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Alibardi L. Immunolabeling for filaggrin and acidic keratins in the granular layer of mammalian epidermis indicates that an acidic-basic interaction is involved in cornification. Tissue Cell 2024; 88:102397. [PMID: 38677234 DOI: 10.1016/j.tice.2024.102397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
The soft epidermis of mammals derives from the accumulation of keratohyaline granules in the granular layer, before maturing into corneocytes. Main proteins accumulated in the granular layer are pro-filaggrin and filaggrin that determine keratin clumping and later moisturization of the stratum corneum that remains flexible. This soft epidermis allows the high sensitivity of mammalian skin. Presence and thickness of the stratum granulosum varies among different species of mammals and even between different body regions of the same animal, from discontinuous to multilayered. These variations are evident using antibodies for filaggrin, a large protein that share common epitopes among placentals. Here we have utilized filaggrin antibodies (8959 and 466) and an acidic keratin antibody (AK2) for labeling placental, marsupial and monotreme epidermis. AK2 labeling appears mainly to detect K24 keratin, and less likely other acidic keratins. Immunoreactivity for filaggrin is absent in platypus, discontinuous in Echidna and in the tested marsupials. In placentals, it is inconstantly or hardly detected in the thin epidermis of bat, rodents, and lagomorphs with a narrow, mono-stratified and/or discontinuous granular layer. In contrast, where the granular layer is continuous or even stratified, both filaggrin and AK2 antibodies decorate granular cells. The ultrastructural analysis using the AK2 antibody on human epidermis reveals that a weak labeling is associated with keratohyalin granules and filamentous keratins of transitional keratinocytes and corneocytes. This observation suggests that basophilic filaggrin interacts with acidic keratins like K24 and determines keratin condensation into corneocytes of the stratum corneum.
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Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab Padova, Italy; Department of Biology, University of Bologna, Italy.
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2
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Gu T, Hu J, Yu L. Evolution and conservation genetics of pangolins. Integr Zool 2024; 19:426-441. [PMID: 38146613 DOI: 10.1111/1749-4877.12796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Pangolins (Pholidota, Manidae) are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology (nail-like scales and a myrmecophagous diet) and being the victim of heavy poaching and worldwide trafficking. As such, pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species. Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics, which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins. This review comprehensively presents the hitherto advances in phylogeny, adaptive evolution, conservation genetics, and conservation genomics that are related to pangolins, which will provide an ample understanding of their diversity, molecular adaptation mechanisms, and evolutionary potentials. In addition, we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.
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Affiliation(s)
- Tongtong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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3
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Pinto B, Valente R, Caramelo F, Ruivo R, Castro LFC. Decay of Skin-Specific Gene Modules in Pangolins. J Mol Evol 2023:10.1007/s00239-023-10118-z. [PMID: 37249590 DOI: 10.1007/s00239-023-10118-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Abstract
The mammalian skin exhibits a rich spectrum of evolutionary adaptations. The pilosebaceous unit, composed of the hair shaft, follicle, and the sebaceous gland, is the most striking synapomorphy. The evolutionary diversification of mammals across different ecological niches was paralleled by the appearance of an ample variety of skin modifications. Pangolins, order Pholidota, exhibit keratin-derived scales, one of the most iconic skin appendages. This formidable armor is intended to serve as a deterrent against predators. Surprisingly, while pangolins have hair on their abdomens, the occurrence of sebaceous and sweat glands is contentious. Here, we explore various molecular modules of skin physiology in four pangolin genomes, including that of sebum production. We show that genes driving wax monoester formation, Awat1/2, show patterns of inactivation in the stem pangolin branch, while the triacylglycerol synthesis gene Dgat2l6 seems independently eroded in the African and Asian clades. In contrast, Elovl3 implicated in the formation of specific neutral lipids required for skin barrier function is intact and expressed in the pangolin skin. An extended comparative analysis shows that genes involved in skin pathogen defense and structural integrity of keratinocyte layers also show inactivating mutations: associated with both ancestral and independent pseudogenization events. Finally, we deduce that the suggested absence of sweat glands is not paralleled by the inactivation of the ATP-binding cassette transporter Abcc11, as previously described in Cetacea. Our findings reveal the sophisticated and complex history of gene retention and loss as key mechanisms in the evolution of the highly modified mammalian skin phenotypes.
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Affiliation(s)
- Bernardo Pinto
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Raul Valente
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Filipe Caramelo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Raquel Ruivo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - L Filipe C Castro
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal.
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4
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Damania B, Dittmer DP. Today's Kaposi sarcoma is not the same as it was 40 years ago, or is it? J Med Virol 2023; 95:e28773. [PMID: 37212317 PMCID: PMC10266714 DOI: 10.1002/jmv.28773] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/23/2023]
Abstract
This review will provide an overview of the notion that Kaposi sarcoma (KS) is a disease that manifests under diverse and divergent circumstances. We begin with a historical introduction of KS and KS-associated herpesvirus (KSHV), highlight the diversity of clinical presentations of KS, summarize what we know about the cell of origin for this tumor, explore KSHV viral load as a potential biomarker for acute KSHV infections and KS-associated complications, and discuss immune modulators that impact KSHV infection, KSHV persistence, and KS disease.
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Affiliation(s)
- Blossom Damania
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, 450 West Drive CB#7295, Rm 12-048, Chapel Hill, NC 27599
| | - Dirk P. Dittmer
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, 450 West Drive CB#7295, Rm 12-048, Chapel Hill, NC 27599
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5
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Yan D, Luo X, Tang J, Xu S, Huang K, Wang X, Feng T, Que T, Jia M, Guo X, Rehman SU, Li Z, Yang Y, Li K, Cui K, Ruan J, Liu Q. High-Quality Genomes of Pangolins: Insights into the Molecular Basis of Scale Formation and Adaption to Myrmecophagous Diet. Mol Biol Evol 2023; 40:msac262. [PMID: 36585823 PMCID: PMC9848057 DOI: 10.1093/molbev/msac262] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 01/01/2023] Open
Abstract
Pangolins are one of nature's most fascinating species being scales covered and myrmecophagous diet, yet relatively little is known about the molecular basis. Here, we combine the multi-omics, evolution, and fundamental proteins feature analysis of both Chinese and Malayan pangolins, highlighting the molecular mechanism of both myrmecophagous diet and scale formation, representing a fascinating evolutionary strategy to occupy the unique ecological niches. In contrast to conserved organization of epidermal differentiation complex, pangolin has undergone large scale variation and gene loss events causing expression pattern and function conversion that contribute to cornified epithelium structures on stomach to adapt myrmecophagous diet. Our assemblies also enable us to discover large copies number of high glycine-tyrosine keratin-associated proteins (HGT-KRTAPs). In addition, highly homogenized tandem array, amino content, and the specific expression pattern further validate the strong connection between the molecular mechanism of scale hardness and HGT-KRTAPs.
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Affiliation(s)
- Dingyu Yan
- Guangxi Forestry Research Institute, 530002 Nanning, China
| | - Xier Luo
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225 Foshan, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Jiabin Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Shanghua Xu
- Guangxi Forestry Research Institute, 530002 Nanning, China
| | - Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225 Foshan, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Xiaobo Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Tong Feng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Tengcheng Que
- Guangxi Terrestrial Wildlife Rescue Research and Epidemic Disease Monitoring Centre, 530003 Nanning, China
| | - Miaomiao Jia
- Guangxi Forestry Research Institute, 530002 Nanning, China
| | - Xiaobing Guo
- Guangxi Forestry Research Institute, 530002 Nanning, China
| | - Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Yufeng Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Kaixiang Li
- Guangxi Forestry Research Institute, 530002 Nanning, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225 Foshan, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225 Foshan, China
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6
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Olatunji-Akioye A, Ogunleye A, Emikpe B, Jarikre T, Omotosho O, Olajumoke AM. Contrast radiographic anatomy of the gastrointestinal tract of white-bellied pangolin. WEST AFRICAN JOURNAL OF RADIOLOGY 2022. [DOI: 10.4103/wajr.wajr_36_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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Genome-wide signatures of mammalian skin covering evolution. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1765-1780. [PMID: 33481165 DOI: 10.1007/s11427-020-1841-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/15/2020] [Indexed: 10/22/2022]
Abstract
Animal body coverings provide protection and allow for adaptation to environmental pressures such as heat, ultraviolet radiation, water loss, and mechanical forces. Here, using a comparative genomics analysis of 39 mammal species spanning three skin covering types (hairless, scaly and spiny), we found some genes (e.g., UVRAG, POLH, and XPC) involved in skin inflammation, skin innate immunity, and ultraviolet radiation damage repair were under selection in hairless ocean mammals (e.g., whales and manatees). These signatures might be associated with a high risk of skin diseases from pathogens and ultraviolet radiation. Moreover, the genomes from three spiny mammal species shared convergent genomic regions (EPHB2, EPHA4, and NIN) and unique positively selected genes (FZD6, INVS, and CDC42) involved in skin cell polarity, which might be related to the development of spines. In scaly mammals, the shared convergent genomic regions (e.g., FREM2) were associated with the integrity of the skin epithelium and epidermal adhesion. This study identifies potential convergent genomic features among distantly related mammals with the same skin covering type.
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8
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Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins ( Manis javanica). Viruses 2019; 11:v11110979. [PMID: 31652964 PMCID: PMC6893680 DOI: 10.3390/v11110979] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022] Open
Abstract
Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.
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9
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Lopes-Marques M, Alves LQ, Fonseca MM, Secci-Petretto G, Machado AM, Ruivo R, Castro LFC. Convergent inactivation of the skin-specific C-C motif chemokine ligand 27 in mammalian evolution. Immunogenetics 2019; 71:363-372. [PMID: 31049641 DOI: 10.1007/s00251-019-01114-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/05/2019] [Indexed: 12/31/2022]
Abstract
The appearance of mammalian-specific skin features was a key evolutionary event contributing for the elaboration of physiological processes such as thermoregulation, adequate hydration, locomotion, and inflammation. Skin inflammatory and autoimmune processes engage a population of skin-infiltrating T cells expressing a specific C-C chemokine receptor (CCR10) which interacts with an epidermal CC chemokine, the skin-specific C-C motif chemokine ligand 27 (CCL27). CCL27 is selectively produced in the skin by keratinocytes, particularly upon inflammation, mediating the adhesion and homing of skin-infiltrating T cells. Here, we examined the evolution and coding condition of Ccl27 in 112 placental mammalian species. Our findings reveal that a number of open reading frame inactivation events such as insertions, deletions, and start and stop codon mutations independently occurred in Cetacea, Pholidota, Sirenia, Chiroptera, and Rodentia, totalizing 18 species. The diverse habitat settings and lifestyles of Ccl27-eroded lineages probably implied distinct evolutionary triggers rendering this gene unessential. For example, in Cetacea, the rapid renewal of skin layers minimizes the need for an elaborate inflammatory mechanism, mirrored by the absence of epidermal scabs. Our findings suggest that the convergent and independent loss of Ccl27 in mammalian evolution concurred with unique adaptive roads for skin physiology.
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Affiliation(s)
| | - Luís Q Alves
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - Miguel M Fonseca
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Giulia Secci-Petretto
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - André M Machado
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - Raquel Ruivo
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - L Filipe C Castro
- CIIMAR-UP, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal. .,Department of Biology, Faculty of Sciences, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal.
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10
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Ma JE, Jiang HY, Li LM, Zhang XJ, Li HM, Li GY, Mo DY, Chen JP. SMRT sequencing of the full-length transcriptome of the Sunda pangolin (Manis javanica). Gene 2019; 692:208-216. [PMID: 30664913 DOI: 10.1016/j.gene.2019.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/26/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
Abstract
It is widely known that transcriptional diversity contributes greatly to biological regulation in eukaryotes. With the development of next-generation sequencing (NGS) technologies, several studies on RNA sequencing have considerably improved our understanding of transcriptome complexity. However, obtaining full-length (FL) transcripts remains a considerable challenge because of difficulties in short read-based assembly. In the present study, single-molecule real-time (SMRT) sequencing and NGS were combined to generate the complete and FL transcriptome of Manis javanica. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of the M. javanica genome. We obtained 45,530 high-confidence transcripts from 19,109 genic loci, of which 8014 genes have not yet been annotated within the M. javanica genome. Furthermore, we revealed 8824 long-chain noncoding RNAs (lncRNAs). A total of 30,199 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events were identified in the sequencing data. The structure and expression level of 59 digestive enzyme genes, including 13 carbohydrase genes, 28 lipase genes and 18 protease genes, were analyzed, which might provide original data for further research on M. javanica.
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Affiliation(s)
- Jing-E Ma
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Hai-Ying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Lin-Miao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Xiu-Juan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Hui-Ming Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Guan-Yu Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Da-Ying Mo
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jin-Ping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China.
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11
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Imam A, Bhagwandin A, Ajao MS, Spocter MA, Ihunwo AO, Manger PR. The brain of the tree pangolin (Manis tricuspis
). II. The olfactory system. J Comp Neurol 2018; 526:2548-2569. [DOI: 10.1002/cne.24510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/27/2018] [Accepted: 07/27/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Aminu Imam
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
- Department of Anatomy, Faculty of Basic Medical Sciences; College of Health Sciences, University of Ilorin; Ilorin Nigeria
| | - Adhil Bhagwandin
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
| | - Moyosore S. Ajao
- Department of Anatomy, Faculty of Basic Medical Sciences; College of Health Sciences, University of Ilorin; Ilorin Nigeria
| | - Muhammed A. Spocter
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
- Department of Anatomy; Des Moines University; Iowa
| | - Amadi O. Ihunwo
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
| | - Paul R. Manger
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
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12
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Ma JE, Li LM, Jiang HY, Zhang XJ, Li J, Li GY, Yuan LH, Wu J, Chen JP. Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin ( Manis javanica). PeerJ 2018; 5:e4140. [PMID: 29302388 PMCID: PMC5742527 DOI: 10.7717/peerj.4140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/15/2017] [Indexed: 12/12/2022] Open
Abstract
The Malayan pangolin (Manis javanica) is an unusual, scale-covered, toothless mammal that specializes in myrmecophagy. Due to their threatened status and continuing decline in the wild, concerted efforts have been made to conserve and rescue this species in captivity in China. Maintaining this species in captivity is a significant challenge, partly because little is known of the molecular mechanisms of its digestive system. Here, the first large-scale sequencing analyses of the salivary gland, liver and small intestine transcriptomes of an adult M. javanica genome were performed, and the results were compared with published liver transcriptome profiles for a pregnant M. javanica female. A total of 24,452 transcripts were obtained, among which 22,538 were annotated on the basis of seven databases. In addition, 3,373 new genes were predicted, of which 1,459 were annotated. Several pathways were found to be involved in myrmecophagy, including olfactory transduction, amino sugar and nucleotide sugar metabolism, lipid metabolism, and terpenoid and polyketide metabolism pathways. Many of the annotated transcripts were involved in digestive functions: 997 transcripts were related to sensory perception, 129 were related to digestive enzyme gene families, and 199 were related to molecular transporters. One transcript for an acidic mammalian chitinase was found in the annotated data, and this might be closely related to the unique digestive function of pangolins. These pathways and transcripts are involved in specialization processes related to myrmecophagy (a form of insectivory) and carbohydrate, protein and lipid digestive pathways, probably reflecting adaptations to myrmecophagy. Our study is the first to investigate the molecular mechanisms underlying myrmecophagy in M. javanica, and we hope that our results may play a role in the conservation of this species.
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Affiliation(s)
- Jing-E Ma
- Guangdong Key Laboratory of Animal Conservation and Resource, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Lin-Miao Li
- Guangdong Key Laboratory of Animal Conservation and Resource, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Hai-Ying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Xiu-Juan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Juan Li
- Guangdong Key Laboratory of Animal Conservation and Resource, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Guan-Yu Li
- Guangdong Key Laboratory of Animal Conservation and Resource, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Li-Hong Yuan
- Guangdong Key Laboratory of Animal Conservation and Resource, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
| | - Jun Wu
- Wildlife Disease Surveillance and Molecular Ecology Research Center, Nanjing Institute of Environmental Sciences under Ministry of Environmental Protection, Nanjing, Jiangsu, China
| | - Jin-Ping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, China
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Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko AA, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli KP, Minx P, Krasheninnikova K, Kotze A, Dalton DL, Vermaak E, Paterson IC, Dobrynin P, Sitam FT, Rovie-Ryan JJ, Johnson WE, Yusoff AM, Luo SJ, Karuppannan KV, Fang G, Zheng D, Gerstein MB, Lipovich L, O'Brien SJ, Wong GJ. Pangolin genomes and the evolution of mammalian scales and immunity. Genome Res 2016; 26:1312-1322. [PMID: 27510566 PMCID: PMC5052048 DOI: 10.1101/gr.203521.115] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 08/04/2016] [Indexed: 11/24/2022]
Abstract
Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins. Strikingly, we found that interferon epsilon (IFNE), exclusively expressed in epithelial cells and important in skin and mucosal immunity, is pseudogenized in all African and Asian pangolin species that we examined, perhaps impacting resistance to infection. We propose that scale development was an innovation that provided protection against injuries or stress and reduced pangolin vulnerability to infection. Further evidence of specialized adaptations was evident from positively selected genes involving immunity-related pathways, inflammation, energy storage and metabolism, muscular and nervous systems, and scale/hair development. Olfactory receptor gene families are significantly expanded in pangolins, reflecting their well-developed olfaction system. This study provides insights into mammalian adaptation and functional diversification, new research tools and questions, and perhaps a new natural IFNE-deficient animal model for studying mammalian immunity.
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Affiliation(s)
- Siew Woh Choo
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia; Genome Solutions Sdn Bhd, Research Management & Innovation Complex, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Mike Rayko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Tze King Tan
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ranjeev Hari
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Wei Yee Wee
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Andrey A Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Sergey Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Klaus-Peter Koepfli
- National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA
| | - Patrick Minx
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Ksenia Krasheninnikova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Antoinette Kotze
- National Zoological Gardens of South Africa, Pretoria 0001, South Africa; Department of Genetics, University of the Free State, Bloemfontein, 9300, South Africa
| | - Desire L Dalton
- National Zoological Gardens of South Africa, Pretoria 0001, South Africa; Department of Genetics, University of the Free State, Bloemfontein, 9300, South Africa
| | - Elaine Vermaak
- National Zoological Gardens of South Africa, Pretoria 0001, South Africa
| | - Ian C Paterson
- Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia; Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Frankie Thomas Sitam
- Ex-Situ Conservation Division, Department of Wildlife and National Parks, 56100 Kuala Lumpur, Malaysia
| | - Jeffrine J Rovie-Ryan
- Ex-Situ Conservation Division, Department of Wildlife and National Parks, 56100 Kuala Lumpur, Malaysia
| | - Warren E Johnson
- National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA
| | - Aini Mohamed Yusoff
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Shu-Jin Luo
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, China 100871
| | - Kayal Vizi Karuppannan
- Ex-Situ Conservation Division, Department of Wildlife and National Parks, 56100 Kuala Lumpur, Malaysia
| | - Gang Fang
- NYU Shanghai, Pudong, Shanghai, China 200122
| | - Deyou Zheng
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA; Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA; Department of Neurology, School of Medicine, Wayne State University, Detroit, Michigan 48201, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004; Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, Florida 33004, USA
| | - Guat Jah Wong
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
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Pellicciari C. Histochemistry in biology and medicine: a message from the citing journals. Eur J Histochem 2015; 59:2610. [PMID: 26708189 PMCID: PMC4698620 DOI: 10.4081/ejh.2015.2610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 02/08/2023] Open
Abstract
Especially in recent years, biomedical research has taken advantage of the progress in several disciplines, among which microscopy and histochemistry. To assess the influence of histochemistry in the biomedical field, the articles published during the period 2011-2015 have been selected from different databases and grouped by subject categories: as expected, biological and biomedical studies where histochemistry has been used as a major experimental approach include a wide of basic and applied researches on both humans and other animal or plant organisms. To better understand the impact of histochemical publications onto the different biological and medical disciplines, it was useful to look at the journals where the articles published in a multidisciplinary journal of histochemistry have been cited: it was observed that, in the five-years period considered, 20% only of the citations were in histochemical periodicals, the remaining ones being in journals of Cell & Tissue biology, general and experimental Medicine, Oncology, Biochemistry & Molecular biology, Neurobiology, Anatomy & Morphology, Pharmacology & Toxicology, Reproductive biology, Veterinary sciences, Physiology, Endocrinology, Tissue engineering & Biomaterials, as well as in multidisciplinary journals.It is easy to foresee that also in the future the histochemical journals will be an attended forum for basic and applied scientists in the biomedical field. It will be crucial that these journals be open to an audience as varied as possible, publishing articles on the application of refined techniques to very different experimental models: this will stimulate non-histochemist scientists to approach histochemistry whose application horizon could expand to novel and possibly exclusive subjects.
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