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Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation

Citation

Hwang, Ui Wook (2021), Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation, Dryad, Dataset, https://doi.org/10.5061/dryad.fbg79cnt4

Abstract

Please refer to the publication Shin et al. (2021): "Shin CR, Choi EH, Kim G. et al. (2021). Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation. Scientific Reports 11: 12239.

The land snail Ellobium chinense (Pulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of E. chinense has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific E. chinense based on COI and 10 microsatellite markers. The analyses of 140 COI data from South Korea and Japan and 54 microsatellite data from South Korea revealed that E. chinense has high haplotype and low nucleotide diversity without showing any genetic structures that reflect geographical isolations. It strongly implies that the subfamily Ellobiinae may have first appeared around the Eocene Optimum immediately after the Paleocene–Eocene Thermal Maximum (PETM; ca. 55 mya) and the examined E. chinense populations in Northwestern Pacific may have been maintained in a metapopulation under the influence of the Kuroshio warm currents through the Late-Middle Pleistocene (0.350−0.126 mya) and Late Pleistocene (0.126−0.012 mya). We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in COI (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four COI hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure.

Methods

We elucidated the genetic diversity and the pattern of genetic structures among populations of northwestern Pacific E. chinense (sampled in South Korea and Japan). Our analyses were based on the popular DNA barcode region of the mitochondrial gene COI and 10 selected SSR microsatellite markers. In total, 140 COI data (consisting of 139 South Korean samples and one Japanese sample), and 54 SSR microsatellite data (from South Korea only) were analyzed. In addition, we employed four distinct covariate adenine/guanine hotspots observed on COI which are distinct key sequences to easily classify phylogenetic groups of E. chinense. Herein, this repository contains the raw data of COI alignments and G-quadruplex motifs. For these results, the population genetic diversity and structure analyses and divergence time estimation were performed. Finally, it was written as a manuscript and accepted for publication in the journal Scientific Reports.

Usage Notes

This data repository contains the following files:

Supplementary Information: Shin_et_al_Supplementary_Information_Online_Final_submitted.docx

This file contains the supplementary data including seven tables and five figures.

Data S1: Data_S1_COI_sequences_of_140_individuals_of_Ellobium_chinense.fas

The alignment set of the 140 COI sequences of Ellobium chinense inhabiting South Korea and Japan, among which 113 COI sequences were obtained from the present study and 27 COI sequences were retrieved from the GenBank database.

Data S2: Data_S2_58_COI_haplotype_sequences_of_Ellobium_chinense.txt

The sequence alignment set of the 58 COI haplotypes observed in 140 individuals of Ellobium chinense inhabiting South Korea and Japan, which are from the results of the present study and retrieved ones from the GenBank database.

Data S3: Data_S3_Co-variance_calculation_result.xlsx

Raw data obtained from the covariance tests performed for constructing a covariance network performed in this study. The four COI hotspots reveal high covariance values in common. The results are summarized and depicted as a network in Figure 2b.

Data S4: Data_S4_QGRS_Conserve_motif_prediction_result_(Correction_needed).xlsx

Putative GQRS-Conserve motifs capable of G-quadruplex structures on CDS of the COI barcoding region of Ellobium chinense inhabiting South Korea and Japan. The green boxes mean the selected plausible G-quadruplex motifs shown in Figure 2c.

Funding

National Institute of Biological Resources, Award: NIBR202005202