1
|
Ferreira JS, Bruschi DP. Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species. J Mol Evol 2023; 91:793-805. [PMID: 37906255 DOI: 10.1007/s00239-023-10135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Olfaction is a crucial capability for most vertebrates and is realized through olfactory receptors in the nasal cavity. The enormous diversity of olfactory receptors has been created by gene duplication, following a birth-and-death model of evolution. The olfactory receptor genes of the amphibians have received relatively little attention up to now, although recent studies have increased the number of species for which data are available. This study analyzed the diversity and chromosomal distribution of the OR genes of three anuran species (Engystomops pustulosus, Bufo bufo and Hymenochirus boettgeri). The OR genes were identified through searches for homologies, and sequence filtering and alignment using bioinformatic tools and scripts. A high diversity of OR genes was found in all three species, ranging from 917 in B. bufo to 1194 in H. boettgeri, and a total of 2076 OR genes in E. pustulosus. Six OR groups were recognized using an evolutionary gene tree analysis. While E. pustulosus has one of the highest numbers of genes of the gamma group (which detect airborne odorants) yet recorded in an anuran, B. bufo presented the smallest number of pseudogene sequences ever identified, with no pseudogenes in either the beta or epsilon groups. Although H. boettgeri shares many morphological adaptations for an aquatic lifestyle with Xenopus, and presented a similar number of genes related to the detection of water-soluble odorants, it had comparatively far fewer genes related to the detection of airborne odorants. This study is the first to describe the complete OR repertoire of the three study species and represents an important contribution to the understanding of the evolution and function of the sense of smell in vertebrates.
Collapse
Affiliation(s)
- Johnny Sousa Ferreira
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil
| | - Daniel Pacheco Bruschi
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil.
| |
Collapse
|
2
|
Zhou C, Wang X, Hu Z, Chen Q, Du C, Liu Y, Song Z. Comparative analyses reveal potential genetic mechanisms for high-altitude adaptation of Schizopygopsis fishes based on chromosome-level genomes. J Hered 2023; 114:654-668. [PMID: 37646645 DOI: 10.1093/jhered/esad050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023] Open
Abstract
The schizothoracine fishes, widely distributed in the Qinghai-Tibetan Plateau and its adjacent areas, are considered as ideal models for investigation of high-altitude adaptation. Schizophygopsis are one group of the highly specialized schizothoracine fishes, and the genetic basis for their high-altitude adaptation is poorly understood. In this study, we performed comparative genomics analyses to investigate the potential genetic mechanisms for high-altitude adaptation of Schizopygopsis malacanthus and Schizopygopsis pylzovi based on the chromosome-level genomes. Functional enrichment analysis revealed that many expanded gene families in Schizopygopsis were associated with immune response while many contracted gene families were functionally associated with olfaction. Among the 123 positively selected genes (PSGs), angpt2a was detected in HIF-1 signaling pathway and possibly related to the hypoxia adaptation of Schizopygopsis. Furthermore, two PSGs cox15 and ndufb10 were distributed in thermogenesis, and there was a Schizopygopsis-specific missense mutation in cox15 (Gln115Glu), which possibly contributed to the cold temperature adaptation of the Schizopygopsis. Kyoto Encyclopedia of Genes and Genomes enrichment of the PSGs revealed three significant pathways including metabolic pathways, cell cycle, and homologous recombination and Gene Ontology enrichment analysis of the PSGs revealed several categories associated with DNA repair, cellular response to DNA damage stimulus, and metabolic process. Chromosome-scale characterization of olfactory receptor (OR) repertoires indicated that Schizopygopsis had the least number of OR genes, and the OR gene contraction was possibly caused by the limited food variety and the environmental factors such as lower air pressure, lower humidity, and lower temperature. Our study will help expand our understanding of the potential adaptive mechanism of Schizopygopsis to cope with the high-altitude conditions.
Collapse
Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaodong Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhengrui Hu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Qian Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chao Du
- Baotou Teachers College, Baotou, China
| | - Yi Liu
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang, China
| | - Zhaobin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| |
Collapse
|
3
|
Silva L, Mendes T, Ramos L, Zhang G, Antunes A. Parallel evolution of fish bi-modal breathing and expansion of olfactory receptor (OR) genes: toward a universal ORs nomenclature. J Genet Genomics 2023; 50:600-610. [PMID: 36935037 DOI: 10.1016/j.jgg.2023.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/27/2023] [Accepted: 03/04/2023] [Indexed: 03/19/2023]
Abstract
Olfactory receptors (ORs) play a key role in the prime sensorial perception, being highly relevant for intra/interspecific interactions. ORs are a subgroup of G-protein coupled receptors that exhibit highly complex subgenomes in vertebrates. However, OR repertoires remain poorly studied in fish lineages, precluding finely retracing their origin, evolution, and diversification, especially in the most basal groups. Here, we conduct an exhaustive gene screening upon 43 high-quality fish genomes exhibiting varied gene repertoires (2-583 genes). While the early vertebrates performed gas exchange through gills, we hypothesize that the emergence of new breathing structures (swim bladder and paired lungs) in early osteichthyans may be associated with expansions in the ORs gene families sensitive to airborne molecules. Additionally, we verify that the OR repertoire of moderns actinopterygians has not increased as expected following a whole genome duplication, likely due to regulatory mechanisms compensating the gene load excess. Finally, we identify 25 distinct OR families, allowing us to propose an updated universal nomenclature for the fish ORs.
Collapse
Affiliation(s)
- Liliana Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Tito Mendes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Luana Ramos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, Guangdong 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
| |
Collapse
|
4
|
Ye M, Lin X, Zhang Y, Huang Y, Li G, Tian C. Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Silver Sillago (Sillago sihama). Animals (Basel) 2023; 13:ani13071232. [PMID: 37048487 PMCID: PMC10093537 DOI: 10.3390/ani13071232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Olfactory receptor (OR) genes are essential in the specific recognition of diverse stimuli in fish. In this study, a total of 141 OR genes were identified in silver sillago (Sillago sihama), a marine fish sensitive to environmental stimuli, including 112 intact genes, 26 truncated genes, and three pseudogenes. A phylogenetic tree analysis elucidated that the OR genes of S. sihama were classified into six groups, of which β, γ, δ, ε, and ζ groups belonged to type I, and the η group belonged to type II. The type I OR genes contained almost all conserved motifs (n = 62), while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2 (n = 39). OR genes were mainly distributed on LG1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The identified OR genes explored the mechanism of environmental stress and ecological adaptation of S. sihama, and provided valuable genomic resources for further research on the olfaction of teleosts.
Collapse
Affiliation(s)
- Minghui Ye
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xinghua Lin
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yulei Zhang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Yang Huang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Guangli Li
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Changxu Tian
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| |
Collapse
|
5
|
Zou X, Chen L, Li B, Xiao J, Xu P. The neuropeptide Y receptor gene repository, phylogeny and comparative expression in allotetraploid common carp. Sci Rep 2022; 12:9449. [PMID: 35676423 PMCID: PMC9177570 DOI: 10.1038/s41598-022-13587-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/29/2022] [Indexed: 11/23/2022] Open
Abstract
NPY-family receptors belong to G protein-coupled receptors (GPCR), which lays a physiological foundation for the transmembrane transport of an endogenous appetite-stimulating factor neuropeptide Y and related peptides. In this study, we investigated the npyr genes in ten representative species, and twelve npyr genes were identified from allotetraploid C. carpio, the npyr gene number of C. carpio was twice the number of its subgenome B progenitor-like diploid Poropuntius huangchuchieni. Phylogenetic analysis showed that all npyr genes were divided into three subgroups, and they underwent strong purifying selection according to selection pressure analysis. Subsequently, synteny analysis showed that most npyr genes were evenly distributed on the homologous chromosomes of two subgenomes in allotetraploid C. carpio, in which npy1r and npy2r were tandem duplicated, respectively. In addition, the global expression of npyr genes during embryonic development in allotetraploid C. carpio suggested the potential function of npyr genes in immunity and reproduction. In adult tissues, npyr genes were mainly distributed in the brain, gonad, and skin, which displayed a similar expression pattern between the C. carpio B subgenome and P. huangchuchieni. In general, our research could provide reference information for future exploration of the NPY receptors and neuroendocrine system of allotetraploid C. carpio and vertebrates.
Collapse
Affiliation(s)
- Xiaoqing Zou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Bijun Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Junzhu Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China. .,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China. .,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China.
| |
Collapse
|
6
|
Lu J, Gao D, Sims Y, Fang W, Collins J, Torrance J, Lin G, Xie J, Liu J, Howe K. Chromosome-level Genome Assembly of Acanthopagrus latus Provides Insights into Salinity Stress Adaptation of Sparidae. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:655-660. [PMID: 35394576 DOI: 10.1007/s10126-022-10119-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
The yellowfin seabream, Acanthopagrus latus, is widely distributed throughout the Indo-West Pacific. This species, as a euryhaline Sparidae fish, inhabits in coastal environments with large and frequent salinity fluctuation. So the A. latus can be considered as an ideal species for elucidating the evolutionary mechanism of salinity stress adaption on teleost fish species. Here, a chromosome-scale assembly of A. latus was obtained with PacBio and Hi-C hybrid sequencing strategy. The final assembly genome of A. latus is 685.14 Mbp. The values of contig N50 and scaffold N50 are 14.88 Mbp and 30.72 Mbp, respectively. 29,227 genes were successfully predicted for A. latus in total. Then, the comparative genomics and phylogenetic analysis were employed for investigating the different osmoregulation strategies of salinity stress adaption on multiple whole genome scale of Sparidae species. The highly accurate chromosomal information provides the important genome resources for understanding the osmoregulation evolutionary pattern of the euryhaline Sparidae species.
Collapse
Affiliation(s)
- Jianguo Lu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, 510275, China.
- Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, China.
| | - Dong Gao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge, UK
| | - Wenyu Fang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | | | | | - Genmei Lin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jingui Xie
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jian Liu
- School of Computer Science, Nankai University, Tianjin, China
| | | |
Collapse
|
7
|
Identification and characterization of olfactory receptor genes and olfactory perception in rapa whelk Rapana venosa (Valenciennes, 1846) during larval settlement and metamorphosis. Gene 2022; 825:146403. [PMID: 35306113 DOI: 10.1016/j.gene.2022.146403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/13/2022] [Accepted: 03/04/2022] [Indexed: 11/23/2022]
Abstract
The rapa whelk Rapana venosa, an economically important marine fishery resource in China but a major invader all over the world, changes from a phytophagous to a carnivorous form following settlement and metamorphosis. However, the low settlement and metamorphosis rates (<1%) of larvae limit the abundance of R. venosa. This critical step (settlement and metamorphosis) remains poorly characterized but may be related to how larvae perceive the presence of shellfish, their new source of food. Here, we report that larvae may use olfactory perception to sense shellfish. Olfactory receptor (OR) genes are involved in odor sensing in animals. We identified a total of 463 OR genes, which could be grouped into nine clades based on phylogenetic analysis. When assessing the attraction of larvae at different developmental stages to oyster odor, R. venosa showed active settlement and metamorphosis behavior only at the J4 stage (competent larva, 1000-1500 μm shell length) and in the presence of shellfish odor at the same time. Expression of OR gene family members differed between stage 2 (four-spiral whorl stage) and stage 1 (single- to three-spiral whorl stage), indicating significant changes in the olfactory system during larval development. These findings broaden our understanding of olfactory perception, settlement, and metamorphosis in gastropods and can be used to improve R. venosa harvesting, as well as the sustainable development and utilization of this resource.
Collapse
|
8
|
Genome-wide mining of gpx gene family provides new insights into cadmium stress responses in common carp (Cyprinus carpio). Gene 2022; 821:146291. [PMID: 35176426 DOI: 10.1016/j.gene.2022.146291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 01/11/2023]
Abstract
Glutathione peroxidase (Gpx) is an important member of antioxidant enzymes, which can play a vital role in metabolizing reactive oxygen species (ROS) and in maintaining cell homeostasis. In order to study the evolutionary dynamics of gpx gene family in allotetraploid fish species, we identified a total of 14 gpx genes in common carp Cyprinus carpio, while 9 gpx genes were discovered in the diploid progenitor-like species Poropuntius huangchuchieni. Comparative genomic analysis and phylogenetic analysis revealed that the common carp gpx genes had significant expansion and were divided into five distinct subclades. Exon-intron distribution patterns and conserved motif analysis revealed highly conserved evolutionary patterns. Transcript profiles suggested that different gpx genes had specific patterns of regulation during early embryonic development. In adult tissues, gpx genes had a relatively broad expression distribution, most of which were highly expressed in the gills, intestines, and gonads. RT-qPCR studies showed that most gpx genes were downregulated during the initial cd2+ treatment stage. Dietary supplementation of Bacillus coagulans at different concentrations (Group 2 of 1.0 × 107 cfu/g, Group 3 of 1.0 × 108 cfu/g, and Group 4 of 1.0 × 109 cfu/g) induced different regulatory responses of gpx subclades. This result suggested that the appropriate concentration of B. coagulans can improve gpx gene expression when exposed to heavy metal cadmium treatment, which may play a vital role in the resistance to oxidative stress and immune responses. This study has expanded our understanding of the functional evolution of the gpx gene family in common carp.
Collapse
|
9
|
Zhou C, Liu Y, Zheng X, Shang K, Cheng M, Wang L, Yang N, Yue B. Characterization of olfactory receptor repertoires provides insights into the high-altitude adaptation of the yak based on the chromosome-level genome. Int J Biol Macromol 2022; 209:220-230. [PMID: 35378160 DOI: 10.1016/j.ijbiomac.2022.03.194] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/15/2022]
Abstract
Olfaction in vertebrates plays pivotal parts in many aspects, such as localizing prey or food, mating behavior, avoiding predators, and social communication. Yak (Bos grunniens) is the only Bos species that can thrive in high-altitude areas. In view of the critical role of olfactory receptors (ORs) in the specific recognition of diverse stimuli, investigating the evolutionary dynamics of ORs in the yak means a lot. In this study, we used the chromosome-level genome of the yak to identify the ORs genes and discussed the effects of high altitude on the yak's olfaction by comparing the yak with other low-altitude living Bos species (Bos frontalis (gayal), Bos gaurus (gaur), Bos indicus (zebu) and Bos taurus (cattle)). The yak had 400 OR genes, including 264 functional genes, 16 partial genes and 120 OR pseudo genes. There were 387 OR genes mapped to yak 31 chromosomes, and chromosomes 13 and 8 had the most OR genes and functional OR genes. Among these five Bos species, yak had the least number of OR gene subfamilies, OR genes and functional OR genes, while the total number of OR genes in gayal (n = 784) was almost twice as many as that of yak, indicating that the olfaction of yak may be less developed. In addition, the phylogenetic relationships of the functional Bos OR genes were illustrated, which comprised 79 families and 466 subfamilies distributed in two classes (Class I and Class II). There were 76 OR gene subfamilies shared by these five Bos species and 17 OR gene subfamilies were unique to the yak. The potential odor specificity of 44 yak OR genes was identified through the similarity to human OR protein sequences. Remarkably, yak lacks β-ionone and Isovaleric acid(IVA)-related ORs, which may be related to the decline of high-altitude herbaceous plant diversity and underdeveloped yak sweat glands. The conserved motifs of OR genes were highly conserved in Bos species. These results provided a solid foundation for further studies on the molecular mechanisms of the yak's adaptation to the high-altitude environment in olfaction.
Collapse
Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Yi Liu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Xiaofeng Zheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Ke Shang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Meiling Cheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Lei Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610064, PR China; Collaborative Innovation Center for Ecological Animal Husbandry of Qinghai- Tibetan plateau, Southwest Minzu University.
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China.
| |
Collapse
|