Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea)

Molecular Biology and Evolution

Volumn 31, Issue 8, 2014, Pages 2223-2237

  Gillett, Conrad P D T ^a,b   Crampton Platt, Alex ^a,c   Timmermans, Martijn J T N ^a,d   Jordal, Bjarte H ^e   Emerson, Brent C ^b,f   Vogler, Alfried P ^a,d  

^a DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^b UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d IMPERIAL COLLEGE LONDON   (United Kingdom)

^e UNIVERSITY OF BERGEN   (Norway)

^f INSTITUTO DE PRODUCTOS NATURALES Y AGROBIOLOGÍA   (Spain)

Author keywords

genomics; MiSeq; mitochondria; next generation sequencing; phylogenetics; wood boring

Indexed keywords

GENOMIC DNA; DNA;

ARTICLE; BEETLE; DNA EXTRACTION; DNA LIBRARY; GENE SEQUENCE; GENOME ANALYSIS; MITOCHONDRIAL GENOME; MOLECULAR PHYLOGENY; MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; TAXON; WEEVIL; ANIMAL; BIOLOGICAL MODEL; CLASSIFICATION; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; INSECT GENOME; MOLECULAR EVOLUTION; PHYLOGENY; PROCEDURES;

ANIMALS; DNA; EVOLUTION, MOLECULAR; GENOME, INSECT; GENOME, MITOCHONDRIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA; WEEVILS;

EID: 84905020686     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu154     Document Type: Article

References (53)

1. Alonso-Zarazaga MA, Lyal CHC. 1999. A world catalogue of families and genera of Curculionoidea (Insecta: Coleoptera) (excepting Scolytidae and Platypodidae). Barcelona: Entomopraxis
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410
3. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. Advance Access published April 1, 2014, doi: 10. 1093/bioinformatics/btu170
4. Botero-Castro F, Tilak MK, Justy F, Catzeflis F, Delsuc F, Douzery EJP. 2013. Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae). Mol Phylogenet Evol. 69: 728-739
5. Bouchard P, Bousquet Y, Davies AE, Alonso-Zarazaga MA, Lawrence JF, Lyal CHC, Newton AF, Reid CAM, Schmitt M, Slipinski SA, et al. 2011. Family-group names in Coleoptera (Insecta). Zookeys 88: 1-972
6. Bernt M, Bleidorn C, Braband A, Dambach J, Donath A, Fritzsch G, Golombek A, Hadrys H, Jühling F, Meusemann K, et al. 2013. A comprehensive analysis of bilateran mitochondrial genomes and phylogeny. Mol Phylogenet Evol. 69:352-364
7. Cameron SL. 2014. Insect mitochondrial genomics: Implications for evolution and phylogeny. Annu Rev Entomol. 59:95-117
8. Cameron SL, Lo N, Bourguignon T, Svenson GJ, Evans TA. 2012. A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): Robust support for interfamilial relationships and molecular synapomorphies define major clades. Mol Phylogenet Evol. 65: 163-173
9. Castoe TA, Sasa MM, Parkinson C. 2005. Modeling nucleotide evolution at the mesoscale: The phylogeny of the neotropical pitvipers of the Porthidium group (Viperidae: Crotalinae). Mol Phylogenet Evol. 37: 881-898
10. Crowson RA. 1955. The natural classification of the families of Coleoptera. London: Nathaniel Lloyd & C.o.
11. Curole JP, Kocher TD. 1999. Mitogenomics: Digging deeper with complete mitochondrial genomes. Trends Ecol Evol. 14:394-398
12. Eddy S, Durbin R. 1994. RNA sequence analysis using covariance models. Nucleic Acids Res. 22:2079-2088
13. Finstermeier K, Zinner D, Brameier M, Meyer M, Kreuz E, Hofreiter M, Roos C. 2013. A mitogenomic phylogeny of living primates. PLoS One 8:e69504
14. Foster PG. 2004. Modeling compositional heterogeneity. Syst Biol. 53: 485-495
15. Franz NM, Engel MS. 2010. Can higher-level phylogenies of weevils explain their evolutionary success? A critical review. Syst Entomol. 35: 597-606
16. Funk DJ, Omland KE. 2003. Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst. 34:397-423
17. Haran J, Timmermans MJTN, Vogler AP. 2013. Mitogenome sequences stabilize the phylogenetics of weevils (Curculionoidea) and establish the monophyly of larval ectophagy. Mol Phylogenet Evol. 67:156-166
18. Hundsdoerfer AK, Rheinheimer J, Wink M. 2009. Towards the phylogeny of the Curculionoidea (Coleoptera): Reconstructions from mitochondrial and nuclear ribosomal DNA sequences. Zool Anz. 248: 9-31
19. Jordal BH, Sequeira AS, Cognato AI. 2011. The age and phylogeny of wood boring weevils and the origin of subsociality. Mol Phylogenet Evol. 59:708-724
20. Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066
21. Kayal E, Roure B, Philippe H, Collins AG, Lavrov DV. 2013. Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evol Biol. 13:5
22. Kuschel G. 1995. A phylogenetic classification of Curculionoidea to families and subfamilies. Mem Entomol Soc Washington. 14:5-33
23. Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 29:1695-1701
24. Langley CH, Crepeau M, Cerdeno C, Corbett-Detig R, Stevens K. 2011. Circumventing heterozygosity: Sequencing the amplified genome of a single haploid Drosophila melanogaster embryo. Genetics 188: 239-246
25. Marvaldi AE. 1997. Higher level phylogeny of Curculionidae (Coleoptera : Curculionoidea) based mainly on larval characters, with special reference to broad-nosed weevils. Cladistics 13:285-312
26. McKenna DD, Sequeira AS, Marvaldi AE, Farrell BD. 2009. Temporal lags and overlap in the diversification of weevils and flowering plants. Proc Natl Acad Sci U S A. 106:7083-7088
27. Meregalli M, Osella G. 2007. Dichotrachelus kahleni sp. n. , a new weevil species from the Carnian Alps, north-eastern Italy (Coleoptera, Curculionidae, Entiminae). Deut Entomol Z. 54:169-177
28. Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing EnvironmentsWorkshop (GCE); 2010 Nov 14. New Orleans (LA): IEEE. p. 1-8
29. Myers EW, Sutton CG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, et al. 2000. A whole-genome assembly of Drosophila. Science 287:2196-2204
30. Oberprieler RG, Marvaldi AE, Anderson RS. 2007. Weevils, weevils, weevils everywhere. Zootaxa 1668:491-520
31. Osigus H-J, Eitel M, Bernt M, Donath A, Schierwater B. 2013. Mitogenomics at the base of Metazoa. Mol Phylogenet Evol. 69:339-351
32. Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S, Escalante AA. 2011. Evolution of modern birds revealed by mitogenomics: Timing the radiation and origin of major orders. Mol Biol Evol. 28: 1927-1942
33. Papadopoulou A, Anastasiou I, Vogler AP. 2010. Revisiting the insect mitochondrial molecular clock: The mid-Aegean trench calibration. Mol Biol Evol. 27:1659-1672
34. Paradis E. 2013. Molecular dating of phylogenies by likelihood methods: A comparison of models and a new information criterion. Mol Phylogenet Evol. 67:436-444
35. Paradis E, Claude J, Strimmer K. 2004. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290
36. Peng Y, Leung HCM, Yiu SM, Chin FYL. 2012. IBDA-UD: A De novo assembler for single-cell and metagenomic sequencing data woth highly uneven depth. Bioinformatics 28:1420-1428
37. Pons J, Ribera I, Bertranpetit J, Balke M. 2010. Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera. Mol Phylogenet Evol. 56:796-807
38. PosaDa D, Buckley T. 2004. Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol. 53:793-808
39. Roos J, Aggarwal RK, Janke A. 2007. Extended mitogenomic phylogenetic analyses yield new insight into crocodylian evolution and their survival of the Cretaceous-Tertiary boundary. Mol Phylogenet Evol. 45: 663-673
40. Rubinstein ND, Feldstein T, Shenkar N, Botero-Castro F, Griggio F, Mastrototaro F, Delsuc F, Douzery EJP, Gissi C, Huchon D. 2013. Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic Ascidian mitochondrial genomes. Genome Biol Evol. 5:1185-1199
41. Sheffield NC, Song H, Cameron SL, Whiting MF. 2008. A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Mol Biol Evol. 25:2499-2509
42. Sheffield NC, Song H, Cameron SL, Whiting MF. 2009. Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenetics. Syst Biol. 58:381-394
43. Sommer DD, Delcher AL, Salzberg SL, Pop M. 2007. Minimus: A fast, lightweight genome assembler. BMC Bioinformatics 8:64
44. Song HJ, Sheffield NC, Cameron SL, Miller KB, Whiting MF. 2010. When phylogenetic assumptions are violated: Base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Syst Entomol. 35:429-448
45. Stamatakis A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690
46. Swofford DL. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4. Sunderland (MA): Sinauer Associates
47. Talavera G, Vila R. 2011. What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny. BMC Evol Biol. 11: 315
48. Thompson RT. 1992. Observations on themorphology and classification of weevils (Coleoptera, Curculionoidea) with a key to major groups. J Nat Hist. 26:835-891
49. Timmermans MJTN, Dodsworth S, Culverwell CL, Bocak L, Ahrens D, Littlewood DTJ, Pons J, Vogler AP. 2010. Why barcode? Highthroughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res. 38:1-14
50. Wei S-j, Shi M, Sharkey MJ, Van Achterberg C, Chen X-X. 2010. Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to holometabolous insects. BMC Genomics 11:371
51. Wernersson R. 2005. FeatureExtract-extraction of sequence annotation made easy. Nucleic Acids Res. 33:W567-W569
52. Williams S, Foster PG, Littlewood DTJ. 2014. The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny. Gene 533:38-47
53. Winkelmann I, Campos PF, Strugnell J, Cherel Y, Smith PJ, Kubodera T, Allcock L, Kampmann M-L, Schroeder H, Guerra A, et al. 2013. Mitochondrial genome diversity and population structure of the giant squid Architeuthis: Genetics sheds new light on one of the most enigmatic marine species. Proc R Soc B. 280:1759.