Asymmetric expression of homoeologous genes contributes to dietary adaption of an allodiploid hybrid fish derived from Megalobrama amblycephala (♀) × Culter alburnus (♂)

Background Hybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with one another in a single nucleus, which may cause subgenome interaction and dominance at the gene expression level and has been observed in some allopolyploid plants. In our previous studies, newly formed allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) had herbivorous characteristic. It is thus interesting to further characterize whether the subgenome interaction and dominance derive dietary adaptation of this hybrid fish. Results Differential expression, homoeolog expression silencing and bias were investigated in the hybrid fish after 70 days of adaptation to carnivorous and herbivorous diets. A total of 2.65 × 108 clean reads (74.06 Gb) from the liver and intestinal transcriptomes were mapped to the two parent genomes based on specific SNPs. A total of 2538 and 4385 differentially expressed homoeologous genes (DEHs) were identified in the liver and intestinal tissues between the two groups of fish, respectively, and these DEHs were highly enriched in fat digestion and carbon metabolism, amino acid metabolism and steroid biosynthesis. Furthermore, subgenome dominance were observed in tissues, with paternal subgenome was more dominant than maternal subgenome. Moreover, subgenome expression dominance controlled functional pathways in metabolism, disease, cellular processes, environment and genetic information processing during the two dietary adaptation processes. In addition, few but sturdy villi in the intestine, significant fat accumulation and a higher concentration of malondialdehyde in the liver were observed in fish fed carnivorous diet compared with fish fed herbivorous diet. Conclusions Our results indicated that diet drives phenotypic and genetic variation, and the asymmetric expression of homoeologous genes (including differential expression, expression silencing and bias) may play key roles in dietary adaptation of hybrid fish. Subgenome expression dominance may contribute to uncovering the mechanistic basis of heterosis and also provide perspectives for fish genetic breeding and application.

Replication alert: behavioural lateralisation in a detour test is not repeatable in fishes

Behavioural lateralisation, defined as the asymmetric expression of cognitive functions, is reported to enhance key fitness-relevant traits such as predator escape performance, multitasking abilities, and group coordination. Therefore, studies reporting negative effects on lateralisation in fish due to environmental stressors such as ocean acidification, hypoxia, and pollutants are worrisome. However, such studies have focussed on population-level measures, without validating whether lateralisation is consistent within individuals across time. We conducted a multi-species, international assessment of the repeatability (R) of lateralisation in four previously studied fish species using the common detour test, and re-analysed a published dataset (on guppies) using new statistical methods. We expected the three shoaling species to exhibit greater within-individual consistency in lateralisation than their non-shoaling counterparts given previous reports of stronger lateralisation in group-living fishes. However, both absolute and relative lateralisation scores were highly non-repeatable in all five species (0.01