured Gammaproteobacteria 63.44 61.53 16.33 39.20 29.77 54.10 14.27 34.04 33.07 22.42 42.88 39.15 94.41
Methylococcales 36.54 36.87 27.13 36.20 35.08 40.56 32.38 43.91 35.76 35.06 34.17 34.17 0.00
Campylobacterales 0 1.60 56.46 24.56 35.12 5.28 53.31 22.00 31.09 42.47 22.89 26.59 0.00
Oceanospirillales 0 0 0 0 0 0 0 0 0 0.00 0.00 0.00 5.48
Others (<1.0%) 0.02 0 0.09 0.04 0.03 0.06 0.04 0.04 0.08 0.05 0.06 0.08 0.11
Taxon name at species level (%)
Thiotrophs of B. septemdierum (OTU-1) 58.65 52.84 13.59 32.76 25.42 45.98 11.85 28.17 27.85 19.01 36.3 35.17 0
Candidatus Thioglobus sp. (OTU-2) 4.75 2.56 2.72 2.25 4.33 8.1 2.38 5.51 4.93 3.37 6.36 1.56 90.28
Thiotrophs of B. azoricus 0 0 0 0 0 0 0 0 0 0 0 0 2.75
Methanotrophs of G. platifrons (OTU-3) 31.04 28.46 21.23 29.08 28.52 33.24 25.33 34.65 28.9 29.11 26.49 17.08 0
Methyloprofundus sp. 5.28 8.39 5.63 6.62 6.46 7.27 6.84 8.78 6.28 5.78 7.2 6.25 0
Methyloprofundus sedimenti 0 0 0 0 0 0 0 0 0 0 0 10.45 0
Sulfurovum sp. (OTU-4) 0 1.4 55.81 24.27 34.57 5.23 52.82 21.72 30.76 42.08 22.63 26.22 0
Kistimonas asteriae 0 0 0 0 0 0 0 0 0 0 0 0 4.43
Kistimonas sp. 0 0 0 0 0 0 0 0 0 0 0 0 1.04
Unclassified in higher taxonomic rank 0.17 6.31 0.33 4.58 0.31 0.08 0.19 0.48 0.26 0.19 0.41 2.27 0.69
Others (<1.0%) 0.1 0.03 0.71 0.44 0.39 0.1 0.58 0.7 1.03 0.45 0.61 1 0.81
Number of reads 8,082 11,568 19,288 18,239 12,067 15,933 18,547 15,333 22,994 15,840 22,703 13,104 16,757
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1

Specimen name, G: Gigantidas vrijenhoeki, B: Bathymodiolus marisindicus.

2. Experimental Design, Materials, and Methods

2.1. Sample collection

All mussel specimens were collected from the Onnuri Vent Field (11°24.88’S, 66°25.42’E) in the Indian Ocean via video-guided hydraulic grab (Oktopu, Germany) during the Korea Institute of Ocean Science and Technology (KIOST) research cruise (Dive number: GTV1809) in 2018. Eleven type specimens of Gigantidas vrijenhoeki were immediately preserved in 95% ethanol at −20°C and transported to a land-based laboratory. Twelve additional specimens of G. vrijenhoeki and one specimen of Bathymodiolus marisindicus were frozen at −80°C in an ultra-low freezer on board for bacterial community analysis. Following this, they were transported to a land-based laboratory on dry ice and stored in −80°C.

2.2. DNA extraction

Genomic DNA of G. vrijenhoeki was extracted from the adductor tissue of eleven type specimens to estimate genetic distance. In addition, genomic DNA was extracted from the gill tissue of an additional twelve specimens for bacterial community analysis. The genomic DNA of B. marisindicus was extracted from the gill tissue of one specimen to compare the bacterial community composition between the two species. DNA extraction was performed using the Qiagen DNeasy Tissue kit (Qiagen Inc., Hilden, Germany).

2.3. PCR amplification and Sanger sequencing for G. vrijenhoeki

Mitochondrial COI and ND4 genes were amplified for molecular analysis. The COI gene was amplified using HCO2148 (5′-CCYCTAGGRTCATAAAAAGA-3′) and LCO1560 (5′-ATRCTDATTCGWATTGA-3′) primers [2]. The ND4 gene was amplified using ArgBL (5′-CAAGACCCTTGATTTCGGCTCA-3′) and NAP2H (5′-TGGAGCTTCTACGTGRGCTTT-3′) primers [3]. The PCR was performed in a 20 μl solution that included 2 μl of 10 × Taq polymerase buffer, 1 μl of 2.5 mM stock solution of dNTPs, 1 μl of each primer (10 μmol/L), 1 μl of 1 mg/ml bovine serum albumin, 1 μl of extracted DNA (30–150 ng), 0.625 units of IP-Taq polymerase (COSMO genetech, South Korea), and sufficient sterile H2O to make up to the final volume. The PCR conditions were 94°C for 4 min; 35 cycles at 94°C for 30 s, 50°C for 60 s, and 72°C for 90 s; and a final extension step at 72°C for 7 min. The PCR products were purified using a Dr. Prep kit (Cat. No. MK02020, MGmed, South Korea). Sequencing reactions were performed using a Big Dye Terminator V3.1 Cycle Sequencing kit on an Applied Biosystems 3730xl DNA Analyzer (Applied Biosystems Inc, South Korea). The sequence data were deposited in National Centre of Biotechnology Information (NCBI) with appropriate accession numbers [1].

2.3.1. Intra- and Inter-specific genetic distance

Genetic distance was estimated at intraspecific level of G. vrijenhoeki and interspecific level among species within genus Gigantidas. The intraspecific genetic distance was calculated based on mitochondrial COI (532 bp) and ND4 (511 bp) sequences. The interspecific genetic distance was calculated based on COI (401 bp) and ND4 (423 bp) with sequence data of Gigantidas species downloaded from NCBI (Table 1). Both estimations of pairwise genetic distance were based on the Kimura-2 parameter (K2P) model implemented in MEGA X.

2.4. Metagenome sequencing

The PCR was conducted with genomic DNA from the gill tissue of mussel specimens, twelve G. vrijenhoeki and one B. marisindicus. 16S rRNA sequences of symbiotic bacteria were amplified using universal primers of the Illumina protocol targeting the V3-V4 region (www.illumina.com, 16S Metagenomic Sequencing Library Preparation, Part #15044223, revB). The amplicons were sequenced using the Illumina Miseq platform with Miseq Reagent Kit v3 (600 cycles) and a 2 × 300 bp paired-end protocol. The paired-end reads were deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA613556.

The raw sequences were analyzed through the microbiome taxonomic profiling pipeline in EzBioCloud (https://www.ezbiocloud.net, Chunlab, Inc., Seoul, Korea). Paired-end reads were filtered by quality (Q <25) [4], and merged using PANDAseq software [5]. Primers are then trimmed with Chunlab's in-house program at a similarity cut off of 0.8. A denoising step was conducted using Dude-seq software with 0.5% error-correction criteria [6] and non-redundant reads are extracted by UCLUST-clustering [7]. After denoising and dereplication, the taxonomic assignment of sequences was performed using USEARCH [7] with a 97% similarity cut-off for species level identification against the EzBioCloud 16S database. Cutoff values are obtained from Yarza et al. [8]. Chimera sequences were removed using the UCHIME algorithm. Sequence data were clustered using CD-HIT [9] and UCLUST [7].

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.

Acknowledgments

This work was supported by the the Ministry of Oceans and Fisheries, Korea [No. 20170411].

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