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      New Mitogenomes of Two Chinese Stag Beetles (Coleoptera, Lucanidae) and Their Implications for Systematics

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          Abstract

          Although conspicuous and well-studied, stag beetles have been slow to join the genomic era. In this study, mitochondrial genomes of two stag beetles, Sinodendron yunnanense and Prosopocoilus confucius, are sequenced for the first time. Both of their genomes consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. The mitogenome of S. yunnanense was 16,921 bp in length, and P. confucius was 16,951 bp. The location of the gene trnL( UUR), between the A + T–rich and control region in S. yunnanense, is the first observed in Lucanidae. In P. confucius, an unexpected noncoding region of 580 bp was discovered. Maximum likelihood and Bayesian inference on the 13 mitochondrial PCGs were used to infer the phylogenetic relationships among 12 representative stag beetles and three scarab beetles. The topology of the two phylogenetic trees was almost identical: S. yunnanense was recovered as the most basal Lucanid, and the genus Prosopocoilus was polyphyletic due to P. gracilis being recovered sister to the genera Dorcus and Hemisodorcus. The phylogenetic results, genetic distances and mitogenomic characteristics call into question the cohesion of the genus Prosopocoilus. The genetic resources and findings herein attempts to redress understudied systematics and mitogenomics of the stag beetles.

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          Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences.

          Mitochondrial DNA (mtDNA) sequences are comonly used for inferring phylogenetic relationships. However, the strand-specific bias in the nucleotide composition of the mtDNA, which is thought to reflect assymetric mutational constraints, combined with the important compositional heterogeneity among taxa, are known to be highly problematic for phylogenetic analyses. Here, nucleotide composition was compared across 49 species of Metazoa (34 arthropods, 2 annelids, 2 molluscs, and 11 deuterosomes), and analyzed for a mtDNA fragment including six protein-coding genes, i.e., atp6, atp8, cox1, cox2, cox3, and nad2. The analyses show that most metazoan species present a clear strand assymetry, where one strand is biased in favor of A and C, whereas the other strand has reverse bias, i.e. in favor of T and G. the origin of this strand bias can be related to assymetric mutational constraints involving deaminations of A and C nucleotides during the replication and/or transcription processes. The analyses reveal that six unrelated genera are characterized by a reversal of the usual strand bias, i.e., Argiope (Araneae), Euscorpius (Scorpiones), Tigrioupus (Maxillopoda), Branchiostoma (Cephalochordata) Florometra (Echinodermata), and Katharina (Mollusca). It is proposed that assymetric mutational constraints have been independantly reversed in these six genera, through an inversion of the control region, i.e., the region that contains most regulatory elements for replication and transcription of the mtDNA. We show that reversals of assymetric mutational constraints have dramatic consequences on the phylogenetic analyses, as taxa characterized by reverse strand bias tend to group together due to long-branch attraction artifacts. We propose a new method for limiting this specific problem in tree reconstruction under the Bayesian approach. We apply our method to deal with the question of phylogenetic relationships of the major lineages of Arthropoda, This new approach provides a better congruence with nuclear analyses based on mtDNA sequences, our data suggest that Chelicerata, Crustacea, Myriapoda, Pancrustacea, and Paradoxopoda are monophyletic.
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            The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths.

            The entire mitochondrial genome of the tobacco hornworm, Manduca sexta (Lepidoptera: Spinghidae) was sequenced -- a circular molecular 15516 bp in size. The arrangement of the protein coding genes (PCGs) was the same as that found in the ancestral insect, however Manduca possessed the derived tRNA arrangement of CR-M-I-Q which has been found in all Lepidoptera sequenced to date. Additionally, Manduca, like all lepidopteran mt genomes, has numerous large intergenic spacer regions and microsatellite-like repeat regions. Nucleotide composition is highly A+T biased, and the lepidopterans have the second most biased nucleotide composition of the insect orders after Hymenoptera. Secondary structural features of the PCGs identified in other Lepidoptera were present but highly modified by the presence of microsatellite-like repeat regions which may significantly alter their function in the post-transcriptional modification of pre-mRNAs. Secondary structure models of the ribosomal RNA genes of Manduca are presented and are similar to those proposed for other insect orders. Conserved regions were identified within non-translated spacer regions which correspond to sites for the origin and termination of replication and transcription. Comparisons of gene variability across the order suggest that the mitochondrial genes most frequently used in phylogenetic analysis of the Lepidoptera, cox1 and cox2, are amongst the least variable genes in the genome and phylogenetic resolution could be improved by using alternative, higher variability genes such as nad2, nad3, nad4 and nad5.
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              How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research

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                Author and article information

                Journal
                J Insect Sci
                J. Insect Sci
                jis
                Journal of Insect Science
                Oxford University Press
                1536-2442
                March 2017
                21 April 2017
                21 April 2017
                : 17
                : 2
                : 63
                Affiliations
                [1 ]Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, P. R. China ( 1056955062@ 123456qq.com ; 1406971729@ 123456qq.com ; wanxia@ 123456ahu.edu.cn )
                [2 ]Department of Entomology, China Agricultural University, West Campus, 2 Yuanmingyuan West Rd., Beijing 100193, P. R. China ( 812532519@ 123456qq.com )
                [3 ]Department of Zoology and Developmental Biology, School of Life Sciences, Lanzhou University, 222 Tianshui South Rd., Lanzhou 730000, P. R. China ( 58032831@ 123456qq.com ),
                Author notes
                [4 ]Corresponding author, e-mail: wanxia@ 123456ahu.edu.cn

                Subject Editor: Yoonseong Park

                Article
                iex041
                10.1093/jisesa/iex041
                5469381
                9629645e-95f7-4e22-9332-4daa8d0b26de
                © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                : 22 October 2016
                Page count
                Pages: 9
                Categories
                Research Article

                Entomology
                mitogenomes,gene rearrangement,noncoding region,chinese stag beetles,phylogenomics
                Entomology
                mitogenomes, gene rearrangement, noncoding region, chinese stag beetles, phylogenomics

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