Complete mitochondrial genome of Ampittia dioscorides (Lepidoptera: Hesperiidae) and its phylogenetic analysis

Abstract

The complete mitochondrial genome of Ampittia dioscorides (Lepidoptera: Hesperiidae) was determined. The sequenced genome is a circular molecule of 15313 bp, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an A+ T-rich region. The gene arrangements and transcribing directions are identical to those in most of the reported lepidopteran mitogenomes. The base composition of the whole genome and genes or regions are also similar to those in other lepidopteran species. All the PCGs are initiated by typical ATN codons; the exception being COI, which begins with a CGA codon. Eight genes (ND2, ATPase8, ATPase6, COIII, ND5, ND4L, ND6, and Cytb) end with a TAA stop codon, and two genes (ND1 and ND3) end with TAG. The remaining three genes (COI and COII, which end with TA-, and ND4, which ends with T-) have incomplete stop codons. All tRNAs have the typical clover-leaf structure of mitochondrial tRNAs, with the exception of tRNA^Ser(AGY). On the basis of the concatenated nucleotide and amino acid sequences of the 13 PCGs and wingless gene of 22 butterfly species, maximum parsimony (MP) and Bayesian inference (BI) trees were constructed, respectively. Both MP and BI trees had the same topological structure: ((((Nymphalidae+ Danaidae) + Lycaenidae) + Pieridae) + Papilionidae) + Hesperiidae). The results provide support for Hesperiidae as a superfamily-level taxon.

Keywords

Ampittia dioscorides / mitochondrial genome / phylogeny

References

[1] Altschul S F, Gish W, Miller W, Myers E W, Lipman D J (1990). Basic local alignment search tool. J Mol Biol, 215(3): 403–410

[2] Anderson S, Bankier A T, Barrell B G, de Bruijn M H, Coulson A R, Drouin J, Eperon I C, Nierlich D P, Roe B A, Sanger F, Schreier P H, Smith A J, Staden R, Young I G (1981). Sequence and organization of the human mitochondrial genome. Nature, 290(5806): 457–465

[3] Brower A V Z (2000). Phylogenetic relationships among the Nymphalidae (Lepidoptera) inferred from partial sequences of the wingless gene. Proc Biol Sci, 267(1449): 1201–1211

[4] Campbell D L, Brower A V, Pierce N E (2000). Molecular evolution of the wingless gene and its implications for the phylogenetic placement of the butterfly family Riodinidae (Lepidoptera: papilionoidea). Mol Biol Evol, 17(5): 684–696

[5] Cha S Y, Yoon H J, Lee E M, Yoon M H, Hwang J S, Jin B R, Han Y S, Kim I (2007). The complete nucleotide sequence and gene organization of the mitochondrial genome of the bumblebee, Bombus ignitus (Hymenoptera: Apidae). Gene, 392(1-2): 206–220

[6] Harvey D J (1991). Higher classification of the Nymphalidae[A], Appendix B. The Development and Evolution of Butterfly Wing Patterns (HF Nijhout, ed)[M]. Smithsonian Institution Press, Washington DC, 255–273

[7] Hong M Y, Lee E M, Jo Y H, Park H C, Kim S R, Hwang J S, Jin B R, Kang P D, Kim K G, Han Y S, Kim I (2008). Complete nucleotide sequence and organization of the mitogenome of the silk moth Caligula boisduvalii (Lepidoptera: Saturniidae) and comparison with other lepidopteran insects. Gene, 413(1-2): 49–57

[8] Hsu R, Briscoe A D, Chang B S, Chang W, Pierce N E (2001). Molecular evolution of a long wavelength-sensitive opsin in mimetic Heliconius butterflies (Lepidoptera: Nymphalidae). Biol J Linn Soc Lond, 72(3): 435–449

[9] Jiang S T, Hong G Y, Yu M, Li N, Yang Y, Liu Y Q, Wei Z J (2009). Characterization of the complete mitochondrial genome of the giant silkworm moth, Eriogyna pyretorum (Lepidoptera: Saturniidae). Int J Biol Sci, 5(4): 351–365

[10] Kim M J, Wan X L, Kim K G, Hwang J S, Kim I (2010). Complete nucleotide sequence and organization of the mitogenome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae). Afr J Biotechnol, 9(5): 735–754

[11] Kim M J, Wang A R, Park J S, Kim I (2014). Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera. Gene, 549(1): 97–112

[12] Lavrov D V, Brown W M, Boore J L (2000). A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proc Natl Acad Sci U S A, 97(25): 13738–13742

[13] Lin C P, Danforth B N (2004). How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets. Mol Phylogenet Evol, 30(3): 686–702

[14] Liu Y, Li Y, Pan M, Dai F, Zhu X, Lu C, Xiang Z (2008). The complete mitochondrial genome of the Chinese oak silkmoth, Antheraea pernyi (Lepidoptera: Saturniidae). Acta Biochim Biophys Sin (Shanghai), 40(8): 693–703

[15] Lowe T M, Eddy S R (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res, 25(5): 955–964

[16] Mutanen M, Wahlberg N, Kaila L (2010). Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies. Proc Biol Sci, 277(1695): 2839–2848

[17] Ojala D, Montoya J, Attardi G (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature, 290(5806): 470–474

[18] Peña C, Wahlberg N, Weingartner E, Kodandaramaiah U, Nylin S, Freitas A V J, Brower A V Z (2006). Higher level phylogeny of Satyrinae butterflies (Lepidoptera: Nymphalidae) based on DNA sequence data. Mol Phylogenet Evol, 40(1): 29–49

[19] Regier J C, Cook C, Mitter C, Hussey A (2008). A phylogenetic study of the ‘bombycoid complex’ (Lepidoptera) using five protein-coding nuclear genes, with comments on the problem of macrolepidopteran phylogeny. Syst Entomol, 33(1): 175–189

[20] Silva-Brandão K L, Wahlberg N, Francini R B, Azeredo-Espin A M L, Brown K S Jr, Paluch M, Lees D C, Freitas A V L (2008). Phylogenetic relationships of butterflies of the tribe Acraeini (Lepidoptera, Nymphalidae, Heliconiinae) and the evolution of host plant use. Mol Phylogenet Evol, 46(2): 515–531

[21] Simon C, Frati F, Bekenbach A (1994). Evolution, weighting, and phylogenetic utility of mitochondrialgene sequences and a compilation of conserved polymerase chain reaction primers. Ann Entomol Soc Am, 87(6): 651–701

[22] Singh V K, Mangalam A K, Dwivedi S, Naik S (1998). Primer premier: program for design of degenerate primers from a protein sequence. Biotechniques, 24(2): 318–319

[23] Wahlberg N, Braby M F, Brower A V,de Jong R, Lee M M, Nylin S, Pierce N E, Sperling F A, Vila R, Warren A D, Zakharov E (2005). Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proc Biol Sci, 272: 1577–1586

[24] Warren A D, Ogawa J R, Blower A V Z (2008). Phylogenetic relationships of subfamilies and circumscription of tribes in the family Hesperiidae (Lepidoptera:Hesperioidea). Cladistics, 24(5): 642–676

[25] Warren A D, Ogawa J R, Brower A V (2009). Revised classification of the family Hesperiidae (Lepidoptera: Hesperioidea) based on combined molecular and morphological data. Syst Entomol, 34(3): 467–523

[26] Weller S J, Pashley D P (1995). In search of butterfly origins. Mol Phylogenet Evol, 4(3): 235–246

[27] Xia X, Xie Z (2001). DAMBE: software package for data analysis in molecular biology and evolution. J Hered, 92(4): 371–373

[28] Zhou Z, Huang Y, Shi F (2007). The mitochondrial genome of Ruspolia dubia (Orthoptera: Conocephalidae) contains a short A+T-rich region of 70 bp in length. Genome, 50(9): 855–866

[29] Zou F Z, Hao J S, Huang D Y, Zhang D X, Zhu G P, Zhu C D (2009). Molecular phylogeny of 12 families of the Chinese butterflies based on mitochondrial ND1 and 16S rRNA gene sequences (Lepidoptera: Ditrysia: Rhopalocera). Acta Entomologica Sinica, 52: 191–201

Acknowledgements

The project was supported by the Guangxi Key Laboratory of Rare and Endangered Animal Ecology Research Foundation (16-A-01-07), Guangxi Normal University, China.

Compliance with ethics guidelines

Xin-Min Qin, Xiao-Wen Yang, Li-Xia Hou, and Hui-Min Li declare that they have no conflict of interests. All institutional and national guidelines for the care and use of laboratory animals were followed.

RIGHTS & PERMISSIONS

2016 Higher Education Press and Springer-Verlag Berlin Heidelberg