Abstract
Larimichthys crocea (large yellow croaker) is a type of perciform fish well known for its peculiar physiological properties and economic value. Here, we constructed an improved version of the L. crocea genome assembly, which contained 26,100 protein-coding genes. Twenty-four pseudo-chromosomes of L. crocea were also reconstructed, comprising 90% of the genome assembly. This improved assembly revealed several expansions in gene families associated with olfactory detection, detoxification, and innate immunity. Specifically, six hepcidin genes (LcHamps) were identified in L. crocea, possibly resulting from lineage-specific gene duplication. All LcHamps possessed similar genomic structures and functional domains, but varied substantially with respect to expression pattern, transcriptional regulation, and biological function. LcHamp1 was associated specifically with iron metabolism, while LcHamp2s were functionally diverse, involving in antibacterial activity, antiviral activity, and regulation of intracellular iron metabolism. This functional diversity among gene copies may have allowed L. crocea to adapt to diverse environmental conditions.
Highlights
Larimichthys crocea is a type of perciform fish well known for its peculiar physiological properties and economic value
Two hepcidins were reported in an amphibian (Western clawed frog, Xenopus tropicalis)[16], while a single hepcidin gene was identified in birds[17]
The overall assembly statistics of our new genome version (L. crocea v2.0) were dramatically better than the original version: scaffold N50 increased from 1.03 Mb to 6.55 Mb, contig N50 increased from 63.11 kb to 282.69 kb, number of contig N90 decreased from 11,3902 to 3097 (Supplementary Tables 5 and 6)
Summary
Larimichthys crocea (large yellow croaker) is a type of perciform fish well known for its peculiar physiological properties and economic value. We constructed a markedly improved genome assembly and chromosome map of L. crocea We used this genome to identify multiple previously unrecognized expansions in genes coding olfactory receptors, cytochrome P450 proteins, pattern recognition receptors, chemokines and antimicrobial peptides. We identified six unique hepcidin (LcHamp) genes in L. crocea and investigated their tissue distributions, promoter characteristics, and functions (as antibacterial/antiviral agents and/or as regulators of iron metabolism). These data afforded new insights into the adaptive mechanisms used by this species to thrive in diverse environmental conditions and provided a framework for the genetic improvement of L. crocea
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