DOI: 10.5061/dryad.ghx3ffc07
title: Genetic diversity of the zigzag ladybird beetle, Cheilomenes sexmaculata F. (Coleoptera: Coccinellidae) with its distribution in India and implications for biological control

description: The zigzag beetle, Cheilomenes sexmaculata, the most important and
 abundant of all ladybird beetles, feeds on a diverse range of prey. The
 study was conducted understand the population structure of C. sexmaculata,
 individuals collected from five different zones, consisting of 25
 subpopulations that uniformly representing India. From the ddRAD sequence
 data we have identified contigs, SNPs, and INDELs were identified for all
 these 25 subpopulations collected across the India.
description: The adult <em>C. sexmaculata </em>were collected from
 five different localities belonging to various zones of India viz., Delhi
 (North), Nagpur (Central), Jorhat (East), Anand (West) and Bengaluru
 (South) from May to June 2019. The samples were stored in 100% ethanol and
 frozen at -70°C. Genomic DNA was isolated from each individual separately
 by grinding in liquid nitrogen, using the method described earlier (Kim et
 al., 2012). We employed, restriction-site associated DNA sequencing
 (RADseq) coupled with Illumina sequencing, produces high coverage of
 homologous SNP (Single Nucleotide Polymorphism) loci. Population genomic
 analyses from ddRADseq depend on denovoassembly of a set of reference
 contigs. Raw SNPs/INDELs calls are represented in a single Hap Map
 file.  Methods for processing the data: For samples
 1-25, 100-1000ng of high-quality genomic DNA was completely digested using
 Sphl and Mluc1 in a 20-50ul reaction volume (2.4 U per enzyme, New England
 Biolabs (NEB), Ipswich, MA, USA) and incubated at 37 °C for 90 min.
 Adapter ligation was done with Adapters A and B by changing their sticky
 ends for SphI and Mluc1, respectively. The dual-indexed primers designed
 were used for the reactions. After adding the indexed primers in PCR, the
 obtained libraries were pooled based on concentration (Qubit 2.0
 fluorometer analysis) and concentrated in a SpeedVac (Eppendorf, Hamburg,
 Germany). A manual size selection was applied (a range between 450 and 550
 bp, which corresponds to DNA fragment size of interest between 310 and
 410bp) in low-melting 1.5% agarose gel electrophoresis (Bio-Rad
 Laboratories, Hercules, CA, USA). The final libraries were quantified by
 Qubit 2.0 fluorometer (dsDNA kit, Thermo Fisher Scientific) and their
 quality was checked on a Fragment Analyzer system (DNA High Sensitivity
 kit, Agilent). The sequencing quality of each sample was checked using
 FastqC. The dDocent version 2.2.10 was used for this project. After
 dDocent checks, it was recognized the proper number of samples in the
 current directory, later dDocent, Trim Galore! Program was used to proceed
 with the quality trimming of sequence data. Without reference material,
 population genomic analyses from ddRADseq depend on denovoassembly of a
 set of reference contigs . After all executions of FreeBayes are
 completed, raw SNPs/INDELs calls are concatenated into a single variant
 call file (VCF) using VCF tools.  VCF file that contains all SNPs, INDELs,
 MNPs and complex events that are called in 90% of all individuals with a
 minimum quality score of 30. This VCF file is converted to HapMap with
 TASSEL.
description: # Genetic diversity of the zigzag ladybird beetle, Cheilomenes sexmaculata
 F. (Coleoptera: Coccinellidae) with its distribution in India and
 implications for biological control This readme file was generated on
 [2024-11-27] by [Narayana Bhat Devate] GENERAL INFORMATION Title of
 Dataset: Data from: Genetic diversity of the zigzag ladybird beetle,
 Cheilomenes sexmaculata F. (Coleoptera: Coccinellidae) with its
 distribution in India and implications for biological control
 Author/Principal Investigator Information Name: Dr H S Rakshith ORCID:
 Institution: ICAR-Indian Agricultural Research Institute, New Delhi, India
 Address: ICAR-Indian Agricultural Research Institute, New Delhi,
 India-110012 Email:
 [rakshithmails@gmail.com](mailto:rakshithmails@gmail.com) Date of data
 collection: 2019-05-01 to 2019-06-30 Geographic location of data
 collection: India viz., Delhi (North), Nagpur (Central), Jorhat (East),
 Anand (West) and Bengaluru (South) Information about funding sources that
 supported the collection of the data: Nil SHARING/ACCESS INFORMATION
 Licenses/restrictions placed on the data: Nil Links to publications that
 cite or use the data: DOI: Links to other publicly accessible locations of
 the data: Links/relationships to ancillary data sets: Nil Was data derived
 from another source? If yes, list source(s): Nil Recommended citation for
 this dataset: Rakshith et al., 2024, Data from: Genetic diversity of the
 zigzag ladybird beetle, Cheilomenes sexmaculata F. (Coleoptera:
 Coccinellidae) with its distribution in India and implications for
 biological control, Dryad, Dataset DATA & FILE OVERVIEW File List:
 NGS_P6481.hmp, HapMap file contains genetic information about SNP and
 INDELs at listed contig for all the 25 subpopulations of zigzag ladybird
 beetle (Cheilomenes sexmaculata) collected across india during 2019,
 NGS_P6481_reference, sequence file in FASTA format for each contig used in
 the study Relationship between files, if important: SNPs and INDELs in Hap
 Map file is generated with reference to sequence information of contigs
 available at NGS_P6481_reference Additional related data collected that
 was not included in the current data package: Nil Are there multiple
 versions of the dataset? If yes, name of file(s) that was updated: Nil Why
 was the file updated? When was the file updated? Instrument- or
 software-specific information needed to interpret the data: NA Standards
 and calibration information, if appropriate: NA Environmental/experimental
 conditions: NA Describe any quality-assurance procedures performed on the
 data: Nil People involved with sample collection, processing, analysis
 and/or submission: H S Rakshith, Sachin S Suroshe, Amolkumar U Solankhe,
 Gopalakrishnan S, Keerthi MC, Narayana Bhat Devate, Sujatha G S, Hari
 Krishna and Ranjith Kumar Ellur DATA-SPECIFIC INFORMATION FOR:
 [NGS_P6481_reference] Number of variables: 69,365 Contigs Number of
 cases/column: NA Variable List: 69,365 Contigs sequence in FASTA format
 Missing data codes: Missing entries are denoted as "NA"
 Specialized formats or other abbreviations used: A - Adinine, G - Guanine,
 C - Cytosine, T - Thymine Data format: FASTA DATA-SPECIFIC INFORMATION
 FOR: [NGS_P6481.hmp] Number of variables: 523,331 Number of cases/column:
 11 identifier + reference alleles + 25 Subpopulations Alleles Variable
 List: 523,331 SNP and INDELs Missing data codes: Missing codes are written
 with the symbol "--" Specialized formats or other abbreviations
 used: A - Adinine, G - Guanine, C - Cytosine, T - Thymine, '--'
 - Missing, '/'-Represents Alleles SNP Data format: HapMap format
 - The Hapmap file format is a table which consists of 11 columns plus one
 column for each sample genotyped. The first row contains the header labels
 of samples, and each additional row contains all the information
 associated with a single SNP/INDELs from contig. first 11 column contains
 details of - 1 : rs# : contains the identifier for contig alleles; 2 :
 alleles : contains alleles according to NCBI database dbSNP; 3 : chrom :
 contains the contig that the SNP/INDEL was mapped; 4 : pos : contains the
 respective position of this SNP on Contig; 5 : strand : contains the
 orientation of the SNP in the DNA strand. Thus, SNPs could be in the
 forward (+) or in the reverse (-) or (.) unknown orientation relative to
 the reference contig; 6 : assembly# : contains the version of reference
 sequence assembly (from NCBI); 7 : center : contains the name of
 genotyping center that produced the genotypes; 8 : protLSID contains the
 identifier for HapMap protocol; 9 : assayLSID contain the identifier
 HapMap assay used for genotyping; 10 : panelLSID contains the identifier
 for panel of individuals genotyped; 11 : QCcode contains the quality
 control for all entries From 12th Column onward SNP/INDEL data of zigzag
 ladybird beetle, Cheilomenes sexmaculata - 12 : Reference : Contig
 reference allele for denovo assembley 13 : DL1 : Sample collected from
 IARI 14 : DL3 : Sample collected from Hissar 15 : DL4 : Sample collected
 from Karnal 16 : DL5 : Sample collected from Jhansi 17 : DL6 : Sample
 collected from Panipat 18 : GN2 : Sample collected from Anand 19 : J11 :
 Sample collected from Navsari 20 : J12 : Sample collected from Dandi 21 :
 J21 : Sample collected from Anand 22 : J31 : Sample collected from
 Junagadh 23 : J32 : Sample collected from Porbandar 24 : KA1 : Sample
 collected from Coimbatore 25 : KA2 : Sample collected from GKVK, Bengaluru
 26 : KA4 : Sample collected from Mudigere 27 : KA5 : Sample collected from
 Tiptur 28 : KA6 : Sample collected from Coorg 29 : MA2 : Sample collected
 from Warud 30 : NA3 : Sample collected from Akola 31 : NA4 : Sample
 collected from chandrapura 32 : NA5 : Sample collected from Akola 33 : NA6
 : Sample collected from Amravati 34 : NB1 : Sample collected from Nagpur
 35 : WB1 : Sample collected from Cooch behar 36 : WB2 : Sample collected
 from Barapani 37 : WB3 : Sample collected from Jorhat