Eur. J. Entomol. 113: 482-488, 2016 | 10.14411/eje.2016.063

The mitochondrial genome of the Mediterranean flour moth, Ephestia kuehniella (Lepidoptera: Pyralidae), and identification of invading mitochondrial sequences (numts) in the W chromosome

Katrin LÄMMERMANN1,3, Heiko VOGEL2, Walther TRAUT3,*
1 Universität zu Lübeck, Institut für Neuro- und Bioinformatik, Ratzeburger Allee 160, D-23538 Lübeck, Germany; e-mail: katrin.laemmermann@hotmail.de
2 Max Planck Institute for Chemical Ecology, Department of Entomology, Hans-Knoell-Strasse 8, D-07745 Jena, Germany; e-mail: hvogel@ice.mpg.de
3 Universität zu Lübeck, Zentrum für Medizinische Strukturbiologie, Institut für Biologie, Ratzeburger Allee 160, D-23538 Lübeck, Germany; e-mail: traut@bio.uni-luebeck.de

The Mediterranean flour moth, Ephestia kuehniella is a widespread pest of stored products and a classical object in experimental biology. In the present study, we determined its complete mitochondrial genome sequence. The genome is circular, consists of 15,327 bp and comprises 13 protein-coding, 2 rRNA- and 22 tRNA-coding genes in an order typical for the Ditrysia clade of the order Lepidoptera. A phylogenetic study of the Lepidoptera based on complete mitochondrial genomes places E. kuehniella correctly in the family Pyralidae and supports major lepidopteran taxa as phylogenetic clades. The W chromosome of E. kuehniella is an exceptionally rich reservoir of originally mitochondrial sequences (numts). Around 0.7% of the W DNA was found to be of mitochondrial origin, 83% of the mitogenome sequence was represented between 1-11 × in the W chromosome. Phylogenetic analysis further revealed that these numts are an evolutionary recent acquisition of the W chromosome.

Keywords: Lepidoptera, Pyralidae, Ephestia kuehniella, mitogenome, Mediterranean flour moth, phylogeny, numts, W chromosome

Received: May 10, 2016; Accepted: July 18, 2016; Published online: September 15, 2016

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References

  1. Bernt M., Braband A., Schierwater B. & Stadler P.F. 2013: Genetic aspects of mitochondrial genome evolution. - Mol. Phylogenet. Evol. 69: 328-338. Go to original source...
  2. Cao Y.-Q., Ma C., Chen J.-Y. & Yang D.-R. 2012: The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera. - BMC Genomics 13: 276. Go to original source...
  3. Dornseifer S. & Sczakiel G. 2013: Computational identification of biologically functional non-hairpin GC-helices in human Argonaute mRNA. - BMC Bioinform. 14: 122, 8 pp. Go to original source...
  4. Felsenstein J. 1973: Maximum-likelihood and minimum steps methods for estimating evolutionary trees from data on discrete characters. - Syst. Zool. 22: 240-249. Go to original source...
  5. Guz N., Kilincer N. & Aksoy S. 2012: Molecular characterization of Ephestia kuehniella (Lepidoptera: Pyralidae) transferrin and its response to parasitoid Venturia canescens (Hymenoptera: Ichneumonidae Gravenhorst). - Insect Mol. Biol. 21: 139-147. Go to original source...
  6. Kobelková A., Závodská R., ©auman I., Bazalová O. & Dole¾el D. 2015: Expression of clock genes period and timeless in the central nervous system of the Mediterranean flour moth, Ephestia kuehniella. - J. Biol. Rhythms 30: 104-116. Go to original source...
  7. Kristensen N.P. & Skalski A.W. 1999: Phylogeny and palaeontology. In Kristensen N.P. (ed.): Handbook of Zoology, Lepidoptera, Moths and Butterflies. Vol. 1: Evolution, Systematics, and Biogeography. Walter de Gruyter, Berlin, New York, pp 7-25.
  8. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R. et al. 2007: Clustal W and Clustal X version 2.0. - Bioinformatics 23: 2947-2948. Go to original source...
  9. Laslett D. & Canbäck B. 2008: ARWEN, a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. - Bioinformatics 24: 172-175. Go to original source...
  10. Liu Q.-N., Chai X.-Y., Bian D.-D., Zhou C.-L. & Tang B.-P. 2016: The complete mitochondrial genome of Plodia interpunctella (Lepidoptera: Pyralidae) and comparison with other Pyraloidea insects. - Genome 59: 37-49. Go to original source...
  11. Lopez J., Yuhki N., Masuda R., Modi W. & O'Brien S.J. 1994: Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. - J. Mol. Evol. 39: 174-190.
  12. Mutanen M., Wahlberg N. & Kaila L. 2010: Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies. - Proc. R. Soc. (B) 277: 2839-2848. Go to original source...
  13. Pamilo P., Viljakainen L. & Vihavainen A. 2007: Exceptionally high density of NUMTs in the honeybee genome. - Mol. Biol. Evol. 24: 1340-1346. Go to original source...
  14. Patzel V., Steidl U., Kronenwett R., Haas R. & Sczakiel G. 1999: A theoretical approach to select effective antisense oligodeoxiribonucleotides at high statistical probability. - Nucl. Acids Res. 27: 4328-4334. Go to original source...
  15. Pytelková J., Hubert J., Lep¹ík M., ©obotník J., ©indelka R., Køí¾ková I., Horn M. & Mare¹ M. 2009: Digestive alpha-amylases of the flour moth Ephestia kuehniella - adaptation to alkaline environment and plant inhibitors. - FEBS J. 276: 3531-3546. Go to original source...
  16. Regier J.C., Mitter C., Zwick A., Bazinet A.L., Cummings M.P., Kawahara A.Y., Sohn J.-C., Zwickl D.J., Cho S., Davis D.R. et al. 2013: A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies). - PLoS ONE 8: e58568. Go to original source...
  17. Rhetsky A. & Nei M. 1993: Theoretical foundation of the minimum-evolution method of phylogenetic inference. - Mol. Biol. Evol. 10: 1073-1095.
  18. Richly E. & Leister D. 2004: NUMTs in sequenced eukaryotic genomes. - Mol. Biol. Evol. 21: 1081-1084. Go to original source...
  19. Robinson R. 1971: Lepidoptera Genetics. Pergamon Press, Oxford, 687 pp.
  20. Rohwedel J., Weichenhan D., Meier C. & Traut W. 1993: Different modes of hypervariability in (GATA)n simple sequence repeat loci. - Insect Mol. Biol. 2: 49-58. Go to original source...
  21. Sahara K., Marec F. & Traut W. 1999: TTAGG telomeric repeats in chromosomes of some insects and other arthropods. - Chromosome Res 7: 449-460. Go to original source...
  22. Saitou N. & Nei M. 1987: The neighbor-joining method: a new method for reconstructing phylogenetic trees. - Mol. Biol. Evol. 4: 406-425.
  23. Sunnucks P. & Hales D.F. 1996: Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). - Mol. Biol. Evol. 13: 510-524. Go to original source...
  24. Tamura K. & Aotsuka T. 1988: Rapid isolation method of animal mitochondrial DNA by the alkaline lysis procedure. - Biochem. Genet. 26: 815-819. Go to original source...
  25. Tamura K., Stecher G., Peterson D., Filipski A. & Kumar S. 2013: MEGA6: Molecular evolutionary genetics analysis version 6.0. - Mol. Biol. Evol. 30: 2725-2729. Go to original source...
  26. Timmermans M.J.T.N., Lees D.C. & Simonsen T.J. 2014: Towards a mitogenomic phylogeny of Lepidoptera. - Mol. Phylogenet. Evol. 79: 169-178. Go to original source...
  27. Traut W., Sahara K., Otto T.D. & Marec F. 1999: Molecular differentiation of sex chromosomes probed by comparative genomic hybridization. - Chromosoma 108: 173-180. Go to original source...
  28. Traut W., Vogel H., Glöckner G., Hartmann E. & Heckel D.G. 2013: High-throughput sequencing of a single chromosome: a moth W chromosome. - Chromosome Res. 21: 491-505. Go to original source...
  29. Wyman S.K., Jansen R.K. & Boore J.L. 2004: Automatic annotation of organellar genomes with DOGMA. - Bioinformatics 20: 3252-3255. Go to original source...