51
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Moyers BT, Morrell PL, McKay JK. Genetic Costs of Domestication and Improvement. J Hered 2017; 109:103-116. [DOI: 10.1093/jhered/esx069] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Brook T Moyers
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN (Morrell)
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO
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Hirimuthugoda NY, Adeola AC, Anthony Perera PW, Chen X, Dewar Asoka Gunawardena WW, Thilini Nisanka Gunawardana HG, Yin TT, Wang MS, Li GM, Ding ZL, Wang WZ, Xie HB, Peng MS, Zhang YP. Sri Lankan pig ancestry revealed by mitochondrial DNA, Y-chromosome, and MC1R. Anim Genet 2017; 48:622-623. [PMID: 28748531 DOI: 10.1111/age.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2017] [Indexed: 12/01/2022]
Affiliation(s)
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | | | - Xing Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | | | | | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Gui-Mei Li
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Zhao-Li Ding
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
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53
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Affiliation(s)
- Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, UK.
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54
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Amiri Ghanatsaman Z, Adeola AC, Asadi Fozi M, Ma YP, Peng MS, Wang GD, Esmailizadeh A, Zhang YP. Mitochondrial DNA sequence variation in Iranian native dogs. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:394-402. [PMID: 28303732 DOI: 10.1080/24701394.2017.1289375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The dog mtDNA diversity picture from wide geographical sampling but from a small number of individuals per region or breed, displayed little geographical correlation and high degree of haplotype sharing between very distant breeds. For a clear picture, we extensively surveyed Iranian native dogs (n = 305) in comparison with published European (n = 443) and Southwest Asian (n = 195) dogs. Twelve haplotypes related to haplogroups A, B and C were shared by Iranian, European, Southwest Asian and East Asian dogs. In Iran, haplotype and nucleotide diversities were highest in east, southeast and northwest populations while western population had the least. Sarabi and Saluki dog populations can be assigned into haplogroups A, B, C and D; Qahderijani and Kurdi to haplogroups A, B and C, Torkaman to haplogroups A, B and D while Sangsari and Fendo into haplogroups A and B, respectively. Evaluation of population differentiation using pairwise FST generally revealed no clear population structure in most Iranian dog populations. The genetic signal of a recent demographic expansion was detected in East and Southeast populations. Further, in accordance with previous studies on dog-wolf hybridization for haplogroup d2 origin, the highest number of d2 haplotypes in Iranian dog as compared to other areas of Mediterranean basin suggests Iran as the probable center of its origin. Historical evidence showed that Silk Road linked Iran to countries in South East Asia and other parts of the world, which might have probably influenced effective gene flow within Iran and these regions. The medium nucleotide diversity observed in Iranian dog calls for utilization of appropriate management techniques in increasing effective population size.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- a Department of Animal Science, Faculty of Agriculture , Shahid Bahonar University of Kerman , Kerman , Iran.,b Yong Researchers Society , Shahid Bahonar University of Kerman , Kerman , Iran
| | - Adeniyi C Adeola
- c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China
| | - Masood Asadi Fozi
- a Department of Animal Science, Faculty of Agriculture , Shahid Bahonar University of Kerman , Kerman , Iran
| | - Ya-Ping Ma
- d State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan , Yunnan University , Kunming , China
| | - Min-Sheng Peng
- c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China
| | - Guo-Dong Wang
- c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China
| | - Ali Esmailizadeh
- a Department of Animal Science, Faculty of Agriculture , Shahid Bahonar University of Kerman , Kerman , Iran.,c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China
| | - Ya-Ping Zhang
- c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China.,d State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan , Yunnan University , Kunming , China
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55
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Zhang L, Zhang P, Li Q, Gaur U, Liu Y, Zhu Q, Zhao X, Wang Y, Yin H, Hu Y, Liu A, Li D. Genetic evidence from mitochondrial DNA corroborates the origin of Tibetan chickens. PLoS One 2017; 12:e0172945. [PMID: 28241078 PMCID: PMC5328412 DOI: 10.1371/journal.pone.0172945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 12/27/2016] [Indexed: 01/23/2023] Open
Abstract
Chicken is the most common poultry species and is important to human societies. Tibetan chicken (Gallus gallus domesticus) is a breed endemic to China that is distributed mainly on the Qinghai-Tibet Plateau. However, its origin has not been well characterized. In the present study, we sequenced partial mitochondrial DNA (mtDNA) control region of 239 and 283 samples from Tibetan and Sichuan indigenous chickens, respectively. Incorporating 1091 published sequences, we constructed the matrilineal genealogy of Tibetan chickens to further document their domestication history. We found that the genetic structure of the mtDNA haplotypes of Tibetan chickens are dominated by seven major haplogroups (A-G). In addition, phylogenetic and network analyses showed that Tibetan chickens are not distinguishable from the indigenous chickens in surrounding areas. Furthermore, some clades of Tibetan chickens may have originated from game fowls. In summary, our results collectively indicated that Tibetan chickens may have diverged from indigenous chickens in the adjacent regions and hybridized with various chickens.
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Affiliation(s)
- Long Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Pu Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Li
- Life Science College, Southwest Forestry University, Kunming, China
| | - Uma Gaur
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yaodong Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- * E-mail:
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56
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Higher immunocompetence is associated with higher genetic diversity in feral honey bee colonies (Apis mellifera). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0942-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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57
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A cryptic mitochondrial DNA link between North European and West African dogs. J Genet Genomics 2016; 44:163-170. [PMID: 28302420 DOI: 10.1016/j.jgg.2016.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/17/2016] [Accepted: 10/21/2016] [Indexed: 01/25/2023]
Abstract
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf (Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1 (but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence, we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.
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58
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Peris D, Langdon QK, Moriarty RV, Sylvester K, Bontrager M, Charron G, Leducq JB, Landry CR, Libkind D, Hittinger CT. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus. PLoS Genet 2016; 12:e1006155. [PMID: 27385107 PMCID: PMC4934787 DOI: 10.1371/journal.pgen.1006155] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/08/2016] [Indexed: 12/05/2022] Open
Abstract
Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Quinn K. Langdon
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ryan V. Moriarty
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kayla Sylvester
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Martin Bontrager
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Jean-Baptiste Leducq
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, Québec, Canada
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagonico de Tecnologías Biológicas y Geoambientales, IPATEC (CONICET-UNComahue), Centro Regional Universitario Bariloche, Bariloche, Río Negro, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Song JJ, Wang WZ, Otecko NO, Peng MS, Zhang YP. Reconciling the conflicts between mitochondrial DNA haplogroup trees of Canis lupus. Forensic Sci Int Genet 2016; 23:83-85. [PMID: 27042801 DOI: 10.1016/j.fsigen.2016.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/25/2016] [Accepted: 03/25/2016] [Indexed: 11/18/2022]
Affiliation(s)
- Jiao-Jiao Song
- Institute of Health Sciences, Anhui University, 111 Jiulong Lu, 230601 Hefei, China; State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Lu, 650204 Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Lu, 650204 Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Lu, 650204 Kunming, China; State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, 2 Cuihu Beilu, 650091 Kunming, China.
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60
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Zhang Q, Gou W, Wang X, Zhang Y, Ma J, Zhang H, Zhang Y, Zhang H. Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-Dose Ultraviolet Radiation in High-Altitude Environments. Genome Biol Evol 2016; 8:765-76. [PMID: 26907498 PMCID: PMC4824011 DOI: 10.1093/gbe/evw032] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tibetan chicken, unlike their lowland counterparts, exhibit specific adaptations to high-altitude conditions. The genetic mechanisms of such adaptations in highland chickens were determined by resequencing the genomes of four highland (Tibetan and Lhasa White) and four lowland (White Leghorn, Lindian, and Chahua) chicken populations. Our results showed an evident genetic admixture in Tibetan chickens, suggesting a history of introgression from lowland gene pools. Genes showing positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune responses, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of nonsynonymous single nucleotide polymorphisms between highland and lowland populations was analyzed using chi-square test, which showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development and adaptations to hypoxia and intense radiation. RNA sequencing revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Several candidate genes involved in the development of cardiorespiratory system (FGFR1, CTGF, ADAM9, JPH2, SATB1, BMP4, LOX, LPR, ANGPTL4, and HYAL1), inflammation and immune responses (AIRE, MYO1F, ZAP70, DDX60, CCL19, CD47, JSC, and FAS), DNA repair, and responses to radiation (VCP, ASH2L, and FANCG) were identified to play key roles in the adaptation to high-altitude conditions. Our data provide new insights into the unique adaptations of highland animals to extreme environments.
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Affiliation(s)
- Qian Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Wenyu Gou
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Jun Ma
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Hongliang Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Ying Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
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61
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Wang GD, Zhai W, Yang HC, Wang L, Zhong L, Liu YH, Fan RX, Yin TT, Zhu CL, Poyarkov AD, Irwin DM, Hytönen MK, Lohi H, Wu CI, Savolainen P, Zhang YP. Out of southern East Asia: the natural history of domestic dogs across the world. Cell Res 2016; 26:21-33. [PMID: 26667385 PMCID: PMC4816135 DOI: 10.1038/cr.2015.147] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/09/2015] [Accepted: 10/10/2015] [Indexed: 12/30/2022] Open
Abstract
The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Weiwei Zhai
- Human Genetics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - He-Chuan Yang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Human Genetics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
- Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Li Zhong
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Ruo-Xi Fan
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Chun-Ling Zhu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Andrei D Poyarkov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Science, 33 Leninskiy Prospect, Moscow 119071, Russia
| | - David M Irwin
- Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Rm 6211, Toronto, ON, Canada M5S 1A8
| | - Marjo K Hytönen
- Research Programs Unit, Molecular Neurology and Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Research Programs Unit, Molecular Neurology and Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Chung-I Wu
- Department of Ecology and Evolution, University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA
| | - Peter Savolainen
- Department of Gene Technology, KTH-Royal Institute of Technology, Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
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62
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Lv FH, Peng WF, Yang J, Zhao YX, Li WR, Liu MJ, Ma YH, Zhao QJ, Yang GL, Wang F, Li JQ, Liu YG, Shen ZQ, Zhao SG, Hehua E, Gorkhali NA, Farhad Vahidi SM, Muladno M, Naqvi AN, Tabell J, Iso-Touru T, Bruford MW, Kantanen J, Han JL, Li MH. Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep. Mol Biol Evol 2015; 32:2515-33. [PMID: 26085518 PMCID: PMC4576706 DOI: 10.1093/molbev/msv139] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Despite much attention, history of sheep (Ovis aries) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences (n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637-0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (∼8-11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20-60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5-6.8 ka (lineages A and B: ∼6.4-6.8 ka; C: ∼4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West-East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a "transportation hub" in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia.
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Affiliation(s)
- Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yue-Hui Ma
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Qian-Jun Zhao
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China College of Life Sciences, Shangqiu Normal University, Shangqiu, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Sheng-Guo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Neena A Gorkhali
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council, Kathmandu, Nepal
| | - S M Farhad Vahidi
- Agricultural Biotechnology Research Institute of Iran-North Branch (ABRII), Rasht, Iran
| | - Muhammad Muladno
- Department of Animal Technology and Production Science, Bogor Agricultural University, Darmaga Campus, Bogor, Indonesia
| | - Arifa N Naqvi
- Faculty of Life Sciences, Karakoram International University, Gilgit, Baltistan, Pakistan
| | - Jonna Tabell
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Terhi Iso-Touru
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences and Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland Department of Biology, University of Eastern Finland, Kuopio, Finland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
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63
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Li A, Zhang J, Zhou Z, Wang L, Sun X, Liu Y. Genome-scale identification of miRNA-mRNA and miRNA-lncRNA interactions in domestic animals. Anim Genet 2015; 46:716-9. [PMID: 26360131 DOI: 10.1111/age.12329] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2015] [Indexed: 02/01/2023]
Abstract
Domestic animals show considerable genetic diversity. Previous studies suggested that animal phenotypes were affected by miRNA-mRNA interplay, but these studies focused mainly on the analysis of one or several miRNA-mRNA interactions. However, in this study, we investigated miRNA-mRNA and miRNA-lncRNA interactions on a genomic scale using miranda and targetscan algorithms. There has been strong directional artificial selection practiced during the domestication of animals. Thus, we investigated SNPs that were located in miRNAs and miRNA binding sites and found that several SNPs located in 3'-UTRs of mRNAs had the potential to affect miRNA-mRNA interactions. In addition, a database, named miRBond, was developed to provide visualization, analysis and downloading of the resulting datasets. Our results open the way to further experimental verification of miRNA-mRNA and miRNA-lncRNA interactions as well as the influence of SNPs upon such interplay.
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Affiliation(s)
- A Li
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China.,School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, 710048, China
| | - J Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Z Zhou
- Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, 230022, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - L Wang
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, 710048, China
| | - X Sun
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Y Liu
- Xi'an DongXing Branch, CMST Development Co. Ltd., Xi'an, 710032, China
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64
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Baker E, Wang B, Bellora N, Peris D, Hulfachor AB, Koshalek JA, Adams M, Libkind D, Hittinger CT. The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts. Mol Biol Evol 2015; 32:2818-31. [PMID: 26269586 PMCID: PMC4651232 DOI: 10.1093/molbev/msv168] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The dramatic phenotypic changes that occur in organisms during domestication leave indelible imprints on their genomes. Although many domesticated plants and animals have been systematically compared with their wild genetic stocks, the molecular and genomic processes underlying fungal domestication have received less attention. Here, we present a nearly complete genome assembly for the recently described yeast species Saccharomyces eubayanus and compare it to the genomes of multiple domesticated alloploid hybrids of S. eubayanus × S. cerevisiae (S. pastorianus syn. S. carlsbergensis), which are used to brew lager-style beers. We find that the S. eubayanus subgenomes of lager-brewing yeasts have experienced increased rates of evolution since hybridization, and that certain genes involved in metabolism may have been particularly affected. Interestingly, the S. eubayanus subgenome underwent an especially strong shift in selection regimes, consistent with more extensive domestication of the S. cerevisiae parent prior to hybridization. In contrast to recent proposals that lager-brewing yeasts were domesticated following a single hybridization event, the radically different neutral site divergences between the subgenomes of the two major lager yeast lineages strongly favor at least two independent origins for the S. cerevisiae × S. eubayanus hybrids that brew lager beers. Our findings demonstrate how this industrially important hybrid has been domesticated along similar evolutionary trajectories on multiple occasions.
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Affiliation(s)
- EmilyClare Baker
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison
| | - Bing Wang
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison
| | - Nicolas Bellora
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Bariloche, Argentina
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison
| | | | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue-CONICET, Bariloche, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison
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65
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Adeola AC, Ommeh SC, Murphy RW, Wu SF, Peng MS, Zhang YP. Mitochondrial DNA variation of Nigerian domestic helmeted guinea fowl. Anim Genet 2015; 46:576-9. [PMID: 26153528 DOI: 10.1111/age.12324] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 11/29/2022]
Abstract
We analyzed genetic diversity of 215 mitochondrial DNA (mtDNA) D-loop sequences from seven populations of domesticated helmeted guinea fowl (Numida meleagris) in Nigeria and compared that with results of samples collected in Kenya (n = 4) and China (n = 22). In total, 241 sequences were assigned to 22 distinct haplotypes. Haplotype diversity in Nigeria was 0.693 ± 0.022. The network grouped most matrilines into two main haplogroups: A and B. There was an absence of a geographic signal, and two haplotypes dominated across all locations with the exception of the Kebbi population in the northwest of the country; AMOVA also confirmed this observation (FST = 0.035). The low genetic diversity may be a result of recent domestication, whereas the lack of maternal genetic structure likely suggests the extensive genetic intermixing within the country. Additionally, the differentiation of the Kebbi population may be due to a certain demographic history and/or artificial selection that shaped its haplotype profile. The current data do not permit us to make further conclusions; therefore, more research evidence from genetics and archaeology is still required.
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Affiliation(s)
- Adeniyi C Adeola
- China-Africa Center for Research and Education & State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals & Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Sheila C Ommeh
- Animal Biotechnology Group, Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, PO Box 62000, City Square 00200, Nairobi, Kenya
| | - Robert W Murphy
- China-Africa Center for Research and Education & State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals & Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada, M5S 2C6
| | - Shi-Fang Wu
- China-Africa Center for Research and Education & State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals & Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Min-Sheng Peng
- China-Africa Center for Research and Education & State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals & Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ya-Ping Zhang
- China-Africa Center for Research and Education & State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals & Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, China
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66
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Peng MS, Fan L, Shi NN, Ning T, Yao YG, Murphy RW, Wang WZ, Zhang YP. DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals. Mol Ecol Resour 2015; 15:1238-42. [PMID: 25655564 DOI: 10.1111/1755-0998.12386] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/01/2015] [Accepted: 02/02/2015] [Indexed: 01/01/2023]
Abstract
Mitochondrial DNA (mtDNA) is widely used in various genetic studies of domesticated animals. Many applications require comprehensive knowledge about the phylogeny of mtDNA variants. Herein, we provide the most up-to-date mtDNA phylogeny (i.e. haplogroup tree or matrilineal genealogy) and a standardized hierarchical haplogroup nomenclature system for domesticated cattle, dogs, goats, horses, pigs, sheep, yaks and chickens. These high-resolution mtDNA haplogroup trees based on 1240 complete or near-complete mtDNA genome sequences are available in open resource DomeTree (http://www.dometree.org). In addition, we offer the software MitoToolPy (http://www.mitotool.org/mp.html) to facilitate the mtDNA data analyses. We will continuously and regularly update DomeTree and MitoToolPy.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Long Fan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999077, China
| | - Ni-Ni Shi
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Tiao Ning
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
| | - Yong-Gang Yao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, M5S 2C6, Canada
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.,Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
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67
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Bai B, Zhao WM, Tang BX, Wang YQ, Wang L, Zhang Z, Yang HC, Liu YH, Zhu JW, Irwin DM, Wang GD, Zhang YP. DoGSD: the dog and wolf genome SNP database. Nucleic Acids Res 2014; 43:D777-83. [PMID: 25404132 PMCID: PMC4383968 DOI: 10.1093/nar/gku1174] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The rapid advancement of next-generation sequencing technology has generated a deluge of genomic data from domesticated dogs and their wild ancestor, grey wolves, which have simultaneously broadened our understanding of domestication and diseases that are shared by humans and dogs. To address the scarcity of single nucleotide polymorphism (SNP) data provided by authorized databases and to make SNP data more easily/friendly usable and available, we propose DoGSD (http://dogsd.big.ac.cn), the first canidae-specific database which focuses on whole genome SNP data from domesticated dogs and grey wolves. The DoGSD is a web-based, open-access resource comprising ∼19 million high-quality whole-genome SNPs. In addition to the dbSNP data set (build 139), DoGSD incorporates a comprehensive collection of SNPs from two newly sequenced samples (1 wolf and 1 dog) and collected SNPs from three latest dog/wolf genetic studies (7 wolves and 68 dogs), which were taken together for analysis with the population genetic statistics, Fst. In addition, DoGSD integrates some closely related information including SNP annotation, summary lists of SNPs located in genes, synonymous and non-synonymous SNPs, sampling location and breed information. All these features make DoGSD a useful resource for in-depth analysis in dog-/wolf-related studies.
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Affiliation(s)
- Bing Bai
- Laboratory for Conservation and Utilization of Bioresource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences,Kunming 650204, China
| | - Wen-Ming Zhao
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bi-Xia Tang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan-Qing Wang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Wang
- Laboratory for Conservation and Utilization of Bioresource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - He-Chuan Yang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences,Kunming 650204, China Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bioresource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Jun-Wei Zhu
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ya-Ping Zhang
- Laboratory for Conservation and Utilization of Bioresource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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68
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Shi NN, Fan L, Yao YG, Peng MS, Zhang YP. Mitochondrial genomes of domestic animals need scrutiny. Mol Ecol 2014; 23:5393-7. [PMID: 25294192 DOI: 10.1111/mec.12955] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/22/2014] [Accepted: 10/03/2014] [Indexed: 12/25/2022]
Abstract
More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives, as well. Nevertheless, few efforts have been performed to evaluate the sequence data quality. Herein, we conducted a phylogenetic survey of these complete or near-complete mtDNA sequences based on mtDNA haplogroup trees for the eight animals. We show that errors due to artificial recombination, surplus of mutations and phantom mutations do exist in 14.5% (194/1342) of mtDNA sequences and all of them should be treated with wide caution. We propose some caveats for future mtDNA studies of domestic animals.
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Affiliation(s)
- Ni-Ni Shi
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
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69
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Cao X, Irwin DM, Liu YH, Cheng LG, Wang L, Wang GD, Zhang YP. Balancing selection on CDH2 may be related to the behavioral features of the Belgian Malinois. PLoS One 2014; 9:e110075. [PMID: 25303325 PMCID: PMC4193869 DOI: 10.1371/journal.pone.0110075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/06/2014] [Indexed: 01/23/2023] Open
Abstract
The Belgian Malinois (BM) is an excellent working dog that typically shows a circling behavior when placed in a confined space. Moreover, individuals showing moderate running in circles (one kind of obsessive compulsive behavior) in confined spaces typically show better work performance compared to those without the circling behavior or to those with a serious circling behavior (which can be defined as an obsessive compulsive disorder (OCD)). To determine whether the candidate gene CDH2, Cadherin 2, which is associated with OCD in the Doberman pinscher breed of dogs and in humans, was linked with this behavioral character in the BM, population genetic analyses were performed on a BM population and a natural population of the Chinese indigenous dog (CID). Many genetic signals of balancing selection were detected for one specific region of the CDH2 gene, which suggests that a genomic block, which is included in the CDH2 gene, experienced balancing selection in the BM, and that the CDH2 gene might be associated with the behavioral characteristics of the BM dog (a balance between circling behavior and work performance). Moreover one specific variant, G63913941A, which creates a predicted transcription factor-binding site, may be the key mutation in the CDH2 gene affecting the behavior of BMs by allowing the binding of a transcription factor and increasing CDH2 expression.
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Affiliation(s)
- Xue Cao
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - David M. Irwin
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Lu-Guang Cheng
- Kunming Police Dog Base, Ministry of Public Security, Kunming, China
| | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- * E-mail: (GDW); (YPZ)
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- * E-mail: (GDW); (YPZ)
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