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Description of new mitochondrial genomes (Spodoptera litura, Noctuoidea and Cnaphalocrocis medinalis, Pyraloidea) and phylogenetic reconstruction of Lepidoptera with the comment on optimization schemes.
Mol Biol Rep. 2013 Nov; 40(11):6333-49.MB

Abstract

We newly sequenced mitochondrial genomes of Spodoptera litura and Cnaphalocrocis medinalis belonging to Lepidoptera to obtain further insight into mitochondrial genome evolution in this group and investigated the influence of optimal strategies on phylogenetic reconstruction of Lepidoptera. Estimation of p-distances of each mitochondrial gene for available taxonomic levels has shown the highest value in ND6, whereas the lowest values in COI and COII at the nucleotide level, suggesting different utility of each gene for different hierarchical group when individual genes are utilized for phylogenetic analysis. Phylogenetic analyses mainly yielded the relationships (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea), evidencing the polyphyly of Macrolepidoptera. The Noctuoidea concordantly recovered the familial relationships (((Arctiidae + Lymantriidae) + Noctuidae) + Notodontidae). The tests of optimality strategies, such as exclusion of third codon positions, inclusion of rRNA and tRNA genes, data partitioning, RY recoding approach, and recoding nucleotides into amino acids suggested that the majority of the strategies did not substantially alter phylogenetic topologies or nodal supports, except for the sister relationship between Lycaenidae and Pieridae only in the amino acid dataset, which was in contrast to the sister relationship between Lycaenidae and Nymphalidae in Papilionoidea in the remaining datasets.

Authors+Show Affiliations

College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, Republic of Korea.No affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24057247

Citation

Wan, Xinlong, et al. "Description of New Mitochondrial Genomes (Spodoptera Litura, Noctuoidea and Cnaphalocrocis Medinalis, Pyraloidea) and Phylogenetic Reconstruction of Lepidoptera With the Comment On Optimization Schemes." Molecular Biology Reports, vol. 40, no. 11, 2013, pp. 6333-49.
Wan X, Kim MJ, Kim I. Description of new mitochondrial genomes (Spodoptera litura, Noctuoidea and Cnaphalocrocis medinalis, Pyraloidea) and phylogenetic reconstruction of Lepidoptera with the comment on optimization schemes. Mol Biol Rep. 2013;40(11):6333-49.
Wan, X., Kim, M. J., & Kim, I. (2013). Description of new mitochondrial genomes (Spodoptera litura, Noctuoidea and Cnaphalocrocis medinalis, Pyraloidea) and phylogenetic reconstruction of Lepidoptera with the comment on optimization schemes. Molecular Biology Reports, 40(11), 6333-49. https://doi.org/10.1007/s11033-013-2748-3
Wan X, Kim MJ, Kim I. Description of New Mitochondrial Genomes (Spodoptera Litura, Noctuoidea and Cnaphalocrocis Medinalis, Pyraloidea) and Phylogenetic Reconstruction of Lepidoptera With the Comment On Optimization Schemes. Mol Biol Rep. 2013;40(11):6333-49. PubMed PMID: 24057247.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Description of new mitochondrial genomes (Spodoptera litura, Noctuoidea and Cnaphalocrocis medinalis, Pyraloidea) and phylogenetic reconstruction of Lepidoptera with the comment on optimization schemes. AU - Wan,Xinlong, AU - Kim,Min Jee, AU - Kim,Iksoo, Y1 - 2013/09/22/ PY - 2012/11/21/received PY - 2013/09/14/accepted PY - 2013/9/24/entrez PY - 2013/9/24/pubmed PY - 2014/6/12/medline SP - 6333 EP - 49 JF - Molecular biology reports JO - Mol Biol Rep VL - 40 IS - 11 N2 - We newly sequenced mitochondrial genomes of Spodoptera litura and Cnaphalocrocis medinalis belonging to Lepidoptera to obtain further insight into mitochondrial genome evolution in this group and investigated the influence of optimal strategies on phylogenetic reconstruction of Lepidoptera. Estimation of p-distances of each mitochondrial gene for available taxonomic levels has shown the highest value in ND6, whereas the lowest values in COI and COII at the nucleotide level, suggesting different utility of each gene for different hierarchical group when individual genes are utilized for phylogenetic analysis. Phylogenetic analyses mainly yielded the relationships (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea), evidencing the polyphyly of Macrolepidoptera. The Noctuoidea concordantly recovered the familial relationships (((Arctiidae + Lymantriidae) + Noctuidae) + Notodontidae). The tests of optimality strategies, such as exclusion of third codon positions, inclusion of rRNA and tRNA genes, data partitioning, RY recoding approach, and recoding nucleotides into amino acids suggested that the majority of the strategies did not substantially alter phylogenetic topologies or nodal supports, except for the sister relationship between Lycaenidae and Pieridae only in the amino acid dataset, which was in contrast to the sister relationship between Lycaenidae and Nymphalidae in Papilionoidea in the remaining datasets. SN - 1573-4978 UR - https://www.unboundmedicine.com/medline/citation/24057247/Description_of_new_mitochondrial_genomes__Spodoptera_litura_Noctuoidea_and_Cnaphalocrocis_medinalis_Pyraloidea__and_phylogenetic_reconstruction_of_Lepidoptera_with_the_comment_on_optimization_schemes_ L2 - https://doi.org/10.1007/s11033-013-2748-3 DB - PRIME DP - Unbound Medicine ER -