| As economically relevant traits, feeding behavior and food preference domestication determine production cost and profitability. Although there are intensive research efforts on feeding behavior and food intake, little is known about food preference. Food preference is an innate behavioral trait subject to genetic influences. However, the genes and genetic factors that determine food preference are largely unknown. Although several genes were shown to be involved in the determination of food preference, very little is currently known about the transcriptome determining the unique food preference, such as live prey in mandarin fish, and food habit transition in grass carp.Mandarin fish, as a demersal piscivore, has very unique food preference. In the wild, once the fry start feeding, it feed solely on live fry of other fish species. In rearing conditions, mandarin fish also accept only live prey fish, refusing dead prey fish or artificial diets. Among major species of mandarin fish, Siniperca scherzeri, is much easier to accept dead prey fish compared to S. chuatsi, and the difference in acceptance of dead prey fish is further amplified in the hybrid F1 of S. chuatsi ((?)) ×S. scherzeri ((?)). We hypothesize that changes in gene expression as well as SNPs account for this dramatic difference. Elucidating the genes regulating the unique food preference (live prey fish) in mandarin fish could lead to a better understanding of mechanisms controlling food preference in animals, including mammals.To obtain an overview of gene expression profile in mandarin fish with different food preferences, cDNA libraries were constructed from dead prey fish feeders (SCX) and nonfeeders (SCW), and sequenced using the Illumina Hiseq2000 system. High quality reads of SCX and SC_W were assembled, yielding 665,466, and 716,044 contigs, respectively. After removing the partial overlapping sequences, a total of 118,218 distinct sequences were obtained (All-Unigene, mean size:506 bp), suggesting the identification of a large number of new genes by transcriptome sequencing reported here. Among these unigenes,69.5%(82,108) were between 100 and 500 bp in length,30.5%(36,110) were longer than 500 bp, of which 9.8%(11,550) were longer than 1,000 bp.49,155 unigenes (41.6% of All-Unigene) were aligned function by BLASTx, and 69,063 (58.4%) assembled sequences could not be matched to any known protein. The BLASTx top-hit species distribution of gene annotations showed highest homology to zebrafish (Danio rerio,52%), followed by Atlantic salmon (Salmo solar,9%) and spotted green pufferfish (Tetraodon nigroviridis,4%). In addition, the mandarin fish sequences also had homologies to four other fish species including Japanese pufferfish (Takifugu rubripes), sablefish (Anoplopoma fimbria), rainbow smelt (Osmerus mordax) and medaka (Oryzias latipes). These results indicated a high level of phylogenetic conservation between mandarin fish and other fish species, especially zebrafish.Of 49,155 annotated sequences in mandarin fish transcriptome,14,228 (28.9%) were assigned with one or more gene ontology (GO) terms. In total,106,024 GO assignments were finally obtained, with 46.1% for biological processes,34.8% for cellular components, and 19.1% for molecular functions. We mapped the 49,155 annotated sequences to the reference canonical pathways in Kyoto Encyclopedia of Genes and Genomes (KEGG) to identify the biological pathways. In total, we assigned 30,964 sequences to 205 known metabolic or signaling pathways. The representative pathways with the differentially expressed genes were mitogen-activated protein kinases (MAPK) signaling pathway (1222 members), calcium signaling pathway (913 members), insulin signaling pathway (711 members), long-term potentiation (LTP) (542 members), long-term depression (369 members), taste transduction (173 members) and mammalian circadian rhythm (92 members).We detected 4,768 potential SNPs in feeders and 41 potential SNPs in nonfeeders. The overall frequency of predicted SNPs in the mandarin fish transcriptome was one per 12,430 bp. A total of 4,809 SNPs were identified, including 1,592 transitions and 3,217 transversions. We identified a total of 22,418 potential Simple Sequence Repeats (SSRs) in 17,933 (15.2%) unigenes with frequency of one SSR per 2.7 kb of the unigenes. Of 17,933 SSR-containing sequences,7,585 (42.3%) had been annotated, and could be considered as preferred candidates for marker development. We foundl,986 and 4,526 unigenes to be differentially expressed between feeders and nonfeeders from transcriptome and DGE analysis (False Discovery Rate (FDR)< 0.001, fold-change> 2), respectively. Analysis of these genes revealed the signaling pathways involved, including retinal photosensitivity (retinal G protein-coupled receptor (Rgr), retinol dehydrogenase 8 (Rdh8), cellular retinol-binding protein (Crbp) and guanylate cyclase (Gc)), circadian rhythm (period 1 (Per1), period 2 (Per1), Rev-erba, casein kinase (Ck) and nocturnin), appetite control (neuropeptide Y (Npy), growth hormone (Gh), pro-opiomelanocortin (Pome), peptide YY (Pyy), insulin and leptin), learning and memory (cyclic AMP-response element-binding protein (Creb), c-fos, fos-related antigen 2 (Fra- 2), CCAAT enhancer binding protein (C/EBP), zif268, brain-derived neurotrophic factor (Bdnf) and synaptotagmin (Syt)). The importance of these genes was further supported by the identification of significant potential SNP, SSR and antisense transcripts in these genes. The acquisition of novel food preference (dead prey fish) might be due to enhanced visual ability, resetting of circadian phase, decreased appetite, deficiency in memory retention and more abundant variant alleles. Interaction of retinal photo sensitivity, circadian rhythm, appetite control, learning and memory outputs might drive the feeding behavior. Elucidating the genes regulating the unique food preference (live prey fish) in mandarin fish could lead to a better understanding of mechanisms controlling food preference in animals, including mammals.Although there are intensive research efforts on feeding behavior and food habit, little is known about the formation and evolution of herbivory. Grass carp (Ctenopharyngodon idella) is an ecologically appealing model of vertebrate herbivore, widely cultivated in the world as edible fish or as biological control agents for aquatic weeds. Little is known about the molecular mechanism of the formation of herbivory. Grass carp goes through a transition from carnivory to herbivory during its life cycle. Grass carp smaller than 3 cm (total length) is carnivorous, fish of 3-5.5 cm (total length) is at the food transition stage from zooplankton or benthos to aquatic macrophytes, whereas fish lager than 5.5 cm (total length) is herbivorous. However, little is currently known about genes determining the food habit transition, and how they could achieve higher growth rates on plant materials, which have a relatively poor nutritional quality.We showed that grass carp fed with duckweed (modeling fish after food habit transition, Group C) had significantly higher relative length of gut than fish before food habit transition (Group A) or those fed with chironomid larvae (fish without transition, Group A). To obtain an overview of gene expression profile in grass carp before and after food habit transition, cDNA libraries were constructed from brain (AB), liver (AL), gut (AG) of grass carp before the food transition (before the feeding trial (Group A)); brain (BB), liver (BL), gut (BG) offish without transition (fed with chironomid larvae (Group B)); brain (CB), liver (CL), gut (CG) of fish after food transition (fed with duckweed (Group C)), and sequenced using the Illumina HiSeq2000 system. After removing the low-quality reads, we obtained 64,914,000 (AB),62,801,686 (AL),62,679,236 (AG), 66,466,322 (BB),65,442,204 (BL),63,096,538 (BG),62,196,672 (CB),62,079,494 (CL), 66,338,198 (CG) clean reads, respectively. About 66.32-76.59%of clean reads could be mapped to grass carp genome and 30.60-55.24% mapped to gene. We examined four major alternative splicing events of each group, including exon skipping, intron retention, alternative 5’splicing and alternative 3’splicing.15,739,16,380 and 16,826 alternative splicing events were identified in Groups A, B and C, respectively. We predicted 69,520, 43,953,26,592,49,109,41,754,16,897,46,457,36,675 and 18,331 novel transcripts in AB, AG, AL, BB, BG, BL, CB, CG and CL, respectively. We detected 65,015,48,001, 17,759,61,761,40,721,16,683,59,601,41,561 and 18,770 potential SNPs in AB, AG, AL, BB, BG, BL, CB, CG and CL, respectively. A total of 369,872 SNPs were identified, including 262,250 transitions and 107,622 transversions.Using transcriptome sequencing, we identified 10,184differentially expressed genes between grass carp before and after transition in brain, liver and gut. By eliminating genes potentially involved in development (via comparing fish with or without food habit transition), we identified changes in expression of genes involved in cell proliferation and differentiation, appetite control, circadian rhythm, and digestion and metabolism between fish before and after food habit transition. We suggest that the food habit transition from carnivory to herbivory in grass carp might be due to enhanced gut growth, increased appetite, resetting of circadian phase and enhanced digestion and metabolism. We also found extensive alternative splicing and novel transcript accompanying food habit transition. These differences together might account for the food habit transition and the formation of herbivory in grass carp. These potential determinants provide a glimpse of genetic architecture of the formation of herbivory.Elucidating the genes regulating these unique food preference, including the live prey in mandarin fish as carnivorous fish, and the food habit transition from carnivory to herbivory in grass carp as herbivorous fish, could lead to a better understanding of mechanisms controlling food habit, promoting the intake and utilization of feedstuff in fish, increasing the replacement of animal protein by plant protein in animal feed, and decreasing the cost of cultivation and the pollution of the environment. |
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