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Urantówka AD, Kroczak A, Strzała T, Zaniewicz G, Kurkowski M, Mackiewicz P. Mitogenomes of Accipitriformes and Cathartiformes Were Subjected to Ancestral and Recent Duplications Followed by Gradual Degeneration. Genome Biol Evol 2021; 13:6357707. [PMID: 34432018 PMCID: PMC8435663 DOI: 10.1093/gbe/evab193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2021] [Indexed: 11/25/2022] Open
Abstract
The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus, as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14–47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland.,Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
| | - Tomasz Strzała
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Grzegorz Zaniewicz
- Department of Vertebrate Ecology and Zoology, Avian Ecophysiology Unit, University of Gdańsk, Poland
| | - Marcin Kurkowski
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, Wrocław University, Poland
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Urantówka AD, Kroczak A, Mackiewicz P. New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves. BMC Genomics 2020; 21:874. [PMID: 33287726 PMCID: PMC7720580 DOI: 10.1186/s12864-020-07284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. RESULTS Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. CONCLUSIONS The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
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Development and characterization of 31 SNP markers for the Crested ibis (Nipponia nippon). CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01174-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D. Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications. Genome Biol Evol 2019; 11:2824-2849. [PMID: 31580435 PMCID: PMC6795242 DOI: 10.1093/gbe/evz209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
| | - Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Dorota Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
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Lan H, Zhou T, Wan QH, Fang SG. Genetic Diversity and Differentiation at Structurally Varying MHC Haplotypes and Microsatellites in Bottlenecked Populations of Endangered Crested Ibis. Cells 2019; 8:E377. [PMID: 31027280 PMCID: PMC6523929 DOI: 10.3390/cells8040377] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/29/2022] Open
Abstract
Investigating adaptive potential and understanding the relative roles of selection and genetic drift in populations of endangered species are essential in conservation. Major histocompatibility complex (MHC) genes characterized by spectacular polymorphism and fitness association have become valuable adaptive markers. Herein we investigate the variation of all MHC class I and II genes across seven populations of an endangered bird, the crested ibis, of which all current individuals are offspring of only two pairs. We inferred seven multilocus haplotypes from linked alleles in the Core Region and revealed structural variation of the class II region that probably evolved through unequal crossing over. Based on the low polymorphism, structural variation, strong linkage, and extensive shared alleles, we applied the MHC haplotypes in population analysis. The genetic variation and population structure at MHC haplotypes are generally concordant with those expected from microsatellites, underlining the predominant role of genetic drift in shaping MHC variation in the bottlenecked populations. Nonetheless, some populations showed elevated differentiation at MHC, probably due to limited gene flow. The seven populations were significantly differentiated into three groups and some groups exhibited genetic monomorphism, which can be attributed to founder effects. We therefore propose various strategies for future conservation and management.
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Affiliation(s)
- Hong Lan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Department of Agriculture, Zhejiang Open University, Hangzhou 310012, China.
| | - Tong Zhou
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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He X, Chen X, Zhang W, Pu Y, Song S, Han J, Dong K, Zhao Q, Guan W, Ma Y, Jiang L. High occurrence of length heteroplasmy in domestic Bactrian camel (Camelus bactrianus). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:851-854. [PMID: 27937010 DOI: 10.1080/24701394.2016.1197219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Heteroplasmy is the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual. In this study, sequence variation was investigated in the control region (CR) of mitochondrial DNA (mtDNA) from 135 individuals belonging to five primary domestic Bactrian camel breeds in China and Mongolia. Due to variation of the repeat unit G(T/C)(AC)n, length heteroplasmy was detected within each camel by direct sequencing and fragment analysis. A high occurrence of mtDNA heteroplasmy, up to 100 percentages was observed in five camel populations. Our study provides the first evidence of extensive length heteroplasmy in Bactrian camels.
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Affiliation(s)
- Xiaohong He
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Xiaofei Chen
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Wenbin Zhang
- c Bactrian Camels Institute of Alxa League , Inner Mongolia Autonomous Region , China
| | - Yabin Pu
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Shen Song
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Jianlin Han
- b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,d International Livestock Research Institute (ILRI) , Nairobi , Kenya
| | - Kunzhe Dong
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Qianjun Zhao
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Weijun Guan
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Yuehui Ma
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Lin Jiang
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
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E GX, Zhao YJ, Huang YF. Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:91-95. [PMID: 27841052 DOI: 10.1080/24701394.2016.1242582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.
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Affiliation(s)
- Guang-Xin E
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Yong-Ju Zhao
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Yong-Fu Huang
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
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Halley YA, Oldeschulte DL, Bhattarai EK, Hill J, Metz RP, Johnson CD, Presley SM, Ruzicka RE, Rollins D, Peterson MJ, Murphy WJ, Seabury CM. Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy. PLoS One 2015; 10:e0144913. [PMID: 26713762 PMCID: PMC4699210 DOI: 10.1371/journal.pone.0144913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/26/2015] [Indexed: 01/09/2023] Open
Abstract
Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (Callipepla squamata) as being explanatory factors for the two bobwhite maternal lineages observed. Instead, our analyses support the supposition that two diverged maternal lineages have survived from pre-expansion to post-expansion population(s), with the segregation of some slightly deleterious nonsynonymous mutations.
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Affiliation(s)
- Yvette A. Halley
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - David L. Oldeschulte
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Eric K. Bhattarai
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Joshua Hill
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Richard P. Metz
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Charles D. Johnson
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Steven M. Presley
- Department of Environmental Toxicology, Institute of Environmental and Human Health, Texas Tech University, Lubbock, Texas, United States of America
| | - Rebekah E. Ruzicka
- Texas A&M AgriLife Extension Service, Dallas, Texas, United States of America
| | - Dale Rollins
- Rolling Plains Quail Research Ranch, 1262 U.S. Highway 180 W., Rotan, Texas, United States of America
| | - Markus J. Peterson
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Christopher M. Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Gorkhali NA, Jiang L, Shrestha BS, He XH, Junzhao Q, Han JL, Ma YH. High occurrence of mitochondrial heteroplasmy in nepalese indigenous sheep (Ovis aries) compared to chinese sheep. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2645-7. [DOI: 10.3109/19401736.2015.1041134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Neena Amatya 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 (NARC), Kathmandu, Nepal, and
| | - Lin Jiang
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,
| | - Bhola Shankar Shrestha
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal, and
| | - Xiao-Hong He
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,
| | - Qian Junzhao
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,
| | - 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
| | - 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,
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Taniguchi Y, Matsumoto K, Matsuda H, Yamada T, Sugiyama T, Homma K, Kaneko Y, Yamagishi S, Iwaisaki H. Structure and polymorphism of the major histocompatibility complex class II region in the Japanese Crested Ibis, Nipponia nippon. PLoS One 2014; 9:e108506. [PMID: 25247679 PMCID: PMC4172706 DOI: 10.1371/journal.pone.0108506] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/21/2014] [Indexed: 12/15/2022] Open
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic genomic region that plays a central role in the immune system. Despite its functional consistency, the genomic structure of the MHC differs substantially among organisms. In birds, the MHC-B structures of Galliformes, including chickens, have been well characterized, but information about other avian MHCs remains sparse. The Japanese Crested Ibis (Nipponia nippon, Pelecaniformes) is an internationally conserved, critically threatened species. The current Japanese population of N. nippon originates from only five founders; thus, understanding the genetic diversity among these founders is critical for effective population management. Because of its high polymorphism and importance for disease resistance and other functions, the MHC has been an important focus in the conservation of endangered species. Here, we report the structure and polymorphism of the Japanese Crested Ibis MHC class II region. Screening of genomic libraries allowed the construction of three contigs representing different haplotypes of MHC class II regions. Characterization of genomic clones revealed that the MHC class II genomic structure of N. nippon was largely different from that of chicken. A pair of MHC-IIA and -IIB genes was arranged head-to-head between the COL11A2 and BRD2 genes. Gene order in N. nippon was more similar to that in humans than to that in chicken. The three haplotypes contained one to three copies of MHC-IIA/IIB gene pairs. Genotyping of the MHC class II region detected only three haplotypes among the five founders, suggesting that the genetic diversity of the current Japanese Crested Ibis population is extremely low. The structure of the MHC class II region presented here provides valuable insight for future studies on the evolution of the avian MHC and for conservation of the Japanese Crested Ibis.
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Affiliation(s)
- Yukio Taniguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- * E-mail:
| | - Keisuke Matsumoto
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hirokazu Matsuda
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takahisa Yamada
- Department of Agrobiology, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Toshie Sugiyama
- Department of Agrobiology, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Kosuke Homma
- Field Center for Sustainable Agriculture and Forestry, Niigata University, Niigata, Japan
| | | | | | - Hiroaki Iwaisaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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11
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Mao X, Dong J, Hua P, He G, Zhang S, Rossiter SJ. Heteroplasmy and ancient translocation of mitochondrial DNA to the nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) complex. PLoS One 2014; 9:e98035. [PMID: 24842827 PMCID: PMC4026475 DOI: 10.1371/journal.pone.0098035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/28/2014] [Indexed: 11/18/2022] Open
Abstract
The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.
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Affiliation(s)
- Xiuguang Mao
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Ji Dong
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Panyu Hua
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Guimei He
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Shuyi Zhang
- Institute of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- * E-mail:
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