Sequencing & Pangenomes
Authors: Melissa Allen (Center For Aquaculture Technologies) , Dev Mashruwala (Center For Aquaculture Technologies) , Jason Stannard (Center For Aquaculture Technologies) , Sabrina Sauri (Center For Aquaculture Technologies) , Pulgarin (Open Blue) , Arlacon (Open Blue) , Castillo (Center For Aquaculture Technologies) , Klara Verbyla (Center For Aquaculture Technologies)
Advancing genomic resources for emerging aquaculture species requires integrated approaches that bridge laboratory innovation and bioinformatics development. In this work, we describe the establishment of a complete workflow for generating and imputing low-pass whole-genome sequencing (WGS) data in Cobia (Rachycentron canadum). The optimized workflow leverages a TnX transposon system, which integrates a combined tagmentation-ligation strategy to minimize positional bias while generating full-length unique dual-index (UDI) libraries compatible with the Element AVITI sequencing platform. Implementation of this approach on various aquatic species, with focus here on Cobia, results in a streamlined workflow capable of maintaining library complexity while increasing sample processing throughput, reducing hands-on bench time, and improving overall cost-efficiency for low-pass WGS applications. On the bioinformatics side, we constructed a phased haplotype reference panel using high-coverage (~20x) WGS data from 104 broodstock individuals, comprising the full set of 94 current male and female broodstock and 10 individuals from a previous generation, and retaining approximately 1.3-1.5 million high-quality genome-wide SNPs after stringent filtering. Variant calling, phasing, and imputation workflows were optimized using GLIMPSE2 to recover dense genotypes from low-pass sequencing data. Pipeline performance was evaluated across multiple coverage depths (0.2x-1x) and reference configurations by downsampling held-out test individuals and comparing imputed genotypes to their corresponding high-coverage calls. Across test datasets, the optimized pipeline achieved a mean genotype concordance of approximately 97% across ~1.3 million SNPs, demonstrating robust imputation accuracy even at low coverage. This workflow establishes a foundation for imputation-enabled genomic selection in Cobia and provides a scalable model for extending low-pass WGS and imputation strategies to other aquaculture species where high-density genotyping resources are limited.
Keywords: 2026
How to Cite: Allen, M. , Mashruwala, D. , Stannard, J. , Sauri, S. , Pulgarin, , Arlacon, , Castillo, & Verbyla, K. (2026) “A low-pass whole-genome sequencing and imputation pipeline for Cobia (Rachycentron Canadum): bridging laboratory innovation and bioinformatics development”, World Congress on Genetics Applied to Livestock Production Digital Archive. 2026(1). doi: https://doi.org/10.31274/wcgalp.24146