Skip to main content Skip to main navigation menu Skip to site footer
Type: Article
Published: 2019-01-29
Page range: 585–593
Abstract views: 134
PDF downloaded: 1

Complete mitochondrial genome of the Western Capercaillie Tetrao urogallus (Phasianidae, Tetraoninae)

Department of Animal and Plant Biology and Ecology, Jaén University, Campus Las Lagunillas, E-23071, Jaén, Spain.
Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva, 18071 Granada, Spain.
Department of Animal and Plant Biology and Ecology, Jaén University, Campus Las Lagunillas, E-23071, Jaén, Spain.
BEOPS, 1 Esplanade Compans Caffarelli, 31000 Toulouse, France
Department of Experimental Biology, Jaén University, Campus Las Lagunillas, E-23071, Jaén, Spain
Aves control region mitogenome Phasianidae Tetrao urogallus

Abstract

The Western Capercaillie (Tetrao urogallus) is a galliform bird of boreal climax forests from Scandinavia to eastern Siberia, with a fragmented population in southwestern Europe. We extracted the DNA of T. urogallus aquitanicus and obtained the complete mitochondrial genome (mitogenome) sequence by combining Illumina and Sanger sequencing sequence data. The mitochondrial genome of T. urogallus is 16,683 bp long and is very similar to that of Lyrurus tetrix (16,677 bp). The T. urogallus mitogenome contains the normal 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and the control region. The number, order, and orientation of the mitochondrial genes are the same as in L. tetrix and in other species of the same and other bird families. The three domains of the control region contained conserved sequences (ETAS; CSBs), boxes (F, E, D, C, B, BS box), the putative origin of replication of the H-strand (OH) and bidirectional promoters of translation (LSP/HSP).

 

References

  1. Baker, A.J. & Marshall, H.D. (1997) Mitochondrial control region sequences as tools for understanding evolution. In: Mindell, D.P. (Ed.), Avian Molecular Evolution and Systematics. Academic Press, San Diego, pp. 51–82.

    https://doi.org/10.1016/B978-012498315-1/50005-4

    Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M. & Stadler, P.F. (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69, 313–319.

    https://doi.org/10.1016/j.ympev.2012.08.023

    Buehler, D.M. & Baker, A.J. (2003) Characterization of the Red Knot (Calidris canutus) mitochondrial control region. Genome, 46, 565–572.

    https://doi.org/10.1139/g03-034

    Canut, J., Garcia, D. & Parellada, X. (2004) Urogallo Pirenaico Tetrao urogallus aquitanicus. In: Madroño, A., González, C. & Atienza, J.C. (Eds.), Libro Rojo de las Aves de España. Dirección General Para la Biodiversidad-SEO/BirdLife, Madrid, pp. 179–181.

    Charra, M. & Sarasa, M. (2018) Applying IUCN Red List criteria to birds at different geographical scales: similarities and differences. Animal Biodiversity and Conservation, 41.1, 75–95.

    https://doi.org/10.32800/abc.2018.41.0075

    Chen, Y., Li, F., Zhang, Q. & Wang, Q. (2017) Complete mitochondrial genome of the Himalayan Monal Lophophorus impejanus (Phasianidae), with phylogenetic implication. Conservation Genetics Resources, 10, 1–4.

    https://doi.org/10.1007/s12686-017-0886-y

    de Juana, E. (1994) Tetraonidae. In: del Hoyo, J., Elliott, A. & Sargatal, J. (Eds.), Handbook of the Birds of the World. Vol 2. Lynx Edicions, Barcelona, pp. 376–411.

    del Hoyo, J., Elliott, A. & Sargatal, J. (1994) Handbook of the Birds of the World, Vol 2. Lynx Ediciones, Barcelona, 638 pp.

    Dimcheff, D.E., Drovetski, S.V. & Mindell, D.P. (2002) Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12s rRNA and ND2 genes. Molecular Phylogenetics and Evolution, 24, 203–215.

    https://doi.org/10.1016/S1055-7903(02)00230-0

    Douzery, E. & Randi, E. (1997) The mitochondrial control region of Cervidae: evolutionary patterns and phylogenetic contents. Molecular Biology and Evolution, 14, 1154–1166.

    https://doi.org/10.1093/oxfordjournals.molbev.a025725

    Fameli, A.F., Morán-Luis, M., Rodríguez-Muñoz, R., Bañuelos, M.J., Quevedo, M. & Mirol, P. (2017) Conservation in the southern edge of Tetrao urogallus distribution: gene flow despite fragmentation in the stronghold of the Cantabrian Capercaillie. European Journal of Wildlife Research, 63, 58.

    https://doi.org/10.1007/s10344-017-1110-9

    Fuller, R.A., Carroll, J.P. & McGowan, P.J.K. (2000) Partridges, Quails, Francolins, Snowcocks, Guineafowl, and Turkeys. Status Survey and Conservation Action Plan 2000–2004. WPA/BirdLife/SSC Partridge, Quail, and Francolin Specialist Group. IUCN, Gland and Cambridge and the World Pheasant Association, Reading, vii + 63 pp.

    Fuller, R.A. & Garson, P.J. (2000) Pheasants. Status Survey and Conservation Action Plan 2000–2004. WPA/BirdLife/SSC Pheasants Specialist Group. IUCN, Gland and Cambridge and the World Pheasant Association, Reading, vii + 68 pp.

    Gée, A., Sarasa, M. & Pays, O. (2018) Long-term variation of demographic parameters in four small game species in Europe: opportunities and limits to test for a global pattern. Animal Biodiversity and Conservation, 41.1, 3360.

    https://doi.org/10.32800/abc.2018.41.0033

    Guan, X.J., Silva, P., Gyenai, K.B., Xu, J., Geng, T.Y., Tu, Z.J., Samuels, D.C. & Smith, E.J. (2010) The mitochondrial genome sequence and molecular phylogeny of the Turkey, Meleagris gallopavo. Animal Genetics, 40, 134–141.

    https://doi.org/10.1111/j.1365-2052.2008.01810.x

    Hahn, C., Bachmann, L. & Chevreux, B. (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Research, 41, e129–e129.

    https://doi.org/10.1093/nar/gkt371

    Haring, E., Herzig-Straschil, B. & Spitzenberger, F. (2000) Phylogenetic analysis of Alpine voles of the Microtus multiplex complex using the mitochondrial control region. Journal of Zoological Systematics and Evolutionary Research, 38, 231–238.

    https://doi.org/10.1046/j.1439-0469.2000.384139.x

    Hosner, P.A., Faircloth, B.C., Glenn, T.C., Braun, E.L. & Kimball, R.T. (2016) Avoiding missing data biases in phylogenomic inference: An empirical study in the landfowl (Aves: Galliformes). Molecular Biology and Evolution, 33, 1110–1125.

    https://doi.org/10.1093/molbev/msv347

    Huang, Z. & Ke, D. (2014) Structure and variation of the Anseriformes mitochondrial DNA control region. Mitochondrial DNA, 27, 2036–2039.

    https://doi.org/10.3109/19401736.2014.974177

    IUCN (2017) The IUCN Red List of Threatened Species. Version 2017-2. Available from: http://www.iucnredlist.org (accessed 20 December 2017)

    Johnsgard, P.A. (1986) The Pheasants of the World. Oxford University Press, Oxford, 300 pp.

    Kan, X.Z., Li, X.F., Lei, Z.P., Wang, M., Chen, L., Gao, H. & Yang, Z.Y. (2010) Complete mitochondrial genome of Cabot’s Tragopan, Tragopan caboti (Galliformes: Phasianidae). Genetics and Molecular Research, 9, 1204–1216.

    https://doi.org/10.4238/vol9-2gmr820

    Kerr, K.C.R., Birks, S.M., Kalyakin, M.V., Red’Kin, Y.A., Koblik, E.A. & Hebert, P.D. (2009) Filling the gap—COI barcode resolution in eastern Palearctic birds. Frontiers in Zoology, 6, 1–13.

    https://doi.org/10.1186/1742-9994-6-29

    Kowalczyk, A.M., Klećkowska-Nawrot, J. & Łukaszewicz, E.T. (2017) Effect of selenium and vitamin E addition to the extender on liquid stored Capercaillie (Tetrao urogallus) semen quality. Reproduction in Domestic Animals, 52, 603–609.

    https://doi.org/10.1111/rda.12955

    L’Abbé, D., Duhaime, J.F., Lang, B.F. & Morais, R. (1991) The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. Journal of Biological Chemistry, 266, 10844–10850.

    Li, B., Zhu, C., Ding, P., Bai, S. & Cui, J. (2016) Complete mitochondrial genome of Black Grouse (Lyrurus tetrix). Mitochondrial DNA, 27, 134–135.

    https://doi.org/10.3109/19401736.2013.878911

    Li, X., Huang, Y. & Lei, F. (2014) Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis. Zoological Systematics, 39, 359–371.

    https://doi.org/10.11865/zs20140302

    Liukkonen-Anttila, T., Ratti, O., Kvist, L., Helle, P. & Orell, M. (2004) Lack of genetic structuring and subspecies differentiation in the Capercaillie (Tetrao urogallus) in Finland. Annales Zoologici Fennici, 41, 619–633. Available from: http://www.jstor.org/stable/23735956 (Accessed 25 Jan. 2019)

    Lohse, M., Drechsel, O., Kahlau, S. & Bock, R. (2013) OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research, 41 (1), 575–581. [W575–W581]

    https://doi.org/10.1093/nar/gkt289

    Lowe, T.M. & Eddy, S.R. (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25, 955–964.

    https://doi.org/10.1093/nar/25.5.955

    Lucchini, V., Höglund, J., Klaus, S., Swenson, J. & Randi, E. (2001) Historical biogeography and a mitochondrial DNA phylogeny of grouse and ptarmigan. Molecular Phylogenetics and Evolution, 20, 149–162.

    https://doi.org/10.1006/mpev.2001.0943

    Mindell, D.P., Sorenson, M.D. & Dimcheff, D.E. (1998) An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles. Molecular Biology and Evolution, 15, 1568–1571.

    https://doi.org/10.1093/oxfordjournals.molbev.a025884

    Mollet, P., Kéry, M., Gardner, B., Pasinelli, G. & Royle, J.A. (2015) Estimating population size for Capercaillie (Tetrao urogallus L.) with spatial capture-recapture models based on genotypes from one field sample. PLoS One, 10, e0129020.

    https://doi.org/10.1371/journal.pone.0129020

    Mouchaty, S.K., Gullberg, A., Janke, A. & Arnason, U. (2000) The phylogenetic position of the Talpidae within Eutheria based on analysis of complete mitochondrial sequences. Molecular Biology and Evolution, 17, 60–67.

    https://doi.org/10.1093/oxfordjournals.molbev.a026238

    Nishibori, M., Hayashi, T., Tsudzuki, M., Yamamoto, Y. & Yasue, H. (2001) Complete sequence of the Japanese Quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species. Animal Genetics, 32, 380–385.

    https://doi.org/10.1046/j.1365-2052.2001.00795.x

    Obeso, J.R. (2004) Urogallo Cantábrico Tetrao urogallus cantabricus. In: Madroño, A., González, C. & Atienza, J.C. (Eds.), Libro Rojo de las Aves de España. Dirección General Para la Biodiversidad-SEO/BirdLife, Madrid, pp. 176–178.

    Ojala, D., Montoya, J. & Attardi, G. (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature, 290, 470–474.

    https://doi.org/10.1038/290470a0

    Pérez, T., Vazquez, J.F., Quirós, F. & Domínguez, A. (2011) Improving non-invasive genotyping in Capercaillie (Tetrao urogallus): redesigning sexing and microsatellite primers to increase efficiency on faeces samples. Conservation Genetics Resources, 3, 483–487.

    https://doi.org/10.1007/s12686-011-9385-8

    Randi, E. & Lucchini, V. (1998) Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. Journal of Molecular Evolution, 47, 449–462.

    https://doi.org/10.1007/PL00006402

    Rodríguez-Muños, R., Mirol, P.M., Segelbacher, G., Fernández, A. & Tregenza, T. (2007) Genetic differentiation of an endangered Capercaillie (Tetrao urogallus) population at the southern edge of the species range. Conservation Genetics, 8, 659–670.

    https://doi.org/10.1007/s10592-006-9212-z

    Ruokonen, M. & Kvist, L. (2002) Structure and evolution of the avian mitochondrial control region. Molecular Phylogenetics and Evolution, 23, 422–432.

    https://doi.org/10.1016/S1055-7903(02)00021-0

    Rutkowski, R., Zawadzka, D., Suchecka, E. & Merta, D. (2017) Conservation genetics of the Capercaillie in Poland—delineation of conservation units. PLoS ONE, 12, e0174901.

    https://doi.org/10.1371/journal.pone.0174901

    Sbisà, E., Tanzariello, F., Reyes, A., Pesole, G. & Saccone, C. (1997) Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene, 205, 125–140.

    https://doi.org/10.1016/S0378-1119(97)00404-6

    Segelbacher, G., Manel, S. & Tomiuk, J. (2008) Temporal and spatial analyses disclose consequences of habitat fragmentation on the genetic diversity in Capercaillie (Tetrao urogallus). Molecular Ecology, 17, 2356–2367.

    https://doi.org/10.1111/j.1365-294X.2008.03767.x

    Shen, Y.Y., Liang, L., Sun, Y.B., Yue, B.S., Yang, X.J., Murphy, R.W. & Zhang, Y.P. (2010) A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evolutionary Biology, 10, 132.

    https://doi.org/10.1186/1471-2148-10-132

    Shi, Q., Liu, Y. & Zhao, H.F. (2017) Characterization of the complete mitochondrial genome of Slaty Bunting Emberiza siemsseni (Passeriformes: Fringillidae). Conservation Genetics Resources, 9, 107–110.

    https://doi.org/10.1007/s12686-016-0632-x

    Storch, I. (2007) Grouse: Status Survey and Conservation Action Plan 2006–2010. IUCN and World Pheasant Association, Gland and Fordingbridge, 112 pp.

    Yang, C., Lian, T., Wang, Q-X., Huang, Y. & Xiao, H. (2015) Structural characteristics of the Relict Gull (Larus relictus) mitochondrial DNA control region and its comparison to other Laridae. Mitochondrial DNA, 27, 2487–2491.

    https://doi.org/10.3109/19401736.2015.1033711

    Zhang, Y.Y., Nie, L.W., Huang, Y.Q., Pu, Y.G. & Zhang, L. (2009) The mitochondrial DNA control region comparative studies of four hinged turtles and its phylogenetic significance of the Genus Cuora sensu lato (Testudinata: Geoemydidae). Genes & Genomics, 31, 349–359.

    https://doi.org/10.1007/BF03191253