Genome assembly and Full-length transcriptome of Malabar Red Snapper, Lutjanus malabaricus

Abstract

The Malabar red snapper (Lutjanus malabaricus) is a high-value marine food fish of growing economic and aquaculture importance across the Indo-Pacific. Despite its significance, genomic resources for this species have remained scarce, hindering the application of genomic tools for selective breeding. Here, we present the first chromosome-level genome assemblies and full-length transcriptome of L. malabaricus. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated high-quality assemblies for unsexed, male, and female individuals, each approximately 1.0 Gb in size and anchored to 24 chromosomes. The assemblies exhibited exceptional contiguity (N50 ≈ 42 Mb) and completeness (BUSCO > 99%), with karyotyping confirming 2n = 48 telocentric chromosomes. Genome annotation identified ~25,000 protein-coding genes, and repeat sequences accounted for almost half of the genome, comparable to other reef-associated teleosts. Comparative analyses of the male and female assemblies revealed strong chromosomal synteny and localized sex-associated regions, suggesting a polygenic or complex mechanism of sex determination. The accompanying multi-tissue full-length transcriptome supports functional and developmental studies. Together, these genomic and transcriptomic datasets provide a comprehensive molecular foundation for population genetics, comparative genomics, and selective breeding in L. malabaricus.