DOI: 10.5061/dryad.k2d05
title: Data from: Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing

description: Imperata cylindrica (Cogongrass, Speargrass) is a diploid C4 grass that is
 a noxious weed in 73 countries and constitutes a significant threat to
 global biodiversity and sustainable agriculture. We used a cost-effective
 genotyping-by-sequencing (GBS) approach to identify the reproductive
 system, genetic diversity and geographic origins of invasions in the
 south-eastern United States. In this work, we demonstrated the advantage
 of employing the closely related, fully sequenced crop species Sorghum
 bicolor (L.) Moench as a proxy reference genome to identify a set of 2320
 informative single nucleotide and insertion–deletion polymorphisms.
 Genetic analyses identified four clonal lineages of cogongrass and one
 clonal lineage of Imperata brasiliensis Trin. in the United States. Each
 lineage was highly homogeneous, and we found no evidence of hybridization
 among the different lineages, despite geographical overlap. We found
 evidence that at least three of these lineages showed clonal reproduction
 prior to introduction to the United States. These results indicate that
 cogongrass has limited evolutionary potential to adapt to novel
 environments and further suggest that upon arrival to its invaded range,
 this species did not require local adaptation through
 hybridization/introgression or selection of favourable alleles from a
 broad genetic base. Thus, cogongrass presents a clear case of broad
 invasive success, across a diversity of environments, in a clonal organism
 with limited genetic diversity.
description: Cogongrass_449G__2320M_US_072514SNP/INDEL data for 449 genotypes with 2320 markersImperata accession collection dataThis file contains the accession numbers of accessions sequenced and used in this manuscript. Data detailing the location in which the accessions were collected is also included.supporting_information_collector_data.xlsxadd_genotype-linenumber_file scriptadd_genotype-linenumber_file: This python script works on csv files that have been exported from the CLC Genomics Workbench. It adds two columns (genotype and line number) at the beginning of each csv file listed in column 1 of an input file. The input file is a csv file. The first row of the input file is considered as a header row. The script also removes the term "mapping" from the chromosome names.add_genotype-linenumber_file.txtremove_header scriptThis python script removes the header row from each csv file that is listed in column 1 of an input csv file.remove_header.txtmerge_sort_enzymes_filesThis perl script merges files listed in column 1 of an input csv file based on various columns within the files to be merged. For example, if chromosome number is found in column 3 and SNP position in column 4, the user could merge all files within the list by columns 3 and then by column 4.extract_SNPs_from_CLC_fileThis python script cleans up the output files that come from the version 6.0 and higher of the CLC software. It removes any SNP calls with length greater than 1 and also all calls where the reference base is a deletion (i.e. a -). It also removes any duplicate entries in the input file.extract_SNPs_from_CLC_file scriptThis python script extracts unique and repetitive rows from an input csv file and puts them into two separate files.extract_unique_SNPsremove_offsite_SNPs scriptThis python script detects those SNPs that aren't within the specific distance of the restriction enzyme used for GBS DNA template preparation and puts good-hits and bad-hits into separate files.remove_offsite_SNPs.txtmerge_CLCv6_SNP_files_with_SAM_files scriptThis python script merges the SNP detection results of CLC(version6 or higher) with the information in SAM files from CLC version 6 or higher. This script requires samtools. The user must specify the path to the samtools software path as well as the reference file name on lines 438 and 439 of this script.merge_CLCv6_SNP_files_with_SAM_files.txt