Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation

Abstract

The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure. The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea.

Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content inLarimichthys crocea

“…To assess the fragment size distribution and the number of potential SNP marker developed, the public large yellow croaker draft genome sequences (Ao et al, 2015) were in silico digested by the four two-enzyme combinations to mimic the genomic fragmentation. As shown in the Fig.…”

“…The raw reads were cleaned by HTSeq to trim low quality ends (average quality < 20) and eliminate short reads (length < 50 bp). The cleaned reads were mapped to large yellow croaker reference genome sequences (Ao et al, 2015) by BWA (Li & Durbin, 2009). To assess the quality of GBS library, the mapped reads distribution of Sample 88 along the linkage groups were illuminated as an example (Fig.…”

Effects of β-glucan on ROS production and energy metabolism in yellow croaker (Pseudosciaena crocea) under acute hypoxic stress

“…However, the high mortality of farmed fish, partly caused by poor water quality including hypoxia, has created significant barriers for commercial aquaculture (Liu et al 1991;Yang et al 2012). Because large yellow croak is especially sensitive to hypoxic stresses (Ao et al 2015), hypoxia is most often associated with high summer temperatures and high-density cultivation and is exacerbated by feeding due to the increase in oxygen demands from postprandial metabolism (Burt et al 2012). Therefore, understanding the defense characteristics against hypoxic stress in large yellow croaker may contribute to the development of Fish Physiol Biochem strategies for long-term sustainability of its culture.…”

Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

“…Many experiments have investigated physiological responses to short-term (herein defined as 1-120 h), often extreme conditions, usually with the aim of discovering "tolerance" genes for breeding or aquaculture (e.g., Liu et al 2013;Xia et al 2013;Ao et al 2015;Sun et al 2015). These challenge studies reveal genes involved in short-term stress responses, many of which quickly return to baseline levels with no consequences to fitness (van Straalen and Feder 2012).…”

“…This stress response substantially overlaps with that induced by hypoxia, both involving the upregulation of many genes involved in oxygen transport (Long et al 2013;Long et al 2015). Hypoxia tolerance has been associated with variation in the expression of genes involved in a variety of processes, including the regulation of epithelial permeability (Sun et al 2015) and repression of cellular apoptosis (Yuan et al 2016) in channel catfish (Ictalurus punctatus), avoiding cerebral inflammation in the large yellow croaker (Larimichthys crocea; Ao et al 2015), and lipid utilization in a hybrid striped bass (Morone sp. ; Beck et al 2016).…”