Abstract
Acronicta rumicis Linnaeus, 1758 is a notorious lepidopteran pest species that feed on economically impotant plants, including pears, apples and peaches. The outbreak of this pest can cause severe financial losses and threatens food security. Herein, we sequenced and annotated the entire mitochondrial genome (mitogenome) of A. rumicis. The A. rumicis mitogenome was 15,384 bp in size, containing 37 genes (13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs)) usually found in lepidopteran mitogenomes. The mitogenome’s nucleotide composition was highly biased towards using A and T, with positive AT skew and negative GC skew. All PCGs were initiated by typical ATN codons, except for the cox1, which was initiated by the CGA codon. The secondary structure of trnS1 lacked the common dihydrouridine (DHU) arm and replaced by a single loop. The seven bp overlapping region ‘ATGATAA’ located between atp6 and atp8, and the spacer region between trnS2 and nad1 contained an ‘ATACTAA’ motif, which are common in other sequenced lepidopterans. The A + T rich region was 370 bp and included a ‘ATAGA’ motif followed by a 19 bp poly-T stretch and a (AT)10 repeats. The phylogenetic analyses using the Maximum Likelihood (ML) and Bayesian Inference (BI) methods supported A. rumicis belonging to the subfamily Acronictinae. Furthermore, this study clarified a novel and monophyly relationship among Noctuidae with mitogenome data.
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References
Agunbiade TA, Coates BS, Sun W et al (2017) Comparison of the mitochondrial genomes of the old and new world strains of the legume pod borer, Maruca vitrata (Lepidoptera: Crambidae). Int J Trop Insect Sci 37(3):125–136. https://doi.org/10.1017/S1742758417000157
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580. https://doi.org/10.1093/nar/27.2.573
Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780. https://doi.org/10.1093/nar/27.8.1767
Chen YX (1999) Fauna Sinica: Vol. 16. Insecta, Lepidoptera, Noctuidae (Chinese edition). Science Press, Beijing
Feng X, Liu DF, Wang NX et al (2010) The mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses. Mol Biol Rep 37:3877–3888. https://doi.org/10.1007/s11033-010-0044-z
Fibiger M, Lafontaine JD (2005) A review of the higher classification of the Noctuoidea (Lepidoptera) with special reference to the Holarctic fauna. Esperiana 11:7–92
Huang Y, Liu Y, Zhu XY et al (2019) Comparative mitochondrial genome analysis of Grammodes geometrica and other noctuid insects reveals conserved mitochondrial genome organization and phylogeny. Int J Biol Macromol 125:1257–1265. https://doi.org/10.1016/j.ijbiomac.2018.09.104
Kitching IJ, Rawlins JE (1998) The Noctuoidea. Walter de Gruyter, New York
Krzywinski J, Grushko OG, Besansky NJ (2006) Analysis of the complete mitochondrial DNA from Anopheles funestus: an improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. Mol Phylogenet Evol 39:417–423. https://doi.org/10.1016/j.ympev.2006.01.006
Larkin MA, Blackshields G, Brown NP et al (2007) Clustal w and clustal x version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404
Lavrov DV, Brown WM, Boore JL (2000) A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proc Natl Acad Sci U S A 97:13738–13742. https://doi.org/10.1073/pnas.250402997
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. https://doi.org/10.1093/nar/25.5.955
Lu HF, Su TJ, Luo AR et al (2013) Characterization of the complete mitochondrion genome of diurnal moth Amata emma(Butler) (Lepidoptera: Erebidae) and its phylogenetic implications. PLoS One 8:e72410. https://doi.org/10.1371/journal.pone.0072410
Lv C, Li Q, Kong L (2018) Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae. PLoS One 13:e0196466. https://doi.org/10.1371/journal.pone.0196466
Minet J, Barbut J, Lalanne-Cassou B (2012) Les noctuelles: classification et clef de détermination des familles (Lepidoptera: Noctuoidea). Alexanor 25:131–151
Mitchell A, Cho S, Regier JC et al (1997) Phylogenetic utility of elongation factor-1 alpha in noctuoidea (Insecta: Lepidoptera): the limits of synonymous substitution. Mol Biol Evol 14(4):381–390. https://doi.org/10.1093/oxfordjournals.molbev.a025774
Mitchell A, Mitter C, Regier JC (2006) Systematics and evolution of the cutworm moths (Lepidoptera: Noctuidae): evidence from two protein-coding nuclear genes. Syst Entomol 31(1):21–46. https://doi.org/10.1111/j.1365-3113.2005.00306.x
Moritz C, Brown WM (1987) Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards. Proc Natl Acad Sci U S A 84:7183. https://doi.org/10.1073/pnas.84.20.7183
Nijman V, Aliabadian M (2013) DNA barcoding as a tool for elucidating species delineation in wide-ranging species as illustrated by owls (Tytonidae and Strigidae). Zool Sci 30(11):1005–1009. https://doi.org/10.2108/zsj.30.1005
Pan MH, Yu QY, Xia YL et al (2008) Characterization of mitochondrial genome of Chinese wild mulberry silkworm, Bomyx mandarina (Lepidoptera: Bombycidae). Science in China Serie C 51:693–701. https://doi.org/10.1007/s11427-008-0097-6
Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41(3):353–358. https://doi.org/10.1007/BF00186547
Regier JC, Zwick A, Cummings MP et al (2009) Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol Biol 9:280–300. https://doi.org/10.1186/1471-2148-9-280
Regier JC, Mitter C, Mitter K et al (2017) Further progress on the phylogeny of Noctuoidea (Insecta: Lepidoptera) using an expanded gene sample. Syst Entomol 42(1):82–93. https://doi.org/10.1111/syen.12199
Simon C, Frati F, Beckenbach A et al (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann Entomol Soc Am 87:651–701. https://doi.org/10.1093/aesa/87.6.651
Sun YX, Wang L, Wei GQ et al (2016) Characterization of the complete mitochondrial genome of Leucoma salicis (Lepidoptera: Lymantriidae) and comparison with other lepidopteran insects. Sci Rep 6:39153. https://doi.org/10.1038/srep39153
Sun Y, Chen C, Gao J et al (2017) Comparative mitochondrial genome analysis of Daphnis nerii and other lepidopteran insects reveals conserved mitochondrial genome organization and phylogenetic relationships. PLoS One 12:e0178773. https://doi.org/10.1371/journal.pone.0178773
Tamura K, Peterson D, Peterson N et al (2011) Mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. https://doi.org/10.1093/molbev/msr121
Trifinopoulos J, Nguyen LT, von Haeseler A et al (2016) W-IQ-TREE: a fast-online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 44(W1):W232–W235. https://doi.org/10.1093/nar/gkw256
Wang H, Wahlberg N, Holloway JD et al (2015) Molecular phylogeny of Lymantriinae (Lepidoptera, Noctuoidea, Erebidae) inferred from eight gene regions. Cladistics 31:579–592. https://doi.org/10.1111/cla.12108
Wilson AC, Cann RL, Carr SM et al (2010) Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linn Soc 26:375–400. https://doi.org/10.1111/j.1095-8312.1985.tb02048.x
Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 141:173–216. https://doi.org/10.1016/s0074-7696(08)62066-5
Yang L, Wei ZJ, Hong GY et al (2009) The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae). Mol Biol Rep 36:1441–1449. https://doi.org/10.1007/s11033-008-9334-0
Yang M, Song L, Mao J et al (2018) Complete mitochondrial genome of the soybean leaffolder, Omiodes indicata, (Lepidoptera: Pyraloidea: Crambidae), and phylogenetic analysis for Pyraloidea. Int J Biol Macromol 115:53–60. https://doi.org/10.1016/j.ijbiomac.2018.03.041
Yang ZH, Yang TT, Liu Y et al (2019) The complete mitochondrial genome of Sinna extrema (Lepidoptera: Nolidae) and its implications for the phylogenetic relationships of Noctuoidea species. Int J Biol Macromol 15(137):317–326. https://doi.org/10.1016/j.ijbiomac.2019.06.238
Yin JA, Hong GY, Wang AM et al (2010) Mitochondrial genome of the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) and comparison with other lepidopterans. Mitochondrial DNA 21:160–169. https://doi.org/10.3109/19401736.2010.503242
Zahiri R, Kitching IJ, Lafontaine JD et al (2011) A new molecular phylogeny offers hope for a stable family level classification of the Noctuoidea (Lepidoptera). Zool Scr 40:158–173. https://doi.org/10.1111/j.1463-6409.2010.00459.x
Zahiri R, Holloway JD, Kitching IJ et al (2012) Molecular phylogenetics of Erebidae (Lepidoptera, Noctuoidea). Syst Entomol 37:102–124. https://doi.org/10.1111/j.1365-3113.2011.00607.x
Zhang BC (1994) Index of economically important Lepidoptera. CAB International, Wallingford
Zhang DX, Hewitt GM (1997) Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies. Biochem Syst Ecol 25:99–120. https://doi.org/10.1016/S0305-1978(96)00042-7
Zhang HL, Zeng HH, Huang Y et al (2013) The complete mitochondrial genomes of three grasshoppers, Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis (Orthoptera: Pamphagidae). Gene 517:89–98. https://doi.org/10.1016/j.gene.2012.12.080
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This study was supported by the Youth Project of Anhui Natural Science Foundation (1908085QC94), General Project of Anhui Natural Science Foundation (1908085MC86) and General Program of Anhui Collage Natural Science Research Projects (KJ2020B22).
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Chen, C., Li, J., Ding, W. et al. First complete mitochondrial genome of Acronictinae (Lepidoptera: Noctuidae): genome description and its phylogenetic implications. Biologia 77, 93–103 (2022). https://doi.org/10.1007/s11756-021-00894-8
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DOI: https://doi.org/10.1007/s11756-021-00894-8