The complete mitogenome of <i>Lamproptera curia</i> (Lepidoptera: Papilionidae) and phylogenetic analyses of Lepidoptera

doi:10.1007/s11515-015-1371-1

Front. Biol.

2015, Vol. 10

Issue (5) : 458-472 https://doi.org/10.1007/s11515-015-1371-1

RESEARCH ARTICLE

The complete mitogenome of Lamproptera curia (Lepidoptera: Papilionidae) and phylogenetic analyses of Lepidoptera

Xin-Min Qin(

),Qing-Xin Guan,Hui-Min Li,Yu Zhang,Yu-Ji Liu,Dan-Ni Guo

Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, China

Download: PDF(1449 KB) HTML
Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks

Abstract

The complete mitochondrial genome sequence of Lamproptera curia was determined in the present study. Our findings showed that the mtDNA of L. curia had a typical organization of insect mitochrondrial DNA − being 15277 base pairs in length, it contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region(CR). The newly determined sequence was used for phylogenetic analyses, together with those of 45 species of Lepidoptera published elsewhere, including sequences of three species of Diptera as outgroups. The phylogenetic trees were constructed using the concatenated amino acid and nucleotide sequences of the 13 protein-coding genes (PCGs) based on the maximum likelihood (ML) and Bayesian inference (BI) methods. Both BI and ML trees revealed a similar topology structure: (((((Bombycoidea+ Geometroidea) + Noctuoide) + Pyraloidea) + (Papilionoidea+ Hesperioidea)) + Tortricoidea). Furthermore, the phylogenetic analyses demonstrated that each of the 16 families belonged to a monophyletic group respectively. The results of molecular phylogeny from the present study were congruent with traditional classification based on morphology but failed to demonstrate the monophyly of Hesperiidae.

Keywords Lamproptera curia phylogeny mitochondrial genome

Corresponding Author(s): Xin-Min Qin

Just Accepted Date: 31 August 2015 Online First Date: 09 October 2015 Issue Date: 30 October 2015

Cite this article:

Xin-Min Qin,Qing-Xin Guan,Hui-Min Li, et al. The complete mitogenome of Lamproptera curia (Lepidoptera: Papilionidae) and phylogenetic analyses of Lepidoptera[J]. Front. Biol., 2015, 10(5): 458-472.

URL:

https://academic.hep.com.cn/fib/EN/10.1007/s11515-015-1371-1
https://academic.hep.com.cn/fib/EN/Y2015/V10/I5/458

Tab.1 List of primers used to amplify and sequence the mitogenome of L. curius

Superfamily/Family	Species	GenBank accession No.
Papilionoidea
	Nymphalidae	Kallima inachus	JN857943
	Acraea issoria	NC_013604
	Apatura ilia	NC_016062
	Apatura metis	NC_015537
	Argynnis hyperbius	NC_015988
	Calinaga davidis	NC_015480
	Hipparchia autonoe	NC_014587
	Sasakia charonda	NC_014224
	Libythea celtis	NC_016724
	Euploea mulciber	NC_016720
	Fabriciana nerippe	NC_016419
	Papilionidae	Lamproptera curius	KJ141168
	Papilio maraho	NC_014055
	Parnassius bremeri	NC_014053
	Teinopalpus aureus	NC_014398
	Troides aeacus	EU625344
	Lycaenidae	Coreana raphaelis	NC_007976
	Protantigius superans	NC_016016
	Spindasis takanonis	NC_016018
	Pieridae	Pieris melete	NC_010568
	Pieris rapae	NC_015895
Hesperioidea
	Hesperiidae	Ctenoptilum vasava	NC_016704
Bombycoidea
	Saturniidae	Antheraea pernyi	NC_004622
		Antheraea yamamai	NC_012739
		Eriogyna pyretorum	NC_012727
		Saturnia boisduvalii	NC_010613
		Samia cynthia ricini	JN215366
	Bombycidae	Bombyx mandarina	NC_003395
		Bombyx mori	NC_002355
	Sphingidae	Manduca sexta	NC_010266
Noctuoide
	Noctuidae	Helicoverpa armigera	NC_014668
		Sesamia inferens	NC_015835
	Notodontidae	Phalera flavescens	NC_016067
		Ochrogaster lunifer	NC_011128
	Arctiidae	Hyphantria cunea	NC_014058
	Lymantriidae	Lymantria dispar	NC_012893
	Pyraloidea
Crambidae	Chilo suppressalis	HQ860290
		Cnaphalocrocis medinalis	NC_015985
		Diatraea saccharalis	NC_013274
		Ostrinia furnacalis	NC_003368
		Ostrinia nubilalis	NC_003367
	Pyralidae	Corcyra cephalonica	NC_016866
Tortricoidea
	Tortricidae	Adoxophyes honmai	NC_008141
		Grapholita molesta	NC_014806
		Spilonota lechriaspis	NC_014294
Geometroidea
	Geometridae	Phthonandria atrilineata	NC_010522
Culicoidea
	Culicidae	Anopheles gambiae	NC_002084
Tephritoidea
	Tephritidae	Bactrocera oleae	NC_005333
Ephydroidea
	Drosophilidae	Drosophila yakuba	NC_001322

Tab.2 list of the complete mitogenome in the phylogenetic analyses

Fig.1 Circular map of the mitochondrial genome of Lamproptera curia. cox1−3: cytochrome oxidase subunit 1−3 genes; atp6, atp 8: ATP synthase subunits 6 and 8 genes; cob: cytochrome oxidase b gene; nad1−6 and nad4L:NADH dehydrogenase subunits 1−6 and 4L. tRNA genes are denoted as one-letter symbol according to the IUPAC-IUB single letter amino acid codes. Gene names that are not underlined indicate the direction of transcription clockwise and with underlines of counter clockwise.

Fig.2 Predicted secondary structures for the 22 tRNA genes of L. curius.

Tab.3 Summary of the mitogenome of L. curius

Fig.3 ML trees based on the nucleotide sequences of the concatenated 13 protein coding genes.

Fig.4 ML trees based on the amino acid sequences of the concatenated 13 protein coding genes.

Fig.5 BI trees based on the nucleotide sequences of the concatenated 13 protein coding genes.

Fig.6 BI trees based on the amino acid sequences of the concatenated 13 protein coding genes.

1	Abascal F, Posada D, Zardoya R (2007). MtArt: a new model of amino acid replacement for arthropoda. Mol Biol Evol, 1: 1–5
2	Ackery P R, De Jong R, Vane-Wright R I (1999). The butterflies: Hedyloidea, Hesperoidea, and Papilionoidea. In: Kristensen NP (Ed.), The butterflies: Hedyloidea, Hesperoidea, and Pilionoidea. De Gruyter, Berlin, 263–300
3	Altschul S F, Gish W, Miller W, Myers E W, Lipman D J (1990). Basic local alignment search tool. J Mol Biol, 3(3): 403–410 https://doi.org/10.1016/S0022-2836(05)80360-2
4	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 https://doi.org/10.1038/290457a0
5	Bae J S, Kim I, Sohn H D, Jin B R (2004). The mitochondrial genome of the firefly, Pyrocoelia rufa: complete DNA sequence, genome organization, and phylogenetic analysis with other insects. Mol Phylogenet Evol, 3(3): 978–985 https://doi.org/10.1016/j.ympev.2004.03.009
6	Boore J L (1999). Animal mitochondrial genomes. Nucleic Acids Res, 8(8): 1767–1780 https://doi.org/10.1093/nar/27.8.1767
7	Clary D O, Wolstenholme D R (1985). The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization and genetic code. J Mol Evol, 22(3): 252–271 https://doi.org/10.1007/BF02099755
8	Clayton D A (1992). Transcription and replication of animal mitochondrial DNA. Int Rev Cytol, 141: 217–232 https://doi.org/10.1016/S0074-7696(08)62067-7
9	Feng X, Liu D F, Wang N X, Zhu C D, Jiang G F (2010). The mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses. Mol Biol Rep, 8(8): 3877–3888 https://doi.org/10.1007/s11033-010-0044-z
10	Flook P K, Rowell C H F, Grellissen G (1995). The sequence organisation, and evolution of the Louocsta migratoria mitochondrial genome. J Mol Evol, 6: 928–941
11	Guindon S, Lethiec F, Duroux P, Gascuel O (2005). PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res, 33(Web Server): W557–W559 https://doi.org/10.1093/nar/gki352
12	Harvey D J (1991). Higher classification of the Nymphalidae [A], Appendix B. In: Nijhout HF. Higher classification of the Nymphalidae. Washington DC: Smithsonian Institution Press, pp 200–273
13	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 https://doi.org/10.1016/j.gene.2008.01.019
14	Horak M (1999). The Tortricoidea. In: Kristensen N P. Lepidoptera: Motha and Butterflies. 1. Evolution,Systematics, and Biogegraphy. Handbook of Zoology Vo1.IV, Part 35: 199–215
15	Hu J, Zhang D X, Hao J S, Huang D Y, Cameron S, Zhu C D (2010). The complete mitochondrial genome of the yellow coaster, Acraea issoria (Lepidoptera: Nymphalidae: Heliconiinae: Acraeini):sequence, gene organization and a unique tRNA translocation event. Mol Biol Rep, 7(7): 3431–3438 https://doi.org/10.1007/s11033-009-9934-3
16	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, 4: 351–365 https://doi.org/10.7150/ijbs.5.351
17	Kawahara A Y, Mignault A A, Regier J C, Kitching I J, Mitter C (2009). Phylogeny and Biogeography of Hawk moths (Lepidoptera: Sphingidae): Evidence from Five Nuclear Genes. PLoS ONE, 5: 1–11
18	Kim M I, Beak J Y, Kim M J (2009). Complete nucleotide sequence and organization of the mitogenome of the red-spotted Apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) and comparison with other lepidopteran insects. Mol Cell, 4(4): 347–363 https://doi.org/10.1007/s10059-009-0129-5
19	Kim M J, Kang A R, Jeong H C, Kim K G, Kim I (2011). Reconstructing intraordinal relationships in Lepidoptera using mitochondrial genome data with the description of two newly sequenced lycaenids, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae). Mol Phy Evol, 2(2): 436–445 https://doi.org/10.1016/j.ympev.2011.07.013
20	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, 5: 735–754
21	Kristensen N P (1976). Remarks on the family-level phylogeny of butterflies (Insecta Lepidoptera, Rhopalocera). Zeit Zool Syst Evol Forsch, 14(1): 25–33 https://doi.org/10.1111/j.1439-0469.1976.tb00515.x
22	Kristensen N P (1999). 11 Evolution, Systematics, and Biogeography, Vol IV. In: Kristensen NP. Lepidoptera: Moths and Butterflies. Berlin and New York: DeGruyter, pp: 491.
23	Kristensen N P, Skalski A W (1999). Phylogeny and palaeontology. In: Kristensen N P (Ed.), Handbuch der Zoologie, vol. IV, Arthropoda: Insecta, Part 35, Lepidoptera, Moths and Butterflies, vol. 1: Evolution, Systematics, and Biogeography. Walter de Gruyter, Berlin & New York, pp. 7–25
24	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 USA, 25(25): 13738–13742 https://doi.org/10.1073/pnas.250402997
25	Lee E S, Shin K S, Kim M S, Park H, Cho S, Kim C B (2006). The mitochondrial genome of the smaller tea tortrix Adoxophyes honmai (Lepidoptera: Tortricidse). Gene, 373: 52–57 https://doi.org/10.1016/j.gene.2006.01.003
26	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 mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae). Int J Biol Sci, 2: 172–186 https://doi.org/10.7150/ijbs.6.172
27	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), 8(8): 693–703 https://doi.org/10.1093/abbs/40.8.693
28	Lowe T M, Eddy S R (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res, 5(5): 955–964 https://doi.org/10.1093/nar/25.5.0955
29	Minet J (1991). Tentative Reconstruction of the ditrysian phylogeny (Lepidiptera, Gloassata). Entomol Scand, 1(1): 69–95 https://doi.org/10.1163/187631291X00327
30	Munroe E, Solis M A (1999). The Pyraloidea. In: Kristensen NP. Lepidoptera: Moths and Butterflies. I. Evolution, Systematics, and Biogeography. Handbook of Zoology, 35: 233–256(Vol IV. In: Kristensen NP. Lepidoptera: Moths and Butterflies. Berlin and New York: DeGruyter, pp: 233–256
31	Mutanen M, Wahlerg N, Kaila L (2010). Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies. Proc Biol Sci, 277(1695): 2839–2848 https://doi.org/10.1098/rspb.2010.0392
32	Nielsen E S (1989) Phylogeny of major lepidopteran groups. In: (eds) The Hierarchy of Life. Amsterdam, Elsevier. pp. 281–294
33	Ojala D, Montoya J, Attardi G (1981). tRNA punctuation model of RNA proeessing in Human mitochondria. Nature, 290(5806): 470–474 https://doi.org/10.1038/290470a0
34	Razowski J (1976). Phylogeny and system of Tortricidae (Lepidoptera). Acta zool Cracov, 5: 73–120
35	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 https://doi.org/10.1111/j.1365-3113.2007.00409.x
36	Regier J C, Zwick A, Cummings M P, Kawahara A, Cho S, Weller S, Roe A, Baixeras J, Brown J W, Parr C, Davis D R, Epstein M, Hallwachs W, Hausmann A, Janzen D H, Kitching I J, Solis M A, Yen S H, Bazinet A L, Mitter C (2009). Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol Biol, 9(1): 280 https://doi.org/10.1186/1471-2148-9-280
37	Ronquist F, Huelsenbeck J P (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 12(12): 1572–1574 https://doi.org/10.1093/bioinformatics/btg180
38	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, 6(6): 651–701 https://doi.org/10.1093/aesa/87.6.651
39	Singh V K, Mangalam A K, Dwivedi S, Naik S (1998). Primer premier:Program for design of degenerate primers from a protein sequence. Biotechniques, 2: 318–319
40	Smart P (1989). The illustrated encyclopedia of the butterfly world (New York, USA: Chartwell Books
41	Thao M L, Baumann L, Baumann P(2004). Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evol Biol, 4: 25–37
42	Wahlberg N, Braby M F, Brower A V Z, de Jong R, Lee M M, Nylin S, Pierce N E, Sperling F A H, 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(1572): 1577–1586 https://doi.org/10.1098/rspb.2005.3124
43	Weller S J, Pashely D P (1995). In search of butterfly origins. Mol Phylogenet Evol, 3(3): 235–246 https://doi.org/10.1006/mpev.1995.1022
44	Wolstenholme D R (1992). Animal mitochondrial DNA: structure and evolution. Int Rev Cytol, 141: 173–216 https://doi.org/10.1016/S0074-7696(08)62066-5
45	Xia X, Xie Z (2001). DAMBE: Data analysis in molecular biology and evolution. J Hered, 4(4): 371–373 https://doi.org/10.1093/jhered/92.4.371
46	Yang Z, Rannala B (1997). Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol Biol Evol, 7(7): 717–724 https://doi.org/10.1093/oxfordjournals.molbev.a025811
47	Yin W Y, Song D X, Yang X K (2008). Study on phylogeny of the Hexapoda (Insect). Beijing, Science Press, pp:193–194
48	Zhou Z J, Huang Y, Shi F M (2007). The mitochondrial genome of the Ruspolia dubia (Orthoptera: Conocephalidae): a short A+T-rich region with 70 bp in length Genome. Genome, 50(9): 855–866 https://doi.org/10.1139/G07-057

[1]	Xin-Min Qin,Xiao-Wen Yang,Li-Xia Hou,Hui-Min Li. *Complete mitochondrial genome of Ampittia dioscorides* (Lepidoptera: Hesperiidae) and its phylogenetic analysis**[J]. Front. Biol., 2017, 12(1): 71-81.
[2]	P. CHELLAPANDI. Molecular evolution of methanogens based on their metabolic facets[J]. Front Biol, 2011, 6(6): 490-503.
[3]	XU Xiaohong, WU Min, ZHANG Huibin, LIU Zhihu. Genetic analysis of the gene in halophilic archaea isolated from Xinjiang region, China[J]. Front. Biol., 2008, 3(4): 392-396.
[4]	ZHU Min, GAI Zhikun. Phylogenetic relationships of Galeaspids (Agnatha)[J]. Front. Biol., 2007, 2(2): 151-169.
[5]	MU Linchun, WANG Li, YAO Li, HAO Bingqing, LUO Qin. Application of pet G-trn P sequence to systematic study of Chinese Cupressus species[J]. Front. Biol., 2006, 1(4): 349-352.
[6]	Xu Xiaohong, Wu Min, Cao Yi, Wu Yuehong, Zhang Ting. Isolation and Phylogenetic Analysis of Halophilic Archaeon AJ6[J]. Front. Biol., 2006, 1(1): 29-34.

Viewed

Full text

Abstract

Cited

Shared

Discussed