Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases

A genome assembly contains the complete DNA sequence of a particular organism. This information is necessary to understand the organism's gene functions and genetic variability of their populations. In this study, the genome of the Pacific whiteleg shrimp Penaeus (Litopenaeus) vannamei was assembled using databases from the GenBank, the repository of DNA sequences of the National Institute of Health of the USA, which is of worldwide public access. The three tables and two figures contain supplementary information of the article JOH-2023-155.R1. The information is relevant for the analysis of the new reference-guided genome assembly of the whiteleg shrimp. The Supplementary Table 1 compares observed to expected chromosome sizes. The location of genetic markers in Supplementary Table 2 will be particularly relevant for future genome-wide association studies, which will look for the association of markers and/or genes to traits of interest for aquaculture, such as disease resistance, growt..., Supplementary Table 1. 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 (1997). The obtained length of each chromosome was calculated counting the number of nucleotides in the genome assembly fasta file.
Supplementary Table 2. The location of each marker was obtained by a Blast alignment to the new reference-guided assembly. Retained markers were those that aligned only once to the genome. The script was:
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 Table 3. The markers listed in this table are those 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.
Supplementary Figure 1. The constru..., , # Supplementary Tables. Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases

[https://doi.org/10.5061/dryad.0k6djhb7n](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 Bl...