DOI: 10.5061/dryad.fbg79cnt4
title: Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation

description: 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.
description: We elucidated the
 genetic diversity and the pattern of genetic structures among populations
 of northwestern Pacific <i>E. chinense </i>(sampled in South
 Korea and Japan). Our analyses were based on the popular DNA barcode
 region of the mitochondrial gene <i>COI</i><i>
 </i>and 10 selected SSR microsatellite markers. In total, 140
 <i>COI </i>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 <i>COI </i>which are
 distinct key sequences to easily classify phylogenetic groups of
 <i>E. chinense.</i> Herein, this repository
 contains the raw data of <em>COI </em>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.
description: This data repository
 contains the following files: <strong>Supplementary
 Information</strong>:
 Shin_et_al_Supplementary_Information_Online_Final_submitted.docx
 This file contains the
 supplementary data including seven tables and five figures.
 <strong>Data
 S1</strong>:
 Data_S1_COI_sequences_of_140_individuals_of_Ellobium_chinense.fas The alignment set of the 140 <i>COI</i> sequences of <i>Ellobium chinense</i> inhabiting South Korea and Japan, among which 113 <i>COI </i>sequences were obtained from the present study and 27 <i>COI </i>sequences were retrieved from the GenBank database. <strong>Data S2</strong>: Data_S2_58_COI_haplotype_sequences_of_Ellobium_chinense.txt The sequence alignment set of the 58 <i>COI</i> haplotypes observed in 140 individuals of <i>Ellobium chinense</i> inhabiting South Korea and Japan, which are from the results of the present study and retrieved ones from the GenBank database. <strong>Data S3</strong>: 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 <i>COI </i>hotspots reveal high covariance values in common. The results are summarized and depicted as a network in Figure 2b. <strong>Data S4</strong>: Data_S4_QGRS_Conserve_motif_prediction_result_(Correction_needed).xlsx Putative GQRS-Conserve motifs capable of G-quadruplex structures on CDS of the <i>COI</i> barcoding region of <i>Ellobium chinense</i> inhabiting South Korea and Japan. The green boxes mean the selected plausible G-quadruplex motifs shown in Figure 2c.