title: Transcriptome-wide identification, molecular evolution and expression analysis of Toll-like receptor family in a Tibet fish, Gymnocypris przewalskii.
abstract: Toll-like receptors (TLR) are key components of innate immunity that play significant roles in immune defense against pathogens invasion. Recent frequent outbreaks of the "white spot disease" caused by parasitic infection in farmed Tibetan fishes had resulted in great economic losses. However, to our knowledge, the roles of TLRs in mediating immune response to parasitic infection in Tibetan fishes remain to be determined. Here, we performed data-mining on a widely-farmed Tibetan fish (Gymnocypris przewalskii or Gp) transcriptome to determine the genetic variation and expression pattern of TLRs. We totally obtained 14 GpTLRs and identified 5 with a complete coding sequence. Phylogenetic analysis verified their identities and supported the classification of TLRs into six families as in other vertebrates. The TLR family motifs, such as leucine rich repeat (LRR) and Toll/interleukin (IL)-1 receptor (TIR) domain, are conserved in GpTLR1-5. Selective pressure test demonstrated that all known GpTLRs are under purifying selection, except GpTLR4 underwent positive selection. Further, site model analysis suggested that 11 positively selected sites are found in LRR domain of GpTLR4. Three positively selected sites are located on outside surface of TLR4 3D structure, indicating that function of GpTLR4 may be affected. Tissue specific expression analysis showed all GpTLRs are present in gill, head-kidney and spleen but the relative abundance varied among tissues. In response to parasite Ichthyophthirius multifiliis infection, 5 GpTLR (GpTLR1, -2, -4, -9 and -20) expressions were induced. Intriguingly, GpTLR4 was significantly up-regulated in gills, while GpTLR19 and GpTLR21 unexpectedly showed no any change. In summary, these results revealed the first genomic resources of TLR family and several parasitic infection responsive TLRs in Tibetan fish. These findings provide key information for future studies aiming to understand the molecular mechanisms underlying the immune response to pathogen invasion in Tibetan fishes.
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Tong
authors.affiliation: College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, China.
authors.forename: Yaqiu
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
authors.forename: Cunfang
authors.initials: C
authors.lastname: Zhang
authors.affiliation: The Rescues Center of Qinghai-Lake Naked Carp, Xining, 810016, China.
authors.forename: Jianquan
authors.initials: J
authors.lastname: Shi
authors.affiliation: The Rescues Center of Qinghai-Lake Naked Carp, Xining, 810016, China.
authors.forename: Hongfang
authors.initials: H
authors.lastname: Qi
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China. Electronic address: zhaokai@nwipb.cas.cn.
authors.forename: Kai
authors.initials: K
authors.lastname: Zhao
mesh_terms: D000818:Animals; D001483:Base Sequence; D002347:Carps / Q000235:genetics* / Q000276:immunology* / Q000469:parasitology; D016770:Ciliophora Infections / Q000235:genetics / Q000276:immunology / Q000662:veterinary; D019143:Evolution, Molecular; D005393:Fish Diseases / Q000235:genetics / Q000276:immunology; D014644:Genetic Variation; D005880:Gills / Q000276:immunology; D060226:Head Kidney / Q000276:immunology; D016803:Hymenostomatida; D008969:Molecular Sequence Data; D010802:Phylogeny; D013154:Spleen / Q000276:immunology; D018609:Tibet; D051193:Toll-Like Receptors / Q000235:genetics* / Q000276:immunology*; D059467:Transcriptome
chemical_list: D051193:Toll-Like Receptors
keywords: Gymnocypris przewalskii; Ichthyophthirius multifiliis infection; Innate immune; Toll-like receptor; Transcriptome