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van Dijk A, Guabiraba R, Bailleul G, Schouler C, Haagsman HP, Lalmanach AC. Evolutionary diversification of defensins and cathelicidins in birds and primates. Mol Immunol 2023; 157:53-69. [PMID: 36996595 DOI: 10.1016/j.molimm.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023]
Abstract
Divergent evolution for more than 310 million years has resulted in an avian immune system that is complex and more compact than that of primates, sharing much of its structure and functions. Not surprisingly, well conserved ancient host defense molecules, such as defensins and cathelicidins, have diversified over time. In this review, we describe how evolution influenced the host defense peptides repertoire, its distribution, and the relationship between structure and biological functions. Marked features of primate and avian HDPs are linked to species-specific characteristics, biological requirements, and environmental challenge.
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Immunity in Sea Turtles: Review of a Host-Pathogen Arms Race Millions of Years in the Running. Animals (Basel) 2023; 13:ani13040556. [PMID: 36830343 PMCID: PMC9951749 DOI: 10.3390/ani13040556] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/05/2023] [Accepted: 01/20/2023] [Indexed: 02/08/2023] Open
Abstract
The immune system of sea turtles is not completely understood. Sea turtles (as reptiles) bridge a unique evolutionary gap, being ectothermic vertebrates like fish and amphibians and amniotes like birds and mammals. Turtles are ectotherms; thus, their immune system is influenced by environmental conditions like temperature and season. We aim to review the turtle immune system and note what studies have investigated sea turtles and the effect of the environment on the immune response. Turtles rely heavily on the nonspecific innate response rather than the specific adaptive response. Turtles' innate immune effectors include antimicrobial peptides, complement, and nonspecific leukocytes. The antiviral defense is understudied in terms of the diversity of pathogen receptors and interferon function. Turtles also mount adaptive responses to pathogens. Lymphoid structures responsible for lymphocyte activation and maturation are either missing in reptiles or function is affected by season. Turtles are a marker of health for their marine environment, and their immune system is commonly dysregulated because of disease or contaminants. Fibropapillomatosis (FP) is a tumorous disease that afflicts sea turtles and is thought to be caused by a virus and an environmental factor. We aim, by exploring the current understanding of the immune system in turtles, to aid the investigation of environmental factors that contribute to the pathogenesis of this disease and provide options for immunotherapy.
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The Two Domains of the Avian Double-β-Defensin AvBD11 Have Different Ancestors, Common with Potential Monodomain Crocodile and Turtle Defensins. BIOLOGY 2022; 11:biology11050690. [PMID: 35625418 PMCID: PMC9138766 DOI: 10.3390/biology11050690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/08/2022] [Accepted: 04/16/2022] [Indexed: 12/12/2022]
Abstract
Simple Summary Vertebrate defensins are a multigene family of antimicrobial peptides that evolved following a series of gene duplication and divergence events during the expansion of vertebrates. In birds, the repertoire of avian defensins contains an atypical defensin, namely AvBD11 (avian beta-defensin 11), which consists of two repeated but divergent defensin units (or domains) while most vertebrate defensins only possess one unit. In this study, we investigated the evolutionary scenario leading to the formation of this double defensin in birds by comparing each defensin unit of AvBD11 with other defensins from birds and closely related reptiles (crocodile, turtles) predicted to have a single defensin unit. Our most outstanding results suggest that the double defensin AvBD11 probably appeared following a fusion of two ancestral genes or from an ancestral double defensin, but not from a recent internal duplication as it can be observed in other types of proteins with domain repeats. Abstract Beta-defensins are an essential group of cysteine-rich host-defence peptides involved in vertebrate innate immunity and are generally monodomain. Among bird defensins, the avian β-defensin 11 (AvBD11) is unique because of its peculiar structure composed of two β-defensin domains. The reasons for the appearance of such ‘polydefensins’ during the evolution of several, but not all branches of vertebrates, still remain an open question. In this study, we aimed at exploring the origin and evolution of the bird AvBD11 using a phylogenetic approach. Although they are homologous, the N- and C-terminal domains of AvBD11 share low protein sequence similarity and possess different cysteine spacing patterns. Interestingly, strong variations in charge properties can be observed on the C-terminal domain depending on bird species but, despite this feature, no positive selection was detected on the AvBD11 gene (neither on site nor on branches). The comparison of AvBD11 protein sequences in different bird species, however, suggests that some amino acid residues may have undergone convergent evolution. The phylogenetic tree of avian defensins revealed that each domain of AvBD11 is distant from ovodefensins (OvoDs) and may have arisen from different ancestral defensins. Strikingly, our phylogenetic analysis demonstrated that each domain of AvBD11 has common ancestors with different putative monodomain β-defensins from crocodiles and turtles and are even more closely related with these reptilian defensins than with their avian paralogs. Our findings support that AvBD11′s domains, which differ in their cysteine spacing and charge distribution, do not result from a recent internal duplication but most likely originate from a fusion of two different ancestral genes or from an ancestral double-defensin arisen before the Testudines-Archosauria split.
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Zhang L, Xiao H, Huang J, Ouyang L, Li S, Tang Y. Identification and expression analysis of the β-defensin genes in the goat small intestine. Gene 2021; 801:145846. [PMID: 34274482 DOI: 10.1016/j.gene.2021.145846] [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: 09/09/2020] [Revised: 03/22/2021] [Accepted: 07/13/2021] [Indexed: 11/24/2022]
Abstract
Defensins represent a family of cysteine-rich peptides that have broad-spectrum antimicrobial activities and serve as a typical kind of effector molecule in the immunity. Ruminant species have a large number of β-defensins in the absence of α- and θ-defensins. It is well-known that the genomes of sheep and cattle harbor at least 43 and 57 β-defensin genes, respectively. However, the repertoire of the goat β-defensin gene family has not been fully elucidated. In this study, we identified a total of 50 β-defensins from the goat genome, including 48 functional genes and 2 pseudogenes. Cross-species genomic and evolutionary analyses showed that all of the β-defensins in goat chromosomes 8, 13 and 23 present one-to-one orthologous relationships to their sheep and cattle counterparts, whereas some β-defensin genes in goat chromosome 27 are goat-specific. Moreover, we observed that some duplicated genes in goat chromosome 27 may be derived from gene copy number variation, and the annotation of sheep and cattle β-defensins appears to be incomplete in the genome. Importantly, real-time PCR analysis showed that 17 β-defensins are expressed in the small intestine with abundant cBD1s expression. These findings significant increased our knowledge of ruminant β-defensin and provided useful information for genetic studies, as well as providing a foundation for future research exploring the role of defensins in the immune response.
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Affiliation(s)
- Long Zhang
- Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China; Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan, China
| | - Haihong Xiao
- Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
| | - Jian Huang
- Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
| | - Linghua Ouyang
- Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China.
| | - Siming Li
- Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
| | - Yanqiang Tang
- Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
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Developmental and Tissue Patterns of the Basal Expression of Chicken Avian β-Defensins. BIOMED RESEARCH INTERNATIONAL 2021; 2020:2567861. [PMID: 33490238 PMCID: PMC7787727 DOI: 10.1155/2020/2567861] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/29/2020] [Accepted: 11/28/2020] [Indexed: 12/21/2022]
Abstract
Defensins are a class of antimicrobial peptides in vertebrates that function as the first line of innate immunity with potent antimicrobial and immunomodulatory activities. Fourteen defensins, namely, avian β-defensin 1 to 14 (AvBD1-14), have been identified in chickens. Before characterizing the role of AvBDs in innate immunity during the early development of chickens, we collected tissue segments from the liver, spleen, and gastrointestinal (GI) tract including the esophagus, crop, proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and colon from broilers at days 1, 3, 7, 14, and 28. After RNA isolation and reverse transcription, we determined the expression levels of the 14 AvBD genes in these tissues during the first 28 days after hatching by real-time PCR. The results suggested the AvBDs were widely expressed in the chicken liver, spleen, and gastrointestinal (GI) tract. Interestingly, we did not detect AvBD11 expressed in the GI tract, even in the liver and spleen. Additionally, AvBDs were differentially expressed in the chicken GI tract. AvBD5 and AvBD14 were expressed most abundantly in the proximal GI tract, especially the esophagus and crop. Moreover, AvBD5, AvBD7, AvBD9, and AvBD14 were expressed in an inverted-V pattern with the peak being the observed expression at days 3, 7, or 14 in the chicken spleen, esophagus, duodenum, and cecum. Other AvBDs presented biphasic or inverted-V expression patterns in different tissues. The expression levels of all detected AvBDs were strengthened after hatching rather than decreasing steadily. Therefore, AvBDs were found to be expressed widely in the chicken liver, spleen, and GI tract and their expression levels were primarily up regulated during the early development of chicken, implying the potential essential roles of AvBDs in early innate defense and infection resistance of chickens.
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Xiao Y, Lyu W, Yang H, Xu X, Zhou C, Lu L, Zhang L. Molecular characterization, mRNA gene expression, and antimicrobial activity of 2 new cathelicidin genes in goose. Poult Sci 2020; 99:2983-2991. [PMID: 32475433 PMCID: PMC7597728 DOI: 10.1016/j.psj.2020.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/30/2020] [Accepted: 03/09/2020] [Indexed: 01/15/2023] Open
Abstract
Cathelicidins represent a major group of host defense peptides (HDPs) that share a highly conserved cathelin-like domain. In birds, this gene family has been identified in many species. However, no information was available in the goose until now. In this study, we present the molecular characterization of 2 goose cathelicidin genes, namely goose CATH2 and goose CATH3, for the first time. The complete cDNA of goose CATH2 and goose CATH3 were 571 bp and 573 bp in length, respectively, and the deduced amino acid sequences exhibited high similarity with other avian cathelicidins. Furthermore, evolutionary analyses indicated that all known cathelicidins form 3 distinct clusters from reptiles, while the oldest cathelicidin member, which is known as CATHB1, is very likely absent in the goose genome. Meanwhile, highly expressed goose CATH2 and goose CATH3 were also observed in primary and secondary lymphoid tissues, same as the observations in other avian species. In addition, chemically synthesized mature peptides of the 2 cathelicidins exerted optimal antimicrobial abilities to a range of gram-negative and gram-positive bacteria. The discovery and characterization of goose cathelicidins complete the knowledge for goose HDPs and might contribute to understanding the evolution of avian cathelicidins as well as for the development of antibacterial agents.
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Affiliation(s)
- Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wentao Lyu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoqin Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Long Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China.
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Contreras G, Shirdel I, Braun MS, Wink M. Defensins: Transcriptional regulation and function beyond antimicrobial activity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 104:103556. [PMID: 31747541 DOI: 10.1016/j.dci.2019.103556] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 05/20/2023]
Abstract
Defensins are one the largest group of antimicrobial peptides and are part of the innate defence. Defensins are produced by animals, plants and fungi. In animals and plants, defensins can be constitutively or differentially expressed both locally or systemically which confer defence before and a stronger response after infection. Immune signalling pathways regulate the gene expression of defensins. These pathways include cellular receptors, which recognise pathogen-associated molecular patterns and are found both in plants and animals. After recognition, signalling pathways and, subsequently, transcriptional factors are activated. There is an increasing number of novel functions in defensins, such as immunomodulators and immune cell attractors. Identification of defensin triggers could help us to elucidate other new functions. The present article reviews the different elicitors of defensins with a main focus on human, fish and marine invertebrate defensins.
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Affiliation(s)
- Gabriela Contreras
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
| | - Iman Shirdel
- Marine Sciences Faculty, Tarbiat Modares University, Noor, Iran
| | - Markus Santhosh Braun
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
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Li JJ, Zhang L, Ren P, Wang Y, Yin LQ, Ran JS, Zhang XX, Liu YP. Genotype frequency distributions of 28 SNP markers in two commercial lines and five Chinese native chicken populations. BMC Genet 2020; 21:12. [PMID: 32019486 PMCID: PMC7001339 DOI: 10.1186/s12863-020-0815-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 01/27/2020] [Indexed: 11/18/2022] Open
Abstract
Background Modern breeding in the poultry industry mainly aims to produce high-performance poultry lines and breeds in two main directions of productivity, meat and eggs. To understand more about the productive potential of lowly selected Chinese native chicken populations, we selected 14 representative SNP markers strongly associated with growth traits or carcass traits and 14 SNP markers strongly associated with egg laying traits through previous reports. By using the MassArray technology, we detected the genotype frequency distributions of these 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line. Results Based on the genotype frequency distributions of these 28 SNP markers in 5 native chicken populations and 2 commercial lines, the results suggested that these Chinese indigenous chicken populations have a relatively close relationship with the commercial broiler line but a marked distinction from the commercial layer line. Two native chicken breeds, Shimian Caoke Chicken and Daheng Broilers, share similar genetic structure with the broiler line. Conclusions Our observations may help us to better select and breed superior domestic chickens and provide new clues for further study of breeding programs in local chicken populations.
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Affiliation(s)
- Jing-Jing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Long Zhang
- Institute of Ecology, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, Sichuan, China
| | - Peng Ren
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ye Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ling-Qian Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jin-Shan Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xian-Xian Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi-Ping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Javůrková VG, Pokorná M, Mikšík I, Tůmová E. Concentration of egg white antimicrobial and immunomodulatory proteins is related to eggshell pigmentation across traditional chicken breeds. Poult Sci 2019; 98:6931-6941. [PMID: 31420680 PMCID: PMC8913977 DOI: 10.3382/ps/pez472] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/30/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
- Veronika Gvoždíková Javůrková
- Department of Animal Science, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague – Suchdol, Czech Republic
- Corresponding author
| | - Monika Pokorná
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Ivan Mikšík
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Eva Tůmová
- Department of Animal Science, Czech University of Life Sciences, Kamýcká 129, 165 00 Prague – Suchdol, Czech Republic
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Yang WR, Li BB, Hu Y, Zhang L, Wang XZ. Oxidative stress mediates heat-induced changes of tight junction proteins in porcine sertoli cells via inhibiting CaMKKβ-AMPK pathway. Theriogenology 2019; 142:104-113. [PMID: 31586867 DOI: 10.1016/j.theriogenology.2019.09.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 08/29/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
Heat stress causes reversible changes in tight junction proteins in immature Sertoli cells via inhibition of the AMPK signaling pathway; these effects are accompanied by an increase in the early apoptotic rate and decrease in the cell viability of Sertoli cells. Since heat stress is known to also cause oxidative damage, in the present study, we investigated whether the earlier mentioned effects of heat stress were brought about via the induction of oxidative stress in boar Sertoli cells. Immature Sertoli cells obtained from 3-week-old piglets were subjected to heat treatment (43 °C, 30 min), and the percentage of ROS-positive cells, the malonaldehyde (MDA) concentration, and the activity of the antioxidases, including superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and catalase (CAT) were measured. Next, the Sertoli cells were treated with N-acetyl-l-cysteine (NAC) (1 mmol/L, 2 h), an antioxidant agent, before they were exposed to heat stress. The effects of NAC on ROS accumulation, MDA levels, antioxidase activity, the CaMKKβ-AMPK signaling pathway and expression of tight junction proteins were assessed. The results showed that heat stress reversibly increased the percentage of ROS-positive cells and MDA levels, and decreased the activity of SOD, GSH-Px, and CAT. Pretreatment with NAC abrogated these effects of heat stress. Additionally, NAC reversed the heat stress-induced decrease in the expression of CaMKKβ and dephosphorylation of AMPK. NAC also obviously rescued the heat stress-induced downregulation of tight junction proteins (claudin-11, JAM-A, occludin, and ZO-1) both at the mRNA and protein level. In conclusion, the findings indicate that oxidative damage participates in heat stress-induced downregulation of tight junction proteins in Sertoli cells by inhibiting the CaMKKβ-AMPK axis. Further, NAC reversed the effects of heat stress on tight junction proteins; this means that it has potential as a protective agent that can prevent reproductive dysfunction in boars under conditions of heat stress.
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Affiliation(s)
- Wei-Rong Yang
- Chongqing Key Laboratory of Forage & Herbivore, College of Animal Science and Technology, Southwest University, Chongqing, 400716, PR China; Institute of Ecological Research, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, 637002, PR China
| | - Bin-Bin Li
- Geomathematics Key Laboratory of Sichuan Province, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Yu Hu
- Chongqing Key Laboratory of Forage & Herbivore, College of Animal Science and Technology, Southwest University, Chongqing, 400716, PR China
| | - Long Zhang
- Institute of Ecological Research, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, 637002, PR China
| | - Xian-Zhong Wang
- Chongqing Key Laboratory of Forage & Herbivore, College of Animal Science and Technology, Southwest University, Chongqing, 400716, PR China.
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Genomic Identification and Expression Analysis of the Cathelicidin Gene Family of the Forest Musk Deer. Animals (Basel) 2019; 9:ani9080481. [PMID: 31344924 PMCID: PMC6719980 DOI: 10.3390/ani9080481] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/21/2019] [Accepted: 07/22/2019] [Indexed: 12/29/2022] Open
Abstract
Simple Summary Cathelicidins are a group of host defense peptides in vertebrates with both antimicrobial and immunomodulatory activities. In the present study, we identified the entire repertoire of the cathelicidin gene family from the forest musk deer genome. Sequence comparison, phylogenetic topology, and gene and genomic organizations collectively suggest that all cathelicidin genes have already been fixed in the genome of forest musk deer before the split of moschidae and bovidae, while independent pseudogenization events have occurred after species divergence. In addition, real-time PCR analysis suggested that all functional cathelicidins play important roles in the immune system. The results of this study will be helpful for further evolutionary and functional studies. Abstract The forest musk deer (Moschus berezovskii) is a small-sized artiodactyl species famous for the musk secreted by adult males. In the captive population, this species is under the threat of infection diseases, which greatly limits the increase of individual numbers. In the present study, we computationally analyzed the repertoire of the cathelicidin (CATHL) family from the genome of forest musk deer and investigated their expression pattern by real-time PCR. Our results showed that the entire genome of forest musk deer encodes eight cathelicidins, including six functional genes and two pseudogenes. Phylogenetic analyses further revealed that all forest musk deer cathelicidin members have emerged before the split of the forest musk deer and cattle and that forest musk deer CATHL3L2 and CATHL9 are orthologous with two cattle pseudogenes. In addition, the gene expression results showed that the six functional genes are not only abundantly expressed in the spleen and lung, but are also differently expressed in response to abscesses, which suggests that forest musk deer cathelicidins may be involved in infections. Taken together, identification and characterization of the forest musk deer cathelicidins provide fundamental data for further investigating their evolutionary process and biological functions.
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Yin L, Yu L, Zhang L, Ran J, Li J, Yang C, Jiang X, Du H, Hu X, Liu Y. Transcriptome analysis reveals differentially expressed genes and pathways for oviduct development and defense in prelaying and laying hens. Am J Reprod Immunol 2019; 82:e13159. [PMID: 31206849 DOI: 10.1111/aji.13159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/01/2019] [Accepted: 06/06/2019] [Indexed: 01/01/2023] Open
Abstract
PROBLEM The oviduct plays an indispensable role in the formation of eggs, especially the magnum and uterus. The identification of oviduct development in different stages will help to target candidate genes and pathways in regulation of albumen and eggshell formation, as well as defense mechanism in oviduct and egg. METHODS To identify the function differences and the molecular defense mechanism of the oviduct and egg, we performed transcriptome sequencing analysis of the magnum and uterus in 120-d-old and 300-d-old Lohmann layers, three birds in each group. RESULTS With fold changes (log2 ratio) ≥ 2 and false discovery rate (FDR) < 0.01, RNA-Seq revealed 1,040 genes expressed differentially in the magnum and 595 genes in the uterus. By combining GO enrichment and KEGG pathway analysis, it served to show that gene activities of the magnum and uterus in prelaying chickens were more likely to concentrate on growth and development, and after egg-laying, they were mainly inclined to enhance the substances transmembrane transport and secretion activities. We further characterized 1579 new genes, while only 803 of them were functionally annotated. A complex mixture of proteins related to defense was measured in this study. A subset of avian β-defensins (AvBDs) and ovodefensins (OvoDs), that is, AvBD12, AvBD11, AvBD10, OvoDA1, OvoDB1, OvoDA2, OvoDA3, and OvoDBβ, was detected to express in the magnum of laying hens at high levels. CONCLUSION Collectively, the identification and functional analysis of these differentially expressed genes (DEGs), as well as specific expression of avian defensins, may contribute to understand the development and defense mechanisms of oviduct and eggs.
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Affiliation(s)
- Lingqian Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Lintian Yu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Guangxi Agricultural Vocational College, Nanning, China
| | - Long Zhang
- Institute of Ecology, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Jinshan Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jingjing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chaowu Yang
- Sichuan Animal Science Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Xiaosong Jiang
- Sichuan Animal Science Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Huarui Du
- Sichuan Animal Science Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Xiaofang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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Molecular Cloning and Expression Analysis of Interleukin-8 and -10 in Yellow Catfish and in Response to Bacterial Pathogen Infection. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9617659. [PMID: 31317044 PMCID: PMC6601492 DOI: 10.1155/2019/9617659] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/15/2019] [Indexed: 01/22/2023]
Abstract
The yellow catfish (Pelteobagrus fulvidraco) is an important economic freshwater aquaculture species in Asia. However, little is known about its immune response to bacterial pathogen infection. Here, two cytokines, the proinflammatory cytokine interleukin-8 (IL-8) and the anti-inflammatory cytokine interleukin-10 (IL-10), were identified and characterized in the yellow catfish for the first time. We found that the full length of the IL-8 cDNA was 784 bp and contained an open reading frame (ORF) of 336 bp, while the IL-10 gene was 973 bp in length with a 549 bp of ORF. In addition, both the IL-8 and the IL-10 had similar tissue-specific expression patterns. They were more abundant in the spleen and lowest expressed in the liver. Furthermore, IL-10 but not IL-8 was significantly upregulated in the intestine of yellow catfish by feed supplementation of Clostridium butyricum (CB). More importantly, the expression levels of intestinal IL-10 and IL-8 were up- and downregulated by pathogen Aeromonas punctata stimuli with the presence of CB, respectively. Collectively, these results suggest that IL-10 and IL-8 mediate important roles in the immunity of yellow catfish, and feed supplementation of CB may able to reduce the intestinal inflammation caused by bacteria infections through regulating the expression of IL-10 and IL-8.
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Yang CW, Ran JS, Yu CL, Qiu MH, Zhang ZR, Du HR, Li QY, Xiong X, Song XY, Xia B, Hu CM, Liu YP, Jiang XS. Polymorphism in MC1R, TYR and ASIP genes in different colored feather chickens. 3 Biotech 2019; 9:203. [PMID: 31065503 DOI: 10.1007/s13205-019-1710-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/08/2019] [Indexed: 01/22/2023] Open
Abstract
Coat color genetics successfully adapted and applied to different animal species, which provides a good demonstration of the concept of comparative genetics. In this study, we sequenced 945 bp fragments of melanocortin 1 receptor (MC1R) gene, 421 bp fragments of exon 1 of tyrosinase (TYR) gene and 266 bp fragments of exon 3 of agouti signaling protein (ASIP) gene for 250 individuals with five plumage color patterns. We detected a total of three SNPs (T398A, T637C, and G920C) in MC1R and built six haplotypes (H1-H6) based on the three SNPs. H5 and H6 haplotypes were mainly concentrated in white and grey chicken. And diplotypes H2H3 occurred in white feather and black-speckle feather with the same frequency. Moreover, a total of three SNPs (C47G, T120C, and T172C) in TYR were found and built six haplotypes (P1-P6) based on the three SNPs. Among them, haplotype P2, P3 and P6 were not occurred in black chicken, the diplotypes P1P6 and P4P6 were only distributed in white, gray and black-speckled feather. We only detected one SNP (T168C) in ASIP gene and found that genotype TT was advantage genotype in the different plumage color groups of chickens. Collectively, our study suggested an association between plumage color and genetic variation of MC1R, TYR and ASIP in chicken.
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Affiliation(s)
- Chao-Wu Yang
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Jin-Shan Ran
- 2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- 3Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, 211 Huimin Road, Wenjiang, 611130 Sichuan Province China
| | - Chun-Lin Yu
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Mo-Han Qiu
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Zeng-Rong Zhang
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Hua-Rui Du
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Qing-Yun Li
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Xia Xiong
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Xiao-Yan Song
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Bo Xia
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Chen-Ming Hu
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
| | - Yi-Ping Liu
- 2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 China
- 3Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, 211 Huimin Road, Wenjiang, 611130 Sichuan Province China
| | - Xiao-Song Jiang
- 1Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066 China
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15
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Li D, Li Y, Li M, Che T, Tian S, Chen B, Zhou X, Zhang G, Gaur U, Luo M, Tian K, He M, He S, Xu Z, Jin L, Tang Q, Dai Y, Xu H, Hu Y, Zhao X, Yin H, Wang Y, Zhou R, Yang C, Du H, Jiang X, Zhu Q, Li M. Population genomics identifies patterns of genetic diversity and selection in chicken. BMC Genomics 2019; 20:263. [PMID: 30940068 PMCID: PMC6446315 DOI: 10.1186/s12864-019-5622-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 03/19/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of genetic variation. There are many local chicken breeds in China. RESULTS Here, we provide a population genome landscape of genetic variations in 86 domestic chickens representing 10 phenotypically diverse breeds. Genome-wide analysis indicated that sex chromosomes have less genetic diversity and are under stronger selection than autosomes during domestication and local adaptation. We found an evidence of admixture between Tibetan chickens and other domestic population. We further identified strong signatures of selection affecting genomic regions that harbor genes underlying economic traits (typically related to feathers, skin color, growth, reproduction and aggressiveness) and local adaptation (to high altitude). By comparing the genomes of the Tibetan and lowland fowls, we identified genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and available food sources. CONCLUSIONS The work provides crucial insights into the distinct evolutionary scenarios occurring under artificial selection for agricultural production and under natural selection for success at high altitudes in chicken. Several genes were identified as candidates for chicken economic traits and other phenotypic traits.
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Affiliation(s)
- Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Miao Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Novogene Bioinformatics Institute, Beijing, China
| | - Binlong Chen
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Guolong Zhang
- Department of Animal Science, Oklahoma State University, Stillwater, OK, USA
| | - Uma Gaur
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Majing Luo
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Kai Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shen He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhongxian Xu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yifei Dai
- Novogene Bioinformatics Institute, Beijing, China
| | - Huailiang Xu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yaodong Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Zhao
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Huadong Yin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chaowu Yang
- Sichuan Animal Science Academy, Chengdu, China
| | - Huarui Du
- Sichuan Animal Science Academy, Chengdu, China
| | | | - Qing Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
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