Interspecific variation in mitochondrial serine transfer RNA (UCN) in Euptychiina butterflies (Lepidoptera: Satyrinae): Structure and alignment

References

• Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. 2007. Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics. 23 13: i19–i28.
   Google Scholar
• Beard CB, Hamm DM, Collins FH. 1993. The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization and comparisons with mitochondrial sequences of other insects. Insect Mol Biol. 2:103–124.
   PubMedGoogle Scholar
• Blum MJ, Bermingham E, Dasmahapatra K. 2003. A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae). Mol Phylogenet Evol. 26:46–55.
   PubMed Web of Science ®Google Scholar
• Braby M, Pierce NE. 2007. Indo-Australian genus Delias Hubner (Lepidoptera: Pieridae): Phylogenetic evidence supports an ‘out-of-Australia’ origin. Syst Entomol. 32:2–25.
   Google Scholar
• Cameron SL, Whiting MF. 2008. The complete mitochondrial genome of the tobacco hornworn, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability with butterflies and moths. Gene. 408:112–123.
   PubMed Web of Science ®Google Scholar
• Cha SY, Yoon HJ, Lee EM, Yoon MH, Hwang JS, Jin BR, Han YS, Kim I. 2007. The complete nucleotide sequence and gene organization of the mitochondrial genome of the bumblebee, Bombus ignitus (Hymenoptera: Apidae). Gene. 392:206–220.
   PubMed Web of Science ®Google Scholar
• Collins FH, Porter CH, Cope SE. 1990. Comparisons or rDNA and mtDNA in the sibling species Anopheles freeborni and A. hermsi. Am J Trop Med Hyg. 42:417–423.
   PubMedGoogle Scholar
• Ding Y, Chan CY, Lawrence CE. 2005. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA. 11:1157–1166.
   PubMed Web of Science ®Google Scholar
• Feng X, Liu D-F, Wang N-X, Zhu C-D, Jiang G-F. 2010. The mitochondrial genome of the butter?y Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses. Mol Biol Rep. 37:3877–3888.
   PubMed Web of Science ®Google Scholar
• Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. 2008. The Vienna RNA Websuite. Nucleic Acids Res. 36:W70–W74.
   PubMed Web of Science ®Google Scholar
• Hall TA. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41:95–98.
   Google Scholar
• Hu J, Zhang D, Hao J, Huang D, Cameron S, Zhu C. 2010. The complete mitochondrial genome of the yellow coaster, Acraea issoria (Lepidoptera: Nymphalidae: Heliconiinae: Acraeini): Sequence, gene organization and unique tRNA translocation event. Mol Biol Rep. 37:3431–3438.
   PubMed Web of Science ®Google Scholar
• Hundsdoerfer AK, Kitching IJ, Wink M. 2005. A molecular phylogeny of the hawkmoth genus Hyles (Lepidoptera: Sphingidae, Macroglossinae). Mol Phylogenet Evol. 35:442–458.
   PubMed Web of Science ®Google Scholar
• Kim I, Lee EM, Seol KY, Yun EY, Lee YB, Hwang JS, Jin BR. 2006. The mitochondrial genome of the Koreana hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). Insect Mol Biol. 15:217–225.
   PubMed Web of Science ®Google Scholar
• Kim MJ, Wan X, Kim K-G, Hwang JS, Kim I. 2010. Complete nucleotide sequence and organization of the mitogenome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae). Afr J Biotechnol. 9:735–754.
   Web of Science ®Google Scholar
• Kumazawa Y, Nishida M. 1993. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J Mol Evol. 37:380–398.
   PubMed Web of Science ®Google Scholar
• Kunte K. 2009. The diversity and evolution of batesian mimicry in Papilio swallowtail butterflies. Evolution. 63:2707–2716.
   PubMed Web of Science ®Google Scholar
• Li X, Ogoh K, Ohba N, Liang X, Ohmiya Y. 2007. Mitochondrial genomes of two luminous beetles, Rhagophthalmus lufengensis and R. ohbai (Arthropoda, Insecta, Coleoptera). Gene. 392:196–205.
   PubMed Web of Science ®Google Scholar
• Liao F, Wang L, Wu S, Li Y-P, Zhao L, Huang G-M, Niu C-J, Liu Y-Q, Li M-G. 2010. The complete mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae). Int J Biol Sci. 6:172–186.
   PubMed Web of Science ®Google Scholar
• Lynch M. 1996. Mutation accumulation in transfer RNAs: Molecular evidence for Muller's ratchet in mitochondrial genomes. Mol Biol Evol. 13:209–220.
   PubMed Web of Science ®Google Scholar
• Marín MA. 2011. Relaciones filogenéticas de Euptychiina (Lepidoptera: Satyrinae) con base en características morfológicas de los adultos, M.Sc. thesis, Universidad Nacional de Colombia, Medellín, Colombia.
   Google Scholar
• Marín MA, López A, Freitas AVL, Uribe SI. 2009. Caracterización molecular de Euptychiina (Lepidoptera: Satyrinae) del norte de la Cordillera Central de los Andes. Rev Colomb Entomol. 35:235–244.
   Web of Science ®Google Scholar
• Masta SE. 2000. Mitochondrial sequence evolution in spiders: Intraspecific variation in tRNAs lacking the TψC arm. Mol Biol Evol. 17:1091–1100.
   PubMed Web of Science ®Google Scholar
• Masta SE, Boore LJ. 2008. Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes. Mol Biol Evol. 25:949–959.
   PubMed Web of Science ®Google Scholar
• Morrison D. 2006. Multiple sequence alignment for phylogenetic purposes. Aust Syst Bot. 19:479–539.
   Web of Science ®Google Scholar
• Mathews DH, Turner DH. 2006. Prediction of RNA secondary structure by free energy minimization. Curr Opin Struc Biol. 16:270–278.
   PubMed Web of Science ®Google Scholar
• Murray DL, Prowell DP. 2005. Molecular phylogenetics and evolutionary history of the neotropical satyrine subtribe Euptychiina (Nymphalidae: Satyrinae). Mol Phylogenet Evol. 34:67–80.
   PubMed Web of Science ®Google Scholar
• Okimoto R, Wolstenholme DR. 1990. A set of tRNAs that lack either the TψC arm or the dihydrouridine arm: Towards a minimal tRNA adaptor. EMBO J. 9:3405–3411.
   PubMedGoogle Scholar
• Oliveira L, Paiva PB, Paiva ACM, Vriend G. 2003. Identification of functionally conserved residues with the use of entropy-variability plots. Proteins. 52:544–552.
   Google Scholar
• Pan MH, Yu QY, Xia YL, Dai FY, Liu YQ, Lu C, Zhang Z, Xiang ZH. 2008. Characterization of mitochondrial genome of Chinese wild mulberry silkworm. Bombyx mandarina (Lepidoptera: Bombycidae). Sci China Ser C. 51:693–701.
   PubMedGoogle Scholar
• Peña C, Nylin S, Freitas AVL, Wahlberg N. 2010. Biogeographic history of the butterfly subtribe Euptychiina (Lepidoptera, Nymphalidae, Satyrinae). Zool Scripta. 39:243–258.
   Web of Science ®Google Scholar
• Pesole G, Gissi C, De Chirico A, Saccone C. 1999. Nucleotide substitution rate of mammalian mitochondrial genomes. J Mol Evol. 48:427–434.
   PubMed Web of Science ®Google Scholar
• Salvato P, Simonato M, Battisti A, Negrisolo E. 2008. The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Genom. 9:331.
   PubMed Web of Science ®Google Scholar
• Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M. 2006. 4SALE – a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics. 7:498.
   PubMed Web of Science ®Google Scholar
• Seibel PN, Müller T, Dandekar T, Wolf M. 2008. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Res Notes. 1:91.
   PubMedGoogle Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731–2739.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res. 22:4673–4680.
   PubMed Web of Science ®Google Scholar
• Vivero RJ, Contreras-Gutiérrez MA, Bejarano EE. 2007. Análisis de la estructura primaria y secundaria del ARN de transferencia mitocondrial para serina en siete especies de Lutzomyia. Biomédica. 27:429–438.
   Google Scholar
• Wolstenholme DR, Macfarlane JL, Okimoto R, Clary DO, Wahleithner JA. 1987. Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Proc Natl Acad Sci USA. 84:1324–1328.
   PubMed Web of Science ®Google Scholar
• Yang F, Du Y, Wang L, Cao J, Yu W. 2011. The complete mitochondrial genome of the leafminer Liriomyza sativae (Diptera: Agromyzidae): Great difference in the A+T-rich region compared to Liriomyza trifolii. Gene. 485:7–15.
   PubMed Web of Science ®Google Scholar
• Yang L, Wei Z-J, Hong G-Y, Jiang S-T, Wen L-P. 2009. The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae). Mol Biol Rep. 36:1441–1449.
   PubMed Web of Science ®Google Scholar