Nutrigenomic marker discovery by de novo transcriptomic sequencing during early development of the tropical gar (Atractosteus tropicus)

We performed transcriptomic profiling from seven larval stages of tropical gar (Atractosteus tropicus), an endemic fish inhabiting the riverscape of southeast Mexico with a growing aquaculture interest. de novo assembly generated 108,932 transcripts, grouped into 80,065 genes, with an average contig length of 792 bp and an N50 value of 1447 bp. A total of 50,377 open reading frames (ORF) were detected, and 34,192 hits were identified against SwissProt; we detected 96% of the metazoan orthologs (BUSCO metazoan odb9) as full-length features. Differential expression (DE) analyses were conducted by grouping samples as biological replicates in three developmental categories or stages: embryo-to-larvae transition (0-1 days after hatch (DAH)), mouth opening larvae (3-5 DAH) and lecithoexotrophic larvae (7-9 DAH). Enrichment analyses of overrepresented gene ontology terms in differentially expressed genes were also performed. Promising candidate nutritional markers were selected by a combination of semantic searches over annotations in three different operational categories: functional role as a digestive enzyme, metabolic hormones and organogenesis of digestive system. The results of this study provide for the first time an overview of early developmental transcriptome profiles in the gar and identify candidate nutritional markers, which can be used as indicators of digestive system development.

Automated summary

The study conducted transcriptomic profiling of seven larval stages of a fish species called tropical gar, with a focus on identifying potential nutritional markers for digestive system development. The results provide a comprehensive overview of the early developmental transcriptome profiles in the gar and offer insights into candidate nutritional markers.