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Jiang YJ, Gao JF, Lin LH, Li H, Meng QG, Qu YF, Ji X. Single-cell transcriptomes from turtle livers reveal sensitivity of hepatic immune cells to bacteria-infection. FISH & SHELLFISH IMMUNOLOGY 2022; 131:847-854. [PMID: 36273515 DOI: 10.1016/j.fsi.2022.10.033] [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: 08/27/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The liver is important in the synthesis, metabolism and storage of nutrients, detoxification and immune response of the body, and the liver immune response against exogenous pathogens from the intestinal tract plays a key role in the immune activities. However, the cellular composition of the liver immune atlas remains sparsely studied in reptiles. We used single-cell RNA sequencing to identify the cellular profile of the liver of the Chinese soft-shelled turtle (Pelodiscus sinensis). We obtained the transcriptional landscape based on 9938 cells from the fractionation of fresh hepatic tissues from two individuals, uninfected and infected with bacteria (Aeromonas hydrophila). We identified seven hepatic immune cell subsets, including plasma, erythroid, T/NK, B, endothelial, dendritic and Kupffer cells. Bacteria-infection altered the number of liver immune cells, as revealed by the fact that the infected turtle had more plasma, endothelial and Kupffer cells and fewer T/NK, dendritic and erythroid cells than did the uninfected turtle. Our study is the first to provide a comprehensive view of the hepatic immune landscape of P. sinensis at the single-cell resolution that outlines the characteristics of immune cells in the turtle liver and provides a liver transcriptome baseline for turtle immunology.
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Affiliation(s)
- Yi-Jin Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Jian-Fang Gao
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Qing-Guo Meng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| | - Xiang Ji
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
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2
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Xie Q, Liu F, Zhang J, Li X, Chen T, Fang G, Ma R, Su S. Development of 105 SNP markers in endangered turtle species Pelodiscus sinensis using RAD-seq. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01238-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kong F, Zhu Q, Xiao F, Hong Z, Zhang H, Shi H. Home Ranges and Movement Patterns of the Chinese Softshell Turtle (Pelodiscus sinensis) in the Yellow River, Northwestern China. CHELONIAN CONSERVATION AND BIOLOGY 2021. [DOI: 10.2744/ccb-1402.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Fei Kong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands; College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China [; ; ; ; ]
| | - Qingjun Zhu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands; College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China [; ; ; ; ]
| | - Fanrong Xiao
- Ministry of Education Key Laboratory for Ecology of Tropical Islands; College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China [; ; ; ; ]
| | - Zhen Hong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands; College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China [; ; ; ; ]
| | - Hongxing Zhang
- Shaanxi Institute of Zoology, Xi'an, 710032, Shaanxi, China []
| | - Haitao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands; College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China [; ; ; ; ]
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Hernández-García J, Pedraza-Lara C, Rangel Mendoza JA, Zenteno-Ruiz CE. Population genetics of wild and captive Trachemysvenusta (Gray, 1856) (Reptilia: Emydidae) in the Usumacinta river basin in Mexico. Zoo Biol 2021; 40:297-305. [PMID: 33792959 DOI: 10.1002/zoo.21604] [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: 06/05/2020] [Revised: 02/09/2021] [Accepted: 03/10/2021] [Indexed: 11/07/2022]
Abstract
The Mesoamerican slider Trachemysvenusta is endemic to Central America and Southern Mexico. Several human-mediated disturbances, including habitat degradation and illegal hunting for food, have impacted its populations along the Usumacinta river basin. The extent to which these disturbances have affected the genetic diversity and population structure of T. venusta inhabiting the basin remains unresolved. To this end, we analyzed eight microsatellite markers in five wild populations of T. venusta from the middle and lower reaches of the basin as well as one captive population. Our results show high levels of genetic diversity for all analyzed populations, low F ST values, high gene flow and no genetic structure, indicating an absence of genetic differentiation across sites and, thus, a single panmictic population for the basin. Evidence of a genetic bottleneck was observed in two of the wild populations (and the captive one), indicating some impact from disturbances, whether from poaching or habitat fragmentation, despite the seemingly high connectivity of most populations. Results are discussed in terms of the relative importance of genetic parameters for the conservation of T. venusta, particularly in light of the importance of demographic stochasticity in local conditions undergoing rapid changes.
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Affiliation(s)
- Jorge Hernández-García
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Tabasco, México
| | - Carlos Pedraza-Lara
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico, México
| | - Judith A Rangel Mendoza
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Tabasco, México
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Analysis of the population structure and genetic diversity of the red swamp crayfish (Procambarus clarkii) in China using SSR markers. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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6
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Liu J, Wang M, Shi Q, Li J, Wang Y, Nie L. Rapid development of novel microsatellite markers from Mauremys reevesii (Testudines: Geoemydidae) using next-generation DNA sequencing technology. THE EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2019.1652359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- J. Liu
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, Anhui, China
| | - M. Wang
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, Anhui, China
| | - Q. Shi
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, Anhui, China
| | - J. Li
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, Anhui, China
| | - Y. Wang
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, Anhui, China
| | - L. Nie
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, Anhui, China
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Gong S, Vamberger M, Auer M, Praschag P, Fritz U. Millennium-old farm breeding of Chinese softshell turtles (Pelodiscus spp.) results in massive erosion of biodiversity. Naturwissenschaften 2018; 105:34. [PMID: 29728774 DOI: 10.1007/s00114-018-1558-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 12/22/2022]
Abstract
Chinese softshell turtles (Pelodiscus spp.) are widely distributed, ranging from the Amur and Ussuri Rivers in the Russian Far East through the Korean Peninsula, Japan, and eastern, central, and southern China to southern Vietnam. In East and Southeast Asia, Chinese softshell turtles are traditionally exploited for food and have been farm-bred in China since the Spring and Autumn Period, more than 2400 years ago. Currently, the annual production of Pelodiscus amounts to 340,000 t in China alone. Using mitochondrial DNA (2428 bp) and five nuclear loci (3704 bp), we examined broad sampling of wild and farm-bred Pelodiscus to infer genetic and taxonomic differentiation. We discovered four previously unknown mitochondrial lineages, all from China. One lineage from Jiangxi is deeply divergent and sister to the mitochondrial lineage of Pelodiscus axenaria. The nuclear loci supported species status for P. axenaria and the new lineage from Jiangxi. Pelodiscus maackii and P. parviformis, both harboring distinct mitochondrial lineages, were not differentiated from P. sinensis in the studied nuclear markers. The same is true for two new mitochondrial lineages from Zhejiang, China, represented by only one individual each, and another new lineage from Anhui, Guangdong, Jiangxi and Zhejiang, China. However, Vietnamese turtles yielding a mitochondrial lineage clustering within P. sinensis were distinct in nuclear markers, suggesting that these populations could represent another unknown species with introgressed mitochondria. Its species status is also supported by the syntopic occurrence with P. sinensis in northern Vietnam and by morphology. In addition, we confirmed sympatry of P. axenaria and P. parviformis in Guangxi, China, and found evidence for sympatry of P. sinensis and the new putative species from Jiangxi, China. We also discovered evidence for hybridization in turtle farms and for the occurrence of alien lineages in the wild (Zhejiang, China), highlighting the risk of genetic pollution of native stock. In the face of the large-scale breeding of Pelodiscus, we claim that the long-term survival of distinct genetic lineages and species can only be assured when an upscale market segment for pure-bred softshell turtles is established, making the breeding of pure lineages lucrative for turtle farms. Our findings underline that the diversity of Pelodiscus is currently underestimated and threatened by anthropogenic admixture. We recommend mass screening of genetic and morphological variation of Chinese softshell turtles as a first step to understand and preserve their diversity.
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Affiliation(s)
- Shiping Gong
- 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, 510260, China
| | - Melita Vamberger
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Markus Auer
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | | | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany.
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Li T, Cao P, Bei YJ, Du WG. Latitudinal and Temperature-Dependent Variation in Embryonic Development Rate and Offspring Performance in a Freshwater Turtle. Physiol Biochem Zool 2018; 91:673-681. [DOI: 10.1086/694856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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9
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Sun Z, Pan T, Wang H, Pang M, Zhang B. Yangtze River, an insignificant genetic boundary in tufted deer ( Elaphodus cephalophus): the evidence from a first population genetics study. PeerJ 2016; 4:e2654. [PMID: 27843712 PMCID: PMC5103815 DOI: 10.7717/peerj.2654] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 10/04/2016] [Indexed: 12/02/2022] Open
Abstract
Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.
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Affiliation(s)
- Zhonglou Sun
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Tao Pan
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Hui Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Mujia Pang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China.,School of Biosciences, Cardiff University, Cardiff, United Kingdom
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Liu F, Guo QS, Shi HZ, Cheng BX, Lu YX, Gou L, Wang J, Shen WB, Yan SM, Wu MJ. Genetic variation in Whitmania pigra, Hirudo nipponica and Poecilobdella manillensis, three endemic and endangered species in China using SSR and TRAP markers. Gene 2015; 579:172-82. [PMID: 26743128 DOI: 10.1016/j.gene.2015.12.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/30/2015] [Accepted: 12/27/2015] [Indexed: 01/12/2023]
Abstract
Leeches are not only important medicinal animals worldwide but also are endangered. We aimed to (i) explore the level of genetic diversity within/among populations of three leeches, (ii) assess genetic differentiation among these three leeches, and (iii) discuss an appropriate strategy for conserving leech germplasm. A total of 315 individuals of Whitmania pigra, Hirudo nipponica and Poecilobdella manillensis from 21 populations were collected in China and Vietnam. The genetic structure and genetic diversity among and within the 21 populations were evaluated using target region amplified polymorphism (TRAP) and simple sequence repeat (SSR) markers. Sixteen pairs of TRAP primers generated a total of 398 fragments, of which 396 (99.50%) were polymorphic; fourteen pairs of SSR primers generated a total of 60 fragments, of which 59 (98.33%) were polymorphic. Shannon's index (I) and Nei's gene diversity index (H) for the three leeches were high at the species level (I=0.4980 and H=0.3323 for TRAPs, I=0.4487 and H=0.2969 for SSRs in W. pigra; I=0.4147/0.3769, H=0.2788/0.2566 for H. nipponica; and I=0.4616/0.4717, H=0.3099/0.3203 for P. manillensis). However, low genetic diversity was determined at the population level; the average genetic diversity measures within populations were H=0.1767/0.1376, I=0.2589/0.2043 for W. pigra, H=0.2149/0.2021, I=0.3184/0.3000 for H. nipponica and H=0.2850/0.2724, I=0.4152/0.3967 for P. manillensis. We conclude that there was limited gene exchange within/among populations and species, as the gene flow number (Nm) was 0.5493/0.5807. However, for all three species, the genetic diversity was different at the population level. Gene differentiation (Gst) and Nm were 0.4682 /0.5364 and 0.5678/0.4321 for W. pigra, 0.2294/0.2127 and 1.6797/1.8512 for H. nipponica and 0.1214/0.1496 and 3.6202/2.8412 for P. manillensis. STRUCTURE analysis, Unweighted Pair-Group Method with Arithmetic means (UPGMA) cluster analysis and Principal Coordinates Analysis (PCOA) all yielded similar results. The isolation-by-distance pattern was not significant for any of the three species by the Mantel test. These data emphasize the need for management, conservation, and rehabilitation of this animal species. Finally, an appropriate strategy for conserving leech is proposed.
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Affiliation(s)
- Fei Liu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China; Biology Post-doctoral Mobile Stations, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China; Key Laboratory for Aquaculture and Ecology of Coastal Pool of Jiangsu Province, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Qiao-Sheng Guo
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hong-Zhuan Shi
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Bo-Xing Cheng
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yu-Xi Lu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ling Gou
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jia Wang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wen-Biao Shen
- Biology Post-doctoral Mobile Stations, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shi-Meng Yan
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Man-Jun Wu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
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