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Xia J, Chang L, Xu D, Jia Y, Ding Y, Cao C, Geng Z, Jin S. Next-Generation Sequencing of the Complete Huaibei Grey Donkey Mitogenome and Mitogenomic Phylogeny of the Equidae Family. Animals (Basel) 2023; 13:ani13030531. [PMID: 36766420 PMCID: PMC9913526 DOI: 10.3390/ani13030531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
The Huaibei grey donkey (HGD) is an endangered species and a vital native breed in Anhui Province, China. However, its complete mitogenome, phylogeny, and maternal origin remain unclear. The objectives of this study were to detect the genetic diversity of the HGD and investigate its phylogenetic relationship with other breeds to inform conservation management. The complete mitogenome of the HGD was sequenced through next-generation sequencing, and the most variable region in the mitochondrial DNA displacement-loop (D-loop) was amplified via a polymerase chain reaction (PCR). Next, we used the median-joining network (MJN) to calculate the genetic relationships among populations and the neighbor-jointing method to build a phylogenetic tree and speculate as to its origin. The results showed that the mitogenome contains 22 tRNAs, 2 rRNAs, 13 PCGs, and 1 D-loop region. Analyzing the D-loop region of the HGDs, we identified 23 polymorphic sites and 11 haplotypes. The haplotype and nucleotide diversity were 0.87000 (Hd) and 0.02115 (Pi), respectively. The MJN analysis indicated that the HGD potentially has two maternal lineages, and phylogenetic analysis indicated that the Somali lineage could be the most probable domestication center for this breed. Therefore, our mitogenome analysis highlights the high genetic diversity of the HGD, which may have originated from the Somali wild ass, as opposed to the Asian wild ass. This study will provide a useful resource for HGD conservation and breeding.
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Affiliation(s)
- Jingjing Xia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Liang Chang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Dashuang Xu
- Anhui Livestock and Poultry Genetic Resources Protection Center, Hefei 231283, China
| | - Yuqing Jia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yuanfei Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Chengcheng Cao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Correspondence: ; Tel.:+86-551-6578-6328; Fax:+86-551-6578-6326
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Alves JS, de Araujo Oliveira CA, Escodro PB, Pinto LFB, Costa RB, de Camargo GMF. Genetic origin of donkeys in Brazil. Trop Anim Health Prod 2022; 54:291. [PMID: 36094617 DOI: 10.1007/s11250-022-03280-x] [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: 03/24/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION The genetic groups of native donkeys in Brazil are characterized by adaptation to the local environment. However, the donkey population in the country is declining, mainly because of agricultural mechanization and transportation that has led to the abandonment and the consequent indiscriminate slaughter of these animals. There are three local genetic groups of distinct geographic and temporal formation. However, analyses of their origin, phylogenetic relationship, and population structure are scarce. Within this context, molecular markers such as the mitochondrial control region (D-loop) are useful for these analyses. MATERIAL AND METHODS This study aimed to evaluate the variation and origin of maternal lineages of groups of naturalized donkeys in Brazil (Brazilian, Nordestino, and Pêga). RESULTS AND DISCUSSION We detected five mitochondrial haplotypes with 19 polymorphic sites, two of them exclusively found in the Nordestino donkey; this group is in fact more distant from the others. Phylogenetic analysis indicates maternal contributions of two clades (Nubian and Somali) to the formation of the genetic groups of donkeys, a fact that explains the high diversity, structure, and distances of the groups, reported here for the first time. CONCLUSION : This analysis contributes production and conservation of native donkey breeds. It also gives clues about the formation of the Iberian breeds from which Brazilian donkeys originated.
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Affiliation(s)
- Jackeline Santos Alves
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Chiara Albano de Araujo Oliveira
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Pierre Barnabé Escodro
- Centro de Engenharias e Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Luis Fernando Batista Pinto
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Raphael Bermal Costa
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil
| | - Gregório Miguel Ferreira de Camargo
- Escola de Medicina Veterinária E Zootecnia, Departamento de Zootecnia, Universidade Federal da Bahia, Avenida Milton Santos, 500, Ondina, Salvador, Bahia, 40170-110, Brazil.
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Kefena E, Rosenbom S, Beja-Pereira A, Kurtu MY, Han JL, Dessie T. Genetic diversity and population genetic structure in native Ethiopian donkeys (Equus asinus) inferred from equine microsatellite markers. Trop Anim Health Prod 2021; 53:334. [PMID: 34018049 DOI: 10.1007/s11250-021-02776-2] [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: 12/12/2020] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
We investigated the genetic diversity and population genetic structure of six morphologically distinct Ethiopian donkey populations using 12 equine microsatellite markers. The donkey populations were Abyssinian (AB), Afar (AF), Hararghe (HA), Ogaden (OG), Omo (OM) and Sinnar (SI). Blood samples were collected from 180 genetically unrelated donkeys (30 individuals per population). Population genetic diversity estimates showed that total number and mean number of observed alleles, average observed and expected heterozygosity were 94, 5.208 ± 0.0229, 0.555 ± 0.023 and 0.588 ± 0.022, respectively. Highly significant deficiency in heterozygote was detected within the overall samples (FIS = 0.055 ± 0.021; P < 0.001). Though highly significant (P < 0.001), heterozygote deficiency within populations relative to total population was moderate (FST = 0.046 ± 0.016), suggesting a higher diversity within the populations (95.4%) than between populations. Various genetic distance estimation methods produced a similar topology of un-rooted dendrograms that grouped the overall Ethiopian donkeys into lowland (Ogaden, Omo and Sinnar) and highland (Abyssinian, Afar and Hararghe) genetic lineages. Likewise, Bayesian clustering analysis produced a similar pattern of clustering that was highly concordant with traditional donkey classification systems in Ethiopia.
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Affiliation(s)
- E Kefena
- Department of Animal Genetics and Breeding, Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia.
| | - S Rosenbom
- Research Center in Biodiversity and Genetic Resources (CIBIO), University of Porto, Campus Agrario de Vairao, Rua Padre Armando, Quintas 7, 4485-661, Vairao, Portugal
| | - A Beja-Pereira
- Research Center in Biodiversity and Genetic Resources (CIBIO), University of Porto, Campus Agrario de Vairao, Rua Padre Armando, Quintas 7, 4485-661, Vairao, Portugal.,Department of Geosciences, Environment and Spatial Planning (DGAOT), Faculty of Sciences, University of Porto, Rua Campo Alegre 687, 4169-007, Porto, Portugal
| | - M Yusuf Kurtu
- Department of Animal and Range Sciences, Haramaya University, P.O. Box 38, Dire Dawa, Ethiopia
| | - J L Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China.,Department of Animal Biosciences, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - T Dessie
- Department of Animal Biosciences, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
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Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region. Animals (Basel) 2020; 10:ani10111970. [PMID: 33120938 PMCID: PMC7692571 DOI: 10.3390/ani10111970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/18/2020] [Accepted: 10/22/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary This paper represents the first fundamental report of mtDNA diversity in Turkish indigenous donkey breeds and presents findings for the origin and genetic characterization of donkey populations dispersed in seven geographical regions in Turkey, and thus reveals insights into their genetic history. The median-joining network and phylogenetic tree exhibit two different maternal lineages of the 16 Turkish indigenous donkey populations. Abstract In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.
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Xia X, Yu J, Zhao X, Yao Y, Zeng L, Ahmed Z, Shen S, Dang R, Lei C. Genetic diversity and maternal origin of Northeast African and South American donkey populations. Anim Genet 2019; 50:266-270. [PMID: 30854699 DOI: 10.1111/age.12774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2019] [Indexed: 11/29/2022]
Abstract
To investigate the mtDNA variation and origin of maternal lineages in South American donkeys and to reassess the domestication of donkeys in northeast Africa, we analyzed sequences (489 bp of the D-loop) from 323 domestic donkeys sampled from Peru, Brazil, Ethiopia and Egypt. Altogether, the 323 sequences displayed 53 different haplotypes (45 in Ethiopia, 14 in Egypt, eight in Peru and six in Brazil). Among the four populations, Egyptian donkeys possessed the highest haplotype diversity (0.910 ± 0.032), followed by Brazilian donkeys (0.879 ± 0.060). The Clade I haplotypes dominated in Peruvian donkeys (65%), whereas Clade II haplotypes dominated in Brazilian donkeys (67%). Estimates of FST values showed a high genetic differentiation between Peruvian and Brazilian donkey populations (FST = 0.4066), which could be explained by the complex introduction history of South American donkeys. Phylogeographic analysis indicates that northeast Africa could be the most probable domestication center for Clade I donkeys. Analysis of molecular variance confirmed a weak genetic structure in domestic donkey populations among four continents (Europe, Asia, Africa and South America).
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Affiliation(s)
- X Xia
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - J Yu
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd., No.78, E-jiao Street, Done-E Country, Shandong Province, 252201, China
| | - X Zhao
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Y Yao
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - L Zeng
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Z Ahmed
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - S Shen
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd., No.78, E-jiao Street, Done-E Country, Shandong Province, 252201, China
| | - R Dang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - C Lei
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Cozzi MC, Valiati P, Cherchi R, Gorla E, Prinsen RTMM, Longeri M, Bagnato A, Strillacci MG. Mitochondrial DNA genetic diversity in six Italian donkey breeds (Equus asinus). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:409-418. [PMID: 28278690 DOI: 10.1080/24701394.2017.1292505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.
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Affiliation(s)
- Maria Cristina Cozzi
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | - Paolo Valiati
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | - Raffaele Cherchi
- b Agenzia per la ricerca in agricoltura-AGRIS Sardegna , Sassari , Italy
| | - Erica Gorla
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | | | - Maria Longeri
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | - Alessandro Bagnato
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
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Jordana J, Ferrando A, Miró J, Goyache F, Loarca A, Martínez López OR, Canelón JL, Stemmer A, Aguirre L, Lara MAC, Álvarez LA, Llambí S, Gómez N, Gama LT, Nóvoa MF, Martínez RD, Pérez E, Sierra A, Contreras MA, Guastella AM, Marletta D, Arsenos G, Curik I, Landi V, Martínez A, Delgado JV. Genetic relationships among American donkey populations: insights into the process of colonization. J Anim Breed Genet 2015; 133:155-64. [PMID: 26364918 DOI: 10.1111/jbg.12180] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/06/2015] [Indexed: 11/29/2022]
Abstract
This study presents the first insights into the genetic diversity and structure of the American donkey metapopulation. The primary objectives were to detect the main structural features underlying variability among American donkey populations, identify boundaries between differentiated gene pools, and draw the main colonization pathways since the introduction of donkeys into America in the 15th century. A panel of 14 microsatellite markers was applied for genotyping 350 American donkeys from 13 countries. The genetic structure of this metapopulation was analysed using descriptive statistics and Bayesian model-based methods. These populations were then compared to a database containing information on 476 individuals from 11 European breeds to identify the most likely ancestral donor populations. Results showed the presence of two distinct genetic pools, with confluence of the two in Colombia. The southern pool showed a unique genetic signature subsequent to an older founder event, but lacked any significant influence of modern gene flow from Europe. The northern pool, conversely, may have retained more ancestral polymorphisms and/or have experienced modern gene flow from Spanish breeds. The Andalusian and, to a lesser extent, the Catalan breeds have left a more pronounced footprint in some of the American donkey populations analysed.
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Affiliation(s)
- J Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - A Ferrando
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - J Miró
- Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - F Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Gijón, Spain
| | - A Loarca
- Ministerio de Agricultura, Ganadería y Alimentación, Quetzaltenango, Guatemala
| | - O R Martínez López
- Dirección General de Investigación Científica y Tecnológica, Centro Multidisciplinario de Investigaciones Tecnológicas, Universidad Nacional de Asunción, Asunción, Paraguay
| | - J L Canelón
- Departamento de Producción e Industria Animal, Decanato de Ciencias Veterinarias, Universidad Centroccidental Lisandro Alvarado, Barquisimeto, Venezuela
| | - A Stemmer
- Facultad de Ciencias Agrícolas y Pecuarias, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - L Aguirre
- Centro Biotecnología Reproductiva Animal, Universidad Nacional de Loja, Loja, Ecuador
| | - M A C Lara
- Instituto de Zootecnia, Nova Odessa, SP, Brazil
| | - L A Álvarez
- Sede Palmira, Universidad Nacional de Colombia, Palmira, Valle del Cauca, Colombia
| | - S Llambí
- Instituto de Producción Animal, Área Genética, Facultad de Veterinaria, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - N Gómez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Micaela Bastidas de Apurímac, Abancay, Peru
| | - L T Gama
- Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Lisboa, Portugal
| | - M F Nóvoa
- AEPGA Associação para o Estudo e Protecção do Gado Asinino, Atenor, Portugal
| | - R D Martínez
- Mejora y Conservación de Recursos Genéticos, Facultad de Ciencias Agrarias, Universidad Nacional de Lomas de Zamora, Llavallol, Argentina
| | - E Pérez
- Departamento de Salud y Explotación Animal, Universidad de Granma, Bayamo, Cuba
| | - A Sierra
- Posgrado e Investigación, Instituto Tecnológico de Conkal, Yucatán, Mexico
| | - M A Contreras
- Escuela de Medicina Veterinaria, UST Sede Santiago, Santiago, Chile
| | - A M Guastella
- Sezione di Scienze delle Produzioni Animali, Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli studi di Catania, Catania, Italy
| | - D Marletta
- Sezione di Scienze delle Produzioni Animali, Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli studi di Catania, Catania, Italy
| | - G Arsenos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - I Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - V Landi
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - A Martínez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - J V Delgado
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
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Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, Fontanesi L. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms. PLoS One 2015; 10:e0131925. [PMID: 26151450 PMCID: PMC4495037 DOI: 10.1371/journal.pone.0131925] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/08/2015] [Indexed: 12/13/2022] Open
Abstract
Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.
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Affiliation(s)
- Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy
| | - Concetta Scimone
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy
| | - Claudia Geraci
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
| | - Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
| | - Vincenzo Chiofalo
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy
- Meat Research Consortium, Polo Universitario dell’Annunziata, Messina, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
- * E-mail:
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Han L, Zhu S, Ning C, Cai D, Wang K, Chen Q, Hu S, Yang J, Shao J, Zhu H, Zhou H. Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys. BMC Evol Biol 2014; 14:246. [PMID: 25433485 PMCID: PMC4263014 DOI: 10.1186/s12862-014-0246-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/17/2014] [Indexed: 11/16/2022] Open
Abstract
Background The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced. Results Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. Conclusions This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.
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Affiliation(s)
- Lu Han
- Key-Lab for Evolution of Past Life and Environment in Northeast Asia, Jilin University, Ministry of Education, Changchun, 130012, PR China. .,Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China. .,Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
| | - Songbiao Zhu
- Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China.
| | - Chao Ning
- Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China.
| | - Dawei Cai
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
| | - Kai Wang
- Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China.
| | - Quanjia Chen
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
| | - Songmei Hu
- Archaeological Research Institute of Shaanxi Province, Xi' an, 710054, PR China.
| | - Junkai Yang
- Institute for Archaeology and Relic Conservation of Xi' an, Xi' an, 710068, PR China.
| | - Jing Shao
- Archaeological Research Institute of Shaanxi Province, Xi' an, 710054, PR China.
| | - Hong Zhu
- Key-Lab for Evolution of Past Life and Environment in Northeast Asia, Jilin University, Ministry of Education, Changchun, 130012, PR China. .,Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
| | - Hui Zhou
- Key-Lab for Evolution of Past Life and Environment in Northeast Asia, Jilin University, Ministry of Education, Changchun, 130012, PR China. .,Ancient DNA Laboratory, School of Life Sciences, Jilin University, Changchun, 130012, PR China. .,Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, PR China.
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Chen J, Sun Y, Manglai D, Min L, Pan Q. Maternal genetic diversity and population structure of four Chinese donkey breeds. Livest Sci 2010. [DOI: 10.1016/j.livsci.2010.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Cytochrome b Genetic Diversity and Maternal Origin of Chinese Domestic Donkey. Biochem Genet 2010; 48:636-46. [DOI: 10.1007/s10528-010-9345-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 03/02/2010] [Indexed: 10/19/2022]
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