Complete mitochondrial genome of the darkling beetle Gonocephalum outreyi (Coleoptera: Tenebrionidae) with phylogenetic implications

Journal of Asia-Pacific Entomology - Tập 21 - Trang 721-730 - 2018
Nan Song1, Hao-Yu Liu2, Xiu-Juan Yang2, Xin-Cheng Zhao1, Ai-Li Lin1
1College of Plant Protection, Henan Agricultural University, Zhengzhou, China
2College of Life Science, Hebei University, Baoding, China

Tài liệu tham khảo

Aalbu, 2006, Where are we at: assessing the current state of tenebrionidae systematics on a global scale (Coleoptera: Tenebrionidae)

Aalbu, 2002, 106. Tenebrionidae Latreille 1802, 463

Allsopp, 1980, The biology of false wireworms and their adults (soil inhabiting Tenebrionidae) (Coleoptera): a review, B. Entomol. Res., 70, 343, 10.1017/S0007485300007628

Arnoldi, 2007, Mitochondrial genome sequence of the Brazilian luminescent click beetle Pyrophorus divergens (Coleoptera: Elateridae): mitochondrial genes utility to investigate the evolutionary history of Coleoptera and its bioluminescence, Gene, 405, 1, 10.1016/j.gene.2007.07.035

Bernt, 2013, MITOS: improved de novo metazoan mitochondrial genome annotation, Mol. Phylogenet. Evol., 69, 313, 10.1016/j.ympev.2012.08.023

Bininda-Emonds, 2005, transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences, BMC Bioinformatics, 6, 156, 10.1186/1471-2105-6-156

Bocak, 2014, Building the Coleoptera tree-of-life for >8000 species: composition of public DNA data and fit with Linnaean classification, Syst. Entomol., 39, 97, 10.1111/syen.12037

Boore, 1999, Survey and summary: animal mitochondrial genomes, Nucleic Acids Res., 27, 1767, 10.1093/nar/27.8.1767

Bouchard, 2005, Synoptic classification of the world Tenebrionidae (Insecta: Coleoptera) with a review of family-group names, Vol. 55, No. 4, 499

Bouchard, 2011, Family-group names in Coleoptera (Insecta), ZooKeys, 88, 1, 10.3897/zookeys.88.807

Cabrera-Brandt, 2015, Phylogenetic analysis of the complete mitogenome sequence of the raspberry weevil, Aegorhinus superciliosus (Coleoptera: Curculionidae), supports monophyly of the tribe Aterpini, Gene, 571, 205, 10.1016/j.gene.2015.06.059

Cameron, 2014, How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research, Syst. Entomol., 39, 400, 10.1111/syen.12071

Cameron, 2014, Insect mitochondrial genomics: implications for evolution and phylogeny, Annu. Rev. Entomol., 59, 95, 10.1146/annurev-ento-011613-162007

Cannone, 2002, The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs, BMC Bioinformatics, 3, 15, 10.1186/1471-2105-3-15

Coates, 2014, Assembly and annotation of full mitochondrial genomes for the corn rootworm species, Diabrotica virgifera virgifera and Diabrotica barberi (Insecta: Coleoptera: Chrysomelidae), using next generation sequence data, Gene, 542, 190, 10.1016/j.gene.2014.03.035

Crampton-Platt, 2015, Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample, Mol. Biol. Evol., 32, 2302, 10.1093/molbev/msv111

Darriba, 2012, JModelTest 2: more models, new heuristics and parallel computing, Nat. Methods, 9, 772, 10.1038/nmeth.2109

Doyen, 1982, Phenetic and cladistic relationships among tenebrionid beetles (Coleoptera), Syst. Entomol., 7, 127, 10.1111/j.1365-3113.1982.tb00129.x

Doyen, 1990, Classification and annotated checklist of the Australian genera of Tenebrionidae (Coleoptera), Invertebr. Taxon., 3, 229, 10.1071/IT9890229

Du, 2016, The complete mitochondrial genome of Epicauta chinensis (Coleoptera: Meloidae) and phylogenetic analysis among Coleopteran insects, Gene, 578, 274, 10.1016/j.gene.2015.12.036

Farris, 1994, Testing significance of incongruence, Cladistics, 10, 315, 10.1111/j.1096-0031.1994.tb00181.x

García-Alcalde, 2012, Qualimap: evaluating next-generation sequencing alignment data, Bioinformatics, 28, 2678, 10.1093/bioinformatics/bts503

Gillespie, 2006, Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements, Insect Mol. Biol., 15, 657, 10.1111/j.1365-2583.2006.00689.x

Gillett, 2014, Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea), Mol. Biol. Evol., 31, 2223, 10.1093/molbev/msu154

Gunter, 2014, Towards a phylogeny of the Tenebrionoidea (Coleoptera), Mol. Phylogenet. Evol., 79, 305, 10.1016/j.ympev.2014.05.028

Hebert, 2003, Biological identifications through DNA barcodes, P Roy. Soc. Lond. B. Biol. Sci., 270, 313, 10.1098/rspb.2002.2218

Hunt, 2007, A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation, Science, 318, 1913, 10.1126/science.1146954

Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010

Kergoat, 2014, Higher level molecular phylogeny of darkling beetles (Coleoptera Tenebrionidae), Syst. Entomol., 39, 486, 10.1111/syen.12065

Kim, 2009, Complete mitochondrial genome sequence of the yellow-spotted long-horned beetle Psacothea hilaris (Coleoptera: Cerambycidae) and phylogenetic analysis among coleopteran insects, Mol. Cells, 27, 429, 10.1007/s10059-009-0064-5

Kuck, 2010, FASconCAT: convenient handling of data matrices, Mol. Phylogenet. Evol., 56, 1115, 10.1016/j.ympev.2010.04.024

Lanfear, 2012, Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses, Mol. Biol. Evol., 29, 1695, 10.1093/molbev/mss020

Lartillot, 2013, PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment, Syst. Biol., 62, 611, 10.1093/sysbio/syt022

Lawrence, 1995, Families and subfamilies of Coleoptera (with selected genera, notes, references and data on family-group names), 779

Lawrence, 2011, Phylogeny of the Coleoptera based on morphological characters of adults and larvae, Ann. Zool., 61, 1, 10.3161/000345411X576725

Li, 2009, Fast and accurate short read alignment with burrows-wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324

Liu, 2014, Complete mitochondrial genome of yellow meal worm (Tenebrio molitor), Zool. Res., 35, 537

Matthews, 2003, Ulomotypus Broun a member of the new subfamily Palorinae, with remarks on Aphtora Bates and Demtrius Broun (Coleoptera, Tenebrionidae), NZ. Entomol., 26, 7

Matthews, E.G., Lawrence, J.F., Bouchard, P., Steiner, W.E., Ślipiński, A.S., 2010. Tenebrionidae Latreille, 1802. Handbook of Zoology. A natural history of the Phyla of the animal kingdom, 574–659. Vol. IV - Arthropoda: Insecta. Part 38. Coleoptera, Beetles, Vol. 2: Systematics (Part 2) (ed. by Leschen R.A.B., Beutel R.G. and Lawrence J.F.), Walter de Gruyter, Berlin.

Mckenna, 2015, The beetle tree of life reveals that Coleoptera survived end-Permian mass extinction to diversify during the Cretaceous terrestrial revolution, Syst. Entomol., 40, 835, 10.1111/syen.12132

Miller, 2010, Creating the CIPRES Science Gateway for inference of large phylogenetic trees, 14

Nie, 2017, The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes, Cladistics, 34, 113, 10.1111/cla.12196

Ouvrard, 2000, 18s rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta: Hemiptera), Mol. Phylogenet. Evol., 16, 403, 10.1006/mpev.2000.0797

Regier, 2010, Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences, Nature, 463, 1079, 10.1038/nature08742

Ronquist, 2012, MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst. Biol., 61, 539, 10.1093/sysbio/sys029

Sheffield, 2009, Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics, Syst. Biol., 58, 381, 10.1093/sysbio/syp037

Simon, 2006, Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA, Annu. Rev. Ecol. Syst., 37, 547

Ślipiński, 2011, Animal biodiversity: an outline of higher-level classification and survey of taxonomic richness, Zootaxa, 3148, 203

Song, 2010, When phylogenetic assumptions are violated base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics, Syst. Entomol., 35, 429, 10.1111/j.1365-3113.2009.00517.x

Song, 2016, All 37 mitochondrial genes of aphid Aphis craccivora obtained from transcriptome sequencing: implications for the evolution of aphids, PLoS One, 11

Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033

Swofford, 2002

Tamura, 2013, MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30, 2725, 10.1093/molbev/mst197

Timmermans, 2010, Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics, Nucleic Acids Res., 38, 10.1093/nar/gkq807

Timmermans, 2016, Family-level sampling of mitochondrial genomes in Coleoptera: compositional heterogeneity and phylogenetics, Genome Biol. Evol., 8, 161, 10.1093/gbe/evv241

Wang, 2016, The complete mitochondrial genome of a medicinal insect Martianus dermestoides (Coleoptera, Tenebrionidae), Mitochondrial DNA A, 27, 1627

Xia, 2013, DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution, Mol. Biol. Evol., 30, 1720, 10.1093/molbev/mst064

Xia, 2003, An index of substitution saturation and its application, Mol. Phylogenet. Evol., 26, 1, 10.1016/S1055-7903(02)00326-3

Xie, 2014, SOAPdenovo-trans: de novo transcriptome assembly with short RNA-Seq reads, Bioinformatics, 30, 1660, 10.1093/bioinformatics/btu077

Zhang, 2015, The mitochondrial genome of Dastarcus helophoroides (Coleoptera: Bothrideridae) and related phylogenetic analyses, Gene, 560, 15, 10.1016/j.gene.2014.12.026

Zhang, 2016, Comparative mitogenomic analysis of species representing six subfamilies in the family Tenebrionidae, Int. J. Mol. Sci., 17, 841, 10.3390/ijms17060841

Zwick, 2012, Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models, PLoS One, 7, 10.1371/journal.pone.0047450

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Journal of Asia-Pacific Entomology

Tập 21

721-730

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