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Deng MX, Xiao B, Yuan JX, Hu JM, Kim KS, Westbury MV, Lai XL, Sheng GL. Ancient Mitogenomes Suggest Stable Mitochondrial Clades of the Siberian Roe Deer. Genes (Basel) 2022; 13:genes13010114. [PMID: 35052455 PMCID: PMC8774404 DOI: 10.3390/genes13010114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 11/16/2022] Open
Abstract
The roe deer (Capreolus spp.) has been present in China since the early Pleistocene. Despite abundant fossils available for detailed morphological analyses, little is known about the phylogenetic relationships of the fossil individuals to contemporary roe deer. We generated near-complete mitochondrial genomes for four roe deer remains from Northeastern China to explore the genetic connection of the ancient roe deer to the extant populations and to investigate the evolutionary history and population dynamics of this species. Phylogenetic analyses indicated the four ancient samples fall into three out of four different haplogroups of the Siberian roe deer. Haplogroup C, distributed throughout Eurasia, have existed in Northeastern China since at least the Late Pleistocene, while haplogroup A and D, found in the east of Lake Baikal, emerged in Northeastern China after the Mid Holocene. The Bayesian estimation suggested that the first split within the Siberian roe deer occurred approximately 0.34 million years ago (Ma). Moreover, Bayesian skyline plot analyses suggested that the Siberian roe deer had a population increase between 325 and 225 thousand years ago (Kya) and suffered a transient decline between 50 and 18 Kya. This study provides novel insights into the evolutionary history and population dynamics of the roe deer.
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Affiliation(s)
- Miao-Xuan Deng
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China;
| | - Bo Xiao
- School of Earth Science, China University of Geosciences, Wuhan 430078, China; (B.X.); (J.-M.H.); (X.-L.L.)
| | - Jun-Xia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China;
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Jia-Ming Hu
- School of Earth Science, China University of Geosciences, Wuhan 430078, China; (B.X.); (J.-M.H.); (X.-L.L.)
| | - Kyung Seok Kim
- Department of Ecology, Evolution, and Organismal Biology, lowa State University, Ames, IA 77575, USA;
| | - Michael V. Westbury
- GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Voldgade 5-7, 1353 Copenhagen, Denmark;
| | - Xu-Long Lai
- School of Earth Science, China University of Geosciences, Wuhan 430078, China; (B.X.); (J.-M.H.); (X.-L.L.)
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China;
| | - Gui-Lian Sheng
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China;
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China;
- Correspondence: ; Tel.: +86-27-6788-3022
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de Jong MJ, Li Z, Qin Y, Quéméré E, Baker K, Wang W, Hoelzel AR. Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene. Mol Ecol 2020; 29:2777-2792. [PMID: 32306438 DOI: 10.1111/mec.15450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/25/2020] [Accepted: 04/03/2020] [Indexed: 01/13/2023]
Abstract
Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C. capreolus) populations. Our analyses were facilitated by the generation of a new high-coverage reference genome for the Siberian roe deer (C. pygargus). We find progressive reductions in effective population size (Ne ), despite very large census sizes in modern C. capreolus populations and show that low Ne has impacted the C. capreolus genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among C. capreolus populations, including a historically documented founder population that has been through a severe bottleneck. During each phylogenetic transition there is evidence for selection (from dN/dS and nucleotide diversity tests), including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even-toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change.
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Affiliation(s)
- Menno J de Jong
- Molecular Ecology Group, Department of Biosciences, Durham University, Durham, UK
| | - Zhipeng Li
- Department of Special Animal nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun City, China
| | - Yanli Qin
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Erwan Quéméré
- Comportement et Ecologie de la Faune Sauvage (CEFS), INRA, Université de Toulouse, Castanet-Tolosan, France.,Ecology and Ecosystems Health, Ouest, INRAE, Rennes, France
| | - Karis Baker
- Molecular Ecology Group, Department of Biosciences, Durham University, Durham, UK
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - A Rus Hoelzel
- Molecular Ecology Group, Department of Biosciences, Durham University, Durham, UK
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Slon V, Hopfe C, Weiß CL, Mafessoni F, de la Rasilla M, Lalueza-Fox C, Rosas A, Soressi M, Knul MV, Miller R, Stewart JR, Derevianko AP, Jacobs Z, Li B, Roberts RG, Shunkov MV, de Lumley H, Perrenoud C, Gušić I, Kućan Ž, Rudan P, Aximu-Petri A, Essel E, Nagel S, Nickel B, Schmidt A, Prüfer K, Kelso J, Burbano HA, Pääbo S, Meyer M. Neandertal and Denisovan DNA from Pleistocene sediments. Science 2017; 356:605-608. [DOI: 10.1126/science.aam9695] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/07/2017] [Indexed: 12/11/2022]
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4
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Lee YS, Markov N, Argunov A, Voloshina I, Bayarlkhagva D, Kim B, Min M, Lee H, Kim KS. Genetic diversity and phylogeography of Siberian roe deer, Caproulus pygargus, in central and peripheral populations. Ecol Evol 2016; 6:7286-7297. [PMID: 28725397 PMCID: PMC5513270 DOI: 10.1002/ece3.2458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/28/2016] [Accepted: 06/28/2016] [Indexed: 11/10/2022] Open
Abstract
Current understanding of phylogeographical structure and genetic diversity of Siberian roe deer remains limited mainly due to small sample size and/or low geographical coverage in previous studies. Published data suggest at least two phylogroups: western (Ural Mountains and Western Siberia) and eastern (east from lake Baikal, including the Korean peninsula), but their phylogenetic relationship remains unclear. Combined sequences of cytochrome b (1140 bp) and the mtDNA control region (963 bp) were analyzed from 219 Siberian roe deer from 12 locations in Russia, Mongolia, and South Korea, which cover a large part of its range, to assess genetic diversity and phylogeographical status. Special emphasis was placed on the demographic history and genetic features of central, peripheral, and isolated populations. Results of median-joining network and phylogenetic tree analyses indicate that Siberian roe deer from the Urals to the Pacific Ocean are genetically diverse and that geographical distribution and composition of haplogroups coincide with previously described ranges of the subspecies Capreolus pygargus pygargus and Capreolus pygargus tianschanicus. We found that peripheral populations in the northwestern parts of the species range (Urals), as well as the isolated population from Jeju Island, are genetically distinct from those in the core part of the range, both in terms of genetic diversity and quantitative composition of haplogroups. We also found that northwestern (Urals) and northern (Yakutia) peripheral populations share the same haplogroup and fall into the same phylogenetic clade with the isolated population from Jeju Island. This finding sheds light on the taxonomic status of the Jeju Island population and leads to hypotheses about the discordance of morphological and genetic evolution in isolated populations and specific genetic features of peripheral populations.
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Affiliation(s)
- Yun Sun Lee
- Conservation Genome Resource Bank for Korean WildlifeCollege of Veterinary Medicine and Research Institute for Veterinary ScienceSeoul National UniversitySeoulKorea
| | - Nickolay Markov
- Institute of Plant and Animal Ecology Urals Branch of Russian Academy of SciencesYekaterinburgRussia
| | - Alexander Argunov
- Institute for Biological Problems of Cryolihtozone Siberian Branch of Russian Academy of SciencesYakutskRussia
| | | | - Damdingiin Bayarlkhagva
- Department of Molecular Biology and GeneticsNational University of MongoliaUlaanbaatarMongolia
| | - Baek‐Jun Kim
- Department of Climate and EcologyNational Institute of EcologyMaseo‐myeonSeocheon‐gunChungcheongnam‐doKorea
| | - Mi‐Sook Min
- Conservation Genome Resource Bank for Korean WildlifeCollege of Veterinary Medicine and Research Institute for Veterinary ScienceSeoul National UniversitySeoulKorea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean WildlifeCollege of Veterinary Medicine and Research Institute for Veterinary ScienceSeoul National UniversitySeoulKorea
| | - Kyung Seok Kim
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIAUSA
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Caldararo N. Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept. J Mol Evol 2016; 83:78-87. [DOI: 10.1007/s00239-016-9755-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/30/2016] [Indexed: 10/21/2022]
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Lee YS, Markov N, Voloshina I, Argunov A, Bayarlkhagva D, Oh JG, Park YS, Min MS, Lee H, Kim KS. Genetic diversity and genetic structure of the Siberian roe deer (Capreolus pygargus) populations from Asia. BMC Genet 2015; 16:100. [PMID: 26282405 PMCID: PMC4539716 DOI: 10.1186/s12863-015-0244-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/29/2015] [Indexed: 11/15/2022] Open
Abstract
Background The roe deer, Capreolus sp., is one of the most widespread meso-mammals of Palearctic distribution, and includes two species, the European roe deer, C. capreolus inhabiting mainly Europe, and the Siberian roe deer, C. pygargus, distributed throughout continental Asia. Although there are a number of genetic studies concerning European roe deer, the Siberian roe deer has been studied less, and none of these studies use microsatellite markers. Natural processes have led to genetic structuring in wild populations. To understand how these factors have affected genetic structure and connectivity of Siberian roe deer, we investigated variability at 12 microsatellite loci for Siberian roe deer from ten localities in Asia. Results Moderate levels of genetic diversity (HE = 0.522 to 0.628) were found in all populations except in Jeju Island, South Korea, where the diversity was lowest (HE = 0.386). Western populations showed relatively low genetic diversity and higher degrees of genetic differentiation compared with eastern populations (mean Ar = 3.54 (east), 2.81 (west), mean FST = 0.122). Bayesian-based clustering analysis revealed the existence of three genetically distinct groups (clusters) for Siberian roe deer, which comprise of the Southeastern group (Mainland Korea, Russian Far East, Trans-Baikal region and Northern part of Mongolia), Northwestern group (Western Siberia and Ural in Russia) and Jeju Island population. Genetic analyses including AMOVA (FRT = 0.200), Barrier and PCA also supported genetic differentiation among regions separated primarily by major mountain ridges, suggesting that mountains played a role in the genetic differentiation of Siberian roe deer. On the other hand, genetic evidence also suggests an ongoing migration that may facilitate genetic admixture at the border areas between two groups. Conclusions Our results reveal an apparent pattern of genetic differentiation among populations inhabiting Asia, showing moderate levels of genetic diversity with an east-west gradient. The results suggest at least three distinct management units of roe deer in continental Asia, although genetic admixture is evident in some border areas. The insights obtained from this study shed light on management of Siberian roe deer in Asia and may be applied in conservation of local populations of Siberian roe deer. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0244-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yun Sun Lee
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Gwanak-gu, Seoul, 151-742, Republic of Korea.
| | - Nickolay Markov
- Institute of Plant and Animal Ecology Urals Branch of Russian Academy of Sciences, Yekaterinburg, 620144, Russia.
| | - Inna Voloshina
- Lazovsky State Nature Reserve, Lazo, Primorsky Krai, 692980, Russia.
| | - Alexander Argunov
- Institute for Biological problems of Cryolihtozone Siberian Branch of Russian Academy of Sciences, Yakutsk, 677980, Russia.
| | - Damdingiin Bayarlkhagva
- Department of Molecular Biology and Genetics, National University of Mongolia, Ulaanbaatar, 210646, Mongolia.
| | - Jang Geun Oh
- Research Institute for Hallasan, Jeju Special Self-Governing Province, Jeju, 690-815, Republic of Korea.
| | - Yong-Su Park
- Department of Conservation Ecology, National Institute of Ecology, 1210, Geumgang-ro, Maseo-myeon, Seocheon-gun, Chungcheongnam-do, 325-813, South Korea.
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Gwanak-gu, Seoul, 151-742, Republic of Korea.
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Gwanak-gu, Seoul, 151-742, Republic of Korea.
| | - Kyung Seok Kim
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Gwanak-gu, Seoul, 151-742, Republic of Korea. .,Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
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Olano-Marin J, Plis K, Sönnichsen L, Borowik T, Niedziałkowska M, Jędrzejewska B. Weak population structure in European roe deer (Capreolus capreolus) and evidence of introgressive hybridization with Siberian roe deer (C. pygargus) in northeastern Poland. PLoS One 2014; 9:e109147. [PMID: 25271423 PMCID: PMC4182808 DOI: 10.1371/journal.pone.0109147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 08/22/2014] [Indexed: 12/02/2022] Open
Abstract
We investigated contemporary and historical influences on the pattern of genetic diversity of European roe deer (Capreolus capreolus). The study was conducted in northeastern Poland, a zone where vast areas of primeval forests are conserved and where the European roe deer was never driven to extinction. A total of 319 unique samples collected in three sampling areas were genotyped at 16 microsatellites and one fragment (610 bp) of mitochondrial DNA (mtDNA) control region. Genetic diversity was high, and a low degree of genetic differentiation among sampling areas was observed with both microsatellites and mtDNA. No evidence of genetic differentiation between roe deer inhabiting open fields and forested areas was found, indicating that the ability of the species to exploit these contrasting environments might be the result of its phenotypic plasticity. Half of the studied individuals carried an mtDNA haplotype that did not belong to C. capreolus, but to a related species that does not occur naturally in the area, the Siberian roe deer (C. pygargus). No differentiation between individuals with Siberian and European mtDNA haplotypes was detected at microsatellite loci. Introgression of mtDNA of Siberian roe deer into the genome of European roe deer has recently been detected in eastern Europe. Such introgression might be caused by human-mediated translocations of Siberian roe deer within the range of European roe deer or by natural hybridization between these species in the past.
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Affiliation(s)
- Juanita Olano-Marin
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
- * E-mail:
| | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Leif Sönnichsen
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Tomasz Borowik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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Matosiuk M, Sheremetyeva IN, Sheremetyev IS, Saveljev AP, Borkowska A. Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer. J Evol Biol 2014; 27:2483-94. [PMID: 25262616 DOI: 10.1111/jeb.12491] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/17/2014] [Accepted: 09/01/2014] [Indexed: 01/29/2023]
Abstract
Introgressive hybridization offers a unique platform for studying the molecular basis of natural selection acting on mitogenomes. Most of the mtDNA protein-coding genes are extremely conserved; however, some of the observed variations have potentially adaptive significance. Here, we evaluated whether the evolution of mtDNA in closely related roe deer species affected by widespread mtDNA introgression is neutral or adaptive. We characterized and compared 16 complete mitogenomes of European (Capreolus capreolus) and Siberian (C. pygargus) roe deer, including four of Siberian origin introgressed into European species. The average sequence divergence of species-specific lineages was estimated at 2.8% and varied across gene classes. Only 21 of 315 fixed differences identified in protein-coding genes represented nonsynonymous changes. Only three of them were determined to have arisen in the C. pygargus lineage since the time to the most recent common ancestor (TMRCA) of both Capreolus species, reflecting a decelerated evolutionary ratio. The almost four-fold higher dN /dS ratio described for the European roe deer lineage is constrained by overall purifying selection, especially pronounced in the ND4 and ND5 genes. We suggest that the highly divergent C. capreolus lineage could have maintained a capability for genomic incorporation of the well-preserved and almost ancestral type of mtDNA present in C. pygargus. Our analyses did not indicate any signs of positive selection for Siberian roe deer mtDNA, suggesting that the present widespread introgression is evolutionarily neutral.
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Affiliation(s)
- M Matosiuk
- Institute of Biology, University of Bialystok, Bialystok, Poland
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9
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Matosiuk M, Borkowska A, Świsłocka M, Mirski P, Borowski Z, Krysiuk K, Danilkin AA, Zvychaynaya EY, Saveljev AP, Ratkiewicz M. Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer. Mol Ecol 2014; 23:2559-72. [PMID: 24697866 DOI: 10.1111/mec.12745] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 11/30/2022]
Abstract
Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective neutral loci and to transfer of fitness-related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer (Capreolus capreolus) in Poland from mitochondrial (CR and cyt b) and sex-linked markers (ZFX, SRY, DBY4 and DBY8). Analyses of CR mtDNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer (C. pygargus) mtDNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mtDNA results, sex-specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after last glacial maximum. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8-10.0 ka BP). Initially, introgressed mtDNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human-mediated introductions of C. pygargus had minimal effect on the extent of mtDNA introgression.
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Affiliation(s)
- Maciej Matosiuk
- Institute of Biology, University of Bialystok, Świerkowa 20B, 15-950, Białystok, Poland
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Lorenzini R, Garofalo L, Qin X, Voloshina I, Lovari S. Global phylogeography of the genusCapreolus(Artiodactyla: Cervidae), a Palaearctic meso-mammal. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12091] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Rita Lorenzini
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana; Centro di Referenza Nazionale per la Medicina Forense Veterinaria; Via Tancia 21 Rieti 02100 Italy
| | - Luisa Garofalo
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana; Centro di Referenza Nazionale per la Medicina Forense Veterinaria; Via Tancia 21 Rieti 02100 Italy
| | - Xuebo Qin
- Tianjin Natural History Museum; 206 Machang Road, Hexi District Tianjin 300074 China
| | - Inna Voloshina
- Department of Science; Lazovsky State Nature Reserve; Centralnaya Street 56, Lazo Primorsky Krai 692890 Russia
| | - Sandro Lovari
- U.R. Ecologia comportamentale, Etologia e Gestione della Fauna, Dipartimento di Scienze della Vita; Università di Siena; Via P.A. Mattioli 4 Siena 53100 Italy
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Trifonov VA, Dementyeva PV, Larkin DM, O'Brien PCM, Perelman PL, Yang F, Ferguson-Smith MA, Graphodatsky AS. Transcription of a protein-coding gene on B chromosomes of the Siberian roe deer (Capreolus pygargus). BMC Biol 2013; 11:90. [PMID: 23915065 PMCID: PMC3751663 DOI: 10.1186/1741-7007-11-90] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/16/2013] [Indexed: 11/25/2022] Open
Abstract
Background Most eukaryotic species represent stable karyotypes with a particular diploid number. B chromosomes are additional to standard karyotypes and may vary in size, number and morphology even between cells of the same individual. For many years it was generally believed that B chromosomes found in some plant, animal and fungi species lacked active genes. Recently, molecular cytogenetic studies showed the presence of additional copies of protein-coding genes on B chromosomes. However, the transcriptional activity of these genes remained elusive. We studied karyotypes of the Siberian roe deer (Capreolus pygargus) that possess up to 14 B chromosomes to investigate the presence and expression of genes on supernumerary chromosomes. Results Here, we describe a 2 Mbp region homologous to cattle chromosome 3 and containing TNNI3K (partial), FPGT, LRRIQ3 and a large gene-sparse segment on B chromosomes of the Siberian roe deer. The presence of the copy of the autosomal region was demonstrated by B-specific cDNA analysis, PCR assisted mapping, cattle bacterial artificial chromosome (BAC) clone localization and quantitative polymerase chain reaction (qPCR). By comparative analysis of B-specific and non-B chromosomal sequences we discovered some B chromosome-specific mutations in protein-coding genes, which further enabled the detection of a FPGT-TNNI3K transcript expressed from duplicated genes located on B chromosomes in roe deer fibroblasts. Conclusions Discovery of a large autosomal segment in all B chromosomes of the Siberian roe deer further corroborates the view of an autosomal origin for these elements. Detection of a B-derived transcript in fibroblasts implies that the protein coding sequences located on Bs are not fully inactivated. The origin, evolution and effect on host of B chromosomal genes seem to be similar to autosomal segmental duplications, which reinforces the view that supernumerary chromosomal elements might play an important role in genome evolution.
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