title: Transcriptome analysis of food habit transition from carnivory to herbivory in a typical vertebrate herbivore, grass carp Ctenopharyngodon idella.
abstract: BACKGROUND
  Although feeding behavior and food habit are ecologically and economically important properties, little is known about 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. Grass carp exhibits food habit transition from carnivory to herbivory during development. However, currently little is known about the genes regulating the unique food habit transition and the formation of herbivory, and how they could achieve higher growth rates on plant materials, which have a relatively poor nutritional quality.
  
  
  RESULTS
  We showed that grass carp fed with duckweed (modeling fish after food habit transition) had significantly higher relative length of gut than fish before food habit transition or those fed with chironomid larvae (fish without transition). Using transcriptome sequencing, we identified 10,184 differentially 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. Up-regulation of GHRb, Egfr, Fgf, Fgfbp1, Insra, Irs2, Jak, STAT, PKC, PI3K expression in fish fed with duckweed, consistent with faster gut growth, could promote the food habit transition. Grass carp after food habit transition had increased appetite signal in brain. Altered expressions of Per, Cry, Clock, Bmal2, Pdp, Dec and Fbxl3 might reset circadian phase of fish after food habit transition. Expression of genes involved in digestion and metabolism were significantly different between fish before and after the transition.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. laile1985@163.com.
authors.forename: Shan
authors.initials: S
authors.lastname: He
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. xufang_liang@hotmail.com.
authors.forename: Xu-Fang
authors.initials: XF
authors.lastname: Liang
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. 20584917@qq.com.
authors.forename: Ling
authors.initials: L
authors.lastname: Li
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. 378340487@qq.com.
authors.forename: Jian
authors.initials: J
authors.lastname: Sun
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. 761612083@qq.com.
authors.forename: Zheng-Yong
authors.initials: ZY
authors.lastname: Wen
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. 916005218@qq.com.
authors.forename: Xiao-Yan
authors.initials: XY
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. 147309817@qq.com.
authors.forename: Ai-Xuan
authors.initials: AX
authors.lastname: Li
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. 332756006@qq.com.
authors.forename: Wen-Jing
authors.initials: WJ
authors.lastname: Cai
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. 328449359@qq.com.
authors.forename: Yu-Hui
authors.initials: YH
authors.lastname: He
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China. wangyp@ihb.ac.cn.
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Wang
authors.affiliation: Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849-5519, USA. taoyaxi@auburn.edu.
authors.forename: Ya-Xiong
authors.initials: YX
authors.lastname: Tao
authors.affiliation: Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Hubei Collaborative Innovation Center for Freshwater Aquaculture, 430070, Wuhan, China. 554962964@qq.com.
authors.forename: Xiao-Chen
authors.initials: XC
authors.lastname: Yuan
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001921:Brain / Q000378:metabolism; D060435:Carnivory; D002347:Carps / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D002874:Chromosome Mapping; D002940:Circadian Rhythm / Q000235:genetics; D005247:Feeding Behavior; D016678:Genome; D060434:Herbivory / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D007413:Intestinal Mucosa / Q000378:metabolism; D007814:Larva / Q000235:genetics / Q000378:metabolism; D008099:Liver / Q000378:metabolism; D017422:Sequence Analysis, DNA; D059467:Transcriptome