Abstract
The Eurasian Wryneck is a species of wryneck woodpecker breeding in temperate regions of Europe and Asia. We sequenced the mitochondrial genome of Jynx torquilla (Aves, Piciformes, Picidae) using the next generation sequencing. The circular genome is 16,832 bp long, encoding 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two control regions. Gene order and orientation are similar to the most common type suggested as ancestral for birds but have a 1,221 bp control region and a 60 bp remnant control region. Phylogenetic analyses of 17 piciform taxa, based on both nucleotide and amino acid sequences of mitochondrial PCGs, strongly support the monophyly of Picidae. All phylogenetic trees indicate that the subfamily Jynginae is a monophyletic lineage sister to other woodpeckers, including monophyletic Picinae. Only the Bayes inferred tree based on the nucleotide dataset, recovered Picumninae as monophyletic. These findings will be helpful for the understanding of the phylogeny and evolution of Picidae.
References
Aleix-Mata, G., Ruiz-Ruano, F.J., Perez, J.M., Sarasa, M. & Sanchez, A. (2019) Complete mitochondrial genome of the Western Capercaillie Tetrao urogallus (Phasianidae, Tetraoninae). Zootaxa, 4550 (4), 585–593.
https://doi.org/10.11646/zootaxa.4550.4.9
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410.
https://doi.org/10.1016/S0022-2836(05)80360-2
Andrews, R.M., Kubacka, I., Chinnery, P.F., Lightowlers, R.N., Turnbull, D.M. & Howell, N. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nature Genetics, 23 (2), 147–147.
Avise, J.C. (1994) Molecular markers, natural history and evolution. Springer Science & Business Media, New York and Philadelphia, 511 pp.
Bi, D., Ding, H., Wang, Q., Jiang, L., Lu, W., Wu, X. & Kan, X. (2019) Two new mitogenomes of Picidae (Aves, Piciformes): Sequence, structure and phylogenetic analyses. International Journal of Biological Macromolecules, 133, 683–692.
https://doi.org/10.1016/j.ijbiomac.2019.04.157
Boore, J.L. (1999) Survey and summary: animal mitochondrial genomes. Nucleic Acids Research, 27, 1767–1780.
https://doi.org/10.1093/nar/27.8.1767
Boore, J.L. (2001) Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii. Molecular Biology and Evolution, 18 (7), 1413–1416.
https://doi.org/10.1093/oxfordjournals.molbev.a003925
Chen, S., Zhou, Y., Chen, Y. & Gu, J. (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34, i884–i890.
https://doi.org/10.1093/bioinformatics/bty560
Chen, Y., Li, F., Zhang, Q. & Wang, Q. (2018) Complete mitochondrial genome of the Himalayan Monal Lophophorus impejanus (Phasianidae), with phylogenetic implication. Conservation Genetics Resources, 10 (4), 877–880.
https://doi.org/10.1007/s12686-017-0886-y
Clary, D.O. & Wolstenholme, D.R. (1985) The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. Journal of Molecular Evolution, 22 (3), 252–271.
https://doi.org/10.1007/BF02099755
Du, C., He, S., Song, X., Liao, Q., Zhang, X. & Yue, B. (2016) The complete mitochondrial genome of Epicauta chinensis (Coleoptera: Meloidae) and phylogenetic analysis among coleopteran insects. Gene, 578 (2), 274–280.
https://doi.org/10.1016/j.gene.2015.12.036
Du, C., Zhang, L., Lu, T., Ma, J., Zeng, C., Yue, B. & Zhang, X. (2017) Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera. BMC Genomics, 18 (1), 698.
https://doi.org/10.1186/s12864-017-4102-y
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797.
https://doi.org/10.1093/nar/gkh340
Fuchs, J., Ohlson, J.I., Ericson, P.G.P. & Pasquet, E. (2006) Molecular phylogeny and biogeographic history of the piculets (Piciformes: Picumninae). Journal of Avian Biology, 37 (5), 487–496.
https://doi.org/10.1111/j.0908-8857.2006.03768.x
Gill, F. & Donsker, D. (2020) IOC World Bird List. Version 10.1. Avaialble from: http://www.worldbirdnames.org/
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(13), e129–e129.
https://doi.org/10.1093/nar/gkt371
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 (2), 1204–1216.
https://doi.org/10.4238/vol9-2gmr820
Lanfear, R., Frandsen, P.B., Wright, A.M., Senfeld, T. & Calcott, B. (2017) PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34 (3), 772–773.
https://doi.org/10.1093/molbev/msw260
Ma, Q., He, K., Wang, X., Jiang, J., Zhang, X., & Song, Z. (2020) Better resolution for Cytochrome b than Cytochrome c Oxidase subunit I to identify Schizothorax species (Teleostei: Cyprinidae) from the Tibetan Plateau and its adjacent area. DNA and Cell Biology, 39 (4), 579–598.
https://doi.org/10.1089/dna.2019.5031
Meng, G., Li, Y., Yang, C. & Liu, S. (2019) MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research, 47 (11), e63–e63.
https://doi.org/10.1093/nar/gkz173
Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE), 14, 1–8.
https://doi.org/10.1109/GCE.2010.5676129
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 (11), 1568–1571.
https://doi.org/10.1093/oxfordjournals.molbev.a025884
Moorea, W.S. & Migliab, K.J. (2009) Woodpeckers, Toucans, and Allies (Piciformes). Oxford University Press, New York, 551 pp.
Ojala, D., Montoya, J. & Attardi, G. (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature, 290 (5806), 470–474.
https://doi.org/10.1038/290470a0
Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D.L., Darling, A., Höhna, S. & Huelsenbeck, J.P. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61 (3), 539–542.
https://doi.org/10.1093/sysbio/sys029
Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, C.A., Chen, W. & Fungal Barcoding Consortium (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences USA, 109 (16), 6241–6246.
https://doi.org/10.1073/pnas.1117018109
Shakya, S.B., Fuchs, J., Pons, J.M., & Sheldon, F.H. (2017) Tapping the woodpecker tree for evolutionary insight. Molecular Phylogenetics and Evolution, 116, 182–191.
https://doi.org/10.1016/j.ympev.2017.09.005
Singh, T.R., Shneor, O. & Huchon, D. (2008) Bird mitochondrial gene order: insight from 3 warbler mitochondrial genomes. Molecular Biology and Evolution, 25 (3), 475–477.
https://doi.org/10.1093/molbev/msn003
Stamatakis, A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30 (9), 1312–1313.
https://doi.org/10.1093/bioinformatics/btu033
Tamashiro, R.A., White, N.D., Braun, M.J., Faircloth, B.C., Braun, E.L. & Kimball, R.T. (2019) What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data? Molecular Phylogenetics and Evolution, 130, 132–142.
https://doi.org/10.1016/j.ympev.2018.10.008
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30 (12), 2725–2729.
https://doi.org/10.1093/molbev/mst197
Webb, D.M. & Moore, W.S. (2005) A phylogenetic analysis of woodpeckers and their allies using 12S, Cyt b, and COI nucleotide sequences (Class Aves; Order Piciformes). Molecular Phylogenetics and Evolution, 36, 233–248.
https://doi.org/10.1016/j.ympev.2005.03.015
Winkler, H. & Christie, D.A. (2020) Grey-capped Woodpecker (Picoides canicapillus). In: del Hoyo, J., Elliott, A., Sargatal, J., Christie, D.A. & de Juana, E. (Eds.), Handbook of the Birds of the World Alive. Lynx Edicions, Barcelona. Avaialble from: https://www.hbw.com/node/56212 (accessed 23 January 2020)
https://doi.org/10.2173/bow.gycwoo1.01
Winkler, H., Gamauf, A., Nittinger, F. & Haring, E. (2014) Relationships of Old World woodpeckers (Aves: Picidae)—new insights and taxonomic implications. Annalen des Naturhistorischen Museums in Wien, Serie B, für Botanik und Zoologie, 116, 69–86.
Wolstenholme, D.R. (1992) Animal mitochondrial DNA: structure and evolution. International Review of Cytology, 141, 173–216.
https://doi.org/10.1016/S0074-7696(08)62066-5
Yukuhiro, K., Sezutsu, H., Itoh, M., Shimizu, K. & Banno, Y. (2002) Significant levels of sequence divergence and gene rearrangements have occurred between the mitochondrial genomes of the wild mulberry silkmoth, Bombyx mandarina, and its close relative, the domesticated silkmoth, Bombyx mori. Molecular Biology and Evolution, 19 (8), 1385–1389.
https://doi.org/10.1093/oxfordjournals.molbev.a004200
Zhou, C., Hao, Y., Ma, J., Zhang, W., Chen, Y., Chen, B. & Yue, B. (2017) The first complete mitogenome of Picumnus innominatus (Aves, Piciformes, Picidae) and phylogenetic inference within the Picidae. Biochemical Systematics and Ecology, 70, 274–282.