https://doi.org/10.5061/dryad.0k6djhb7n

Description of the data and file structure

The supplementary Tables from the article are contained in an Excel file.

The Supplementary Table 1 contains a comparison between the observed and expected shrimp’s chromosomes sizes in nucleotides. The expected size of the chromosomes was estimated by dividing the calculated genome size (Zhang et al. 2019) by the physical size of each chromosome reported by Campos-Ramos (1997). The observed length of each chromosome was calculated counting the number of nucleotides in the genome assembly contained in the fasta file (NCBI bioproject PRJNA1022566).

The Supplementary Table 2 indicates the location of each genetic marker (SNPs or microsatellites) relative to the shrimp chromosomes, derived from a Blast alignment. The information includes the ID of the markers, the chromosome number where the marker aligned to the genome assembly, the percentage of coverage and similitude, the probability of random alignment, the position in base pairs both of the aligned sequence of the query and the reference chromosome, the strand where the marker is aligned (+: left to right; - right to left), and the author who published the marker (some markers do not have authorship but GenBank accession number). Only markers that aligned in a single position are shown. Data can be filtered by chromosome, position, author, etc.

The Supplementary Table 3 contains the ID of markers that aligned more than once in the Blast alignment described in Supplementary Table 2. The markers are ordered from those that aligned most to those that aligned to two sites.

The Supplementary Figure 1 is the output from the analysis with the GenomeScope software which is found in https://github.com/tbenavi1/genomescope2.0

The Supplementary Figure 2 is a linear regression between observed and expected values in The Supplementary Table 1.

note: figures are also uploaded as .png files for easier reuse

The Supplementary Materials 1 contains the file in Perl format containing the instructions to remove mtDNA sequences from the raw data files.

Sharing/Access information

Links to other publicly accessible locations of the data:

• DOI: 10.1093/jhered/esae015
• https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1022566

To make the "genetic_markers.fasta" files for the alignment analysis of Supplementary Table 2, the DNA sequence of the markers have to be searched in the GenBank following the accession numbers cited in each authors' published article, which are referenced in the cited literature of the study.

Code/Software

Supplementary Tables 2 and 3. The blast analysis to align the published marker sequences (contained in a fasta format file “genetic_markers.fasta”) to the new assembly is done with the blastn program. To run it, the new assembly in fasta format (“new_reference-guided_genome.fasta”), in this case linked to bioproject PRJNA1022566 in the GenBank, is put into a database format, and then run with the desired parameters. The scripts are:

makeblastdb -in new_reference-guided_genome.fasta -input_type fasta -dbtype nucl

blastn -db new_reference-guided_genome.fasta -query genetic_markers.fasta -out genetic_markers_out.txt -evalue 1e-50 -outfmt "7 qseqid sseqid pident qcovs qcovhsp length qstart qend sstart send"

Supplementary Materials 1. Simply run in Linux the script contained in the file “0.mtDNA_extraction.pl” with the instruction:

This script uses an one-column file with IDs that are going to be used to remove entries from a fasta file.

Usage:

./0.mtDNA_extraction.pl [name of the fasta file, from which sequences are going to be removed]  [name of the file with ids that are going to be removed]