A molecular characteristic of the Anatidae mitochondrial control region – a review

Joanna Warzecha; Agnieszka Fornal; Maria Oczkowicz; Monika Bugno-Poniewierska

doi:10.1515/aoas-2017-0016

Abstract

Mitochondrial DNA (mtDNA) is a molecular tool that is very effective in genetic research, including phylogenetic analysis. The non-coding region is the most variable fragment of mtDNA, showing variability in length and nucleobase composition and containing three domains: two hypervariable peripheral regions and the conserved domain (D-loop) in the middle. The Anseriformes are amongst the best studied avian groups, including approximately 150 species and containing geese, swans, ducks (Anatidae), the Magpie goose (Anseranatidae) and screamers (Anhimidae). The most numerous family is the Anatidae, appearing in close relationships within the phylogenetic branches of the species. There are differences between the non-coding region of the Anatidae in comparison to other avian control regions. In the article presented below the control region sequences and the phylogeny of the Anatidae were reviewed.

References

Allen J.F. (1996). Separate sexes and the mitochondrial theory of ageing. J. Theor. Biol., 180: 135-140.
Search in Google Scholar Back to article
Boore J.L. (1999). Animal mitochondrial genomes. Nucleic Acids Res., 27: 1767-1780.
Search in Google Scholar Back to article
Brown G.G., Gadaleta G., Pepe G., Saccone C., Sbisa E. (1986). Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol., 192: 503-511.
Search in Google Scholar Back to article
Brown W.M., Prager E.M., Wang A., Wilson A.C. (1982). Mitochondrial DNAsequences of primates: tempo and mode of evolution. J. Mol. Evol., 18: 225-239.10.1007/BF01734101
Open DOI Search in Google Scholar Back to article
Bucheli S.R., Wenzel J. (2005). Gelechioidea (Insecta: Lepidoptera) systematics:areexamination using combined morphology and mitochondrial DNAdata. Mol. Phylogenet. Evol., 35: 380-394.10.1016/j.ympev.2005.02.003
Open DOI Search in Google Scholar Back to article
Castro J.A., Picornell A., Ramon M. (1998). Mitochondrial DNA:atool for populational genetics studies. Int. Microbiol., 1: 327-332.
Search in Google Scholar Back to article
Desjardins P., Morais R. (1990). Sequence and gene organization of the chicken mitochondrial genome:anovel gene order in higher vertebrates. J. Mol. Biol., 212: 599-634.
Search in Google Scholar Back to article
Donne- Goussé C., Laudet V., Hänni C. (2002). Amolecular phylogeny of anseriformes based on mitochondrial DNAanalysis. Mol. Phylogenet. Evol., 23: 339-356.10.1016/S1055-7903(02)00019-2
Open DOI Search in Google Scholar Back to article
Feinstein J. (2006). The mitochondrial genome of Cygnus columbianus, the Whistling Swan: Full Length Research Paper. DNA Sequence, 17: 99-106. 10.1080/1042517060062486717076251
Open DOI Search in Google Scholar Back to article
Gen Bank (www.ncbi.nlm.nih.gov/genbank), 22.10.2016.
Search in Google Scholar Back to article
Gonzalez J., Düttmann H., Wink M. (2009). Phylogenetic relationships based on two mitochondrial genes and hybridization patterns in Anatidae. J. Zool., 279: 310-318.
Search in Google Scholar Back to article
Guan X., Silva P., Gyenai K.B., Xu J., Geng T., Tu Z., Samuels D.C., Smith E.J. (2009). The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo. Anim. Genet., 40: 134-141.
Search in Google Scholar Back to article
Heikkinen M.E., Ruokonen M., Alexander M., Aspi J., Pyhäjärvi T., Searle J.B. (2015). Relationship between wild greylag and European domestic geese based on mitochondrial DNA. Anim. Genet., 46: 485-497.
Search in Google Scholar Back to article
Holland M.M., Parsons T.J. (1999). Mitochondrial DNAsequence analysis - validation and use for forensic casework. Forensic Sci. Rev., 11: 21-50.
Search in Google Scholar Back to article
IOC World Bird List (www.worldbirdnames.org/ bow /waterfowl) 30.03.2016.
Search in Google Scholar Back to article
Jiang F., Miao Y., Liang W., Ye H., Liu H., Liu B. (2010). The complete mitochondrial genomes of the whistling duck (Dendrocygna javanica) and black swan (Cygnus atratus): dating evolutionary divergence in Galloanserae. Mol. Biol. Rep., 6: 3001-3015.10.1007/s11033-009-9868-919823953
Open DOI Search in Google Scholar Back to article
Jiang G.T., Lin Q., He P., Zhang X., Yun L., Li X., Liu G., Li C., He X., Dai Q.Z. (2014). The complete mitochondrial genome of the Wugangtong white goose. Mitochondr. DNA, 1-3: 3890-3892.
Search in Google Scholar Back to article
Lee J.H., Ryu S.H., Kang S.G., Hwang U.W. (2012). Complete mitochondrial genome of the Bewick’s swan Cygnus columbianus bewickii (Aves, Anseriformes, Anatidae). Mitochondr. DNA, 23: 129-130.
Search in Google Scholar Back to article
Lee S.Y., Scott G.R., Milsom W.K. (2008). Have wing morphology or flight kinematics evolved for extreme high altitude migration in the bar-headed goose? Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology, 148: 324-331.10.1016/j.cbpc.2008.05.00918635402
Search in Google Scholar Back to article
Lin Q., Cao R., Jiang G.T., Liu G., Dai Q.Z., Zhang S.R., Hou D.X., He X. (2014 a). Determination and analysis of the complete mitochondrial genome sequence of Yanling white goose. Mitochondr. DNA Part A, 27: 1012-1013.10.3109/19401736.2014.92652924938094
Search in Google Scholar Back to article
Lin Q., Cao R., Jiang G.T., Liu G., Qiu L., Hu G.B., Dai Q.Z., Zhang S.R., Hou D.X., He X. (2014 b). The complete mitochondrial genome sequence of the Xupu goose. Mitochondr. DNA Part A, 27: 1010-1011.10.3109/19401736.2014.92652824938098
Search in Google Scholar Back to article
Liu C.Z., Wei G.H., Hu J.H., Liu X.Y. (2015). Complete mitochondrial genome of the Swan Goose (Anser cygnoides L.) and its phylogenetic analysis. Mitochondr. DNA Part A, 27: 2427- -2428.
Search in Google Scholar Back to article
Liu G., Zhou L., Zhang L., Luo Z., Xu W. (2013). The complete mitochondrial genome of Bean goose (Anser fabalis) and implications for Anseriformes taxonomy. PLOS ONE, 8: e63334.
Search in Google Scholar Back to article
Livezey B.C. (1997). Aphylogenetic analysis of basal Anseriformes, the fossil Presbyornis, and the interordinal relationships of waterfowl. Zool. J. Linn. Soc-Lond., 121: 361-428.
Search in Google Scholar Back to article
Mindell D.P., Sorenson M.D., Dimcheff D.E. (1998). Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci, 95: 10693-10697.
Search in Google Scholar Back to article
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. Anim. Genet., 32: 380-385.
Search in Google Scholar Back to article
Nishibori M., Tsudzuki M., Hayashi T., Yamamoto Y., Yasue H. (2002). Complete nucleotide sequence of the Coturnix chinensis (Blue-breasted quail) mitochondorial genome and a phylogenetic analysis with related species. J. Hered., 93: 439-444.10.1093/jhered/93.6.43912642645
Open DOI Search in Google Scholar Back to article
Nishibori M., Hayashi T., Yasue H. (2004). Complete nucleotide sequence of Nurrada meleagris (Helmeted guineafowl) mitochondrial genome. J. Poultry Sci., 41: 259-268.10.2141/jpsa.41.259
Open DOI Search in Google Scholar Back to article
Olson S.L., Feduccia A. (1980). Presbyornis and the origin of the Anseriformes (Aves: Charadriomorphae). Smithsonian Institution Press, 323.10.5479/si.00810282.323
Search in Google Scholar Back to article
Park C.E., Park G.S., Kwak Y., Hong S.J., Khan A.R., Jung B.K., Park Y.J., Kim J.G., Park H.C., Shin J.H. (2015). Complete mitochondrial genome of Cygnus olor (Aves, Anseriformes, Anatidae). Mitochondr. DNA Part A, 27: 3442-3443.
Search in Google Scholar Back to article
Ramirez V., Savoie P., Morais R. (1993). Molecular characterization and evolution ofaduck mitochondrial genome. J. Mol. Evol., 37: 296-310.
Search in Google Scholar Back to article
Randi E., Lucchini V. (1998). Organization and evolution of the mitochondrial DNAcontrol region in the avian genus Alectoris. J. Mol. Evol., 47: 449-462.10.1007/PL00006402
Open DOI Search in Google Scholar Back to article
Ruokonen M., Kvist L. (2002). Structure and evolution of the avian mitochondrial control region. Mol. Phylogenet. Evol., 23: 422-432.10.1016/S1055-7903(02)00021-0
Open DOI Search in Google Scholar Back to article
Ruokonen M., Kvist L., Lumme J. (2000). Close relatedness between mitochondrial DNAfrom seven Anser goose species. J. Evolution. Biol., 13: 532-540.10.1046/j.1420-9101.2000.00184.x
Open DOI Search in Google Scholar Back to article
Ryu S.H., Hwang U.W. (2011). Complete mitochondrial genome of the Baikal teal Anas formosa (Aves, Anseriformes, Anatidae). Mitochondr. DNA, 22: 74-76.
Search in Google Scholar Back to article
Saccone C., Pesole G., Sbisá E. (1991). The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J. Mol. Evol., 33: 83-91.
Search in Google Scholar Back to article
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.
Search in Google Scholar Back to article
Slack K.E., Janke A., Penny D., Arnason U. (2003). Two new avian mitochondrial genomes (penguin and goose) andasummary of bird and reptile mitogenomic features. Gene, 302: 43-52.
Search in Google Scholar Back to article
Snyder J.C., Mackaness C.A., Sopher M.R., Huber J.P., Disantis E.J., Senecal A.J., Byron P. Vaughn B.P., Desantis R.S., Tobelmann P.E., Hecht Balauff N.M., Barry P.M., Show M.D., Speering L.H., Genareo C.A., Brenner F.J., Dur-wood B.R. (2013). The complete mitochondrial genome sequence of the Canada goose (Branta canadensis). Mitochondr. DNA, 26: 672-673.
Search in Google Scholar Back to article
Solano A., Playán A., López- Pérez M.J., Montoya J. (2001). Genetic diseases of human mitochondrial DNA. Salud Pública Mex., 43: 151-161
Search in Google Scholar Back to article
Taanman J.W. (1999). The mitochondrial genome: structure, transcription, translation and replication. BBA-Bioenergetics, 1410: 103–123.10.1016/S0005-2728(98)00161-3
Open DOI Search in Google Scholar Back to article
Tu J., Si F., Wu Q., Cong B., Xing X., Yang F.H. (2013). The complete mitochondrial genome of the Muscovy duck, Cairina moschata (Anseriformes, Anatidae, Cairina). Mitochondr. DNA, 25:102–103.
Search in Google Scholar Back to article
Wallace D.C. (2005). The mitochondrial genome in human adaptive radiation and disease: on the road to therapeutics and performance enhancement. Gene, 354: 169–180.
Search in Google Scholar Back to article
Wang J., Liu G., Zhou L., Qing H., Li L., Li B., Zhang L. (2014). Complete mitochondrial genome of Tundra swan Cygnus columbianus jankowskii (Anseriformes: Anatidae). Mitochondr. DNA Part A, 27: 90–91.
Search in Google Scholar Back to article
Wolstenholme D.R. (1992). Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol., 141: 173–216.
Search in Google Scholar Back to article
Xie Z., Zhang Y., Xie L., Deng X., Xie Z., Huang L., Huang J., Zeng T. (2014). Sequence and gene organization of the Xilin small partridge duck (Anseriformes, Anatidae, Anas) mitochondrial DNA. Mitochondr. DNA Part A, 27: 1579–1580.
Search in Google Scholar Back to article
Zhu H., Li B., Li L., Zhou L. (2015). Complete mitochondrial genome of Swan goose Anser cygnoides (Anseriformes: Anatidae). Mitochondr. DNA Part A, 27: 3177–3178.
Search in Google Scholar Back to article

A molecular characteristic of the Anatidae mitochondrial control region – a review

Abstract

Paradigm

My account