Metagenome skimming of insect specimen pools: Potential for comparative genomics

Genome Biology and Evolution

Volumn 7, Issue 6, 2015, Pages 1474-1489

  Linard, Benjamin ^a   Crampton Platt, Alex ^a,b   Gillett, Conrad P D T ^a   Timmermans, Martijn J T N ^a,c   Vogler, Alfried P ^a,c  

^a DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Bacterial endosymbionts; Coleoptera; Environmental genomics; Genome evolution; Histone genes; Repetitive DNA

Indexed keywords

DNA; HISTONE; PLANT DNA;

ANIMAL; BACTERIUM; BEETLE; CHEMISTRY; GENE LIBRARY; GENETICS; GENOMICS; METAGENOME; METAGENOMICS; MICROBIOLOGY; MULTIGENE FAMILY; NUCLEOTIDE REPEAT; PHYLOGENY; PROCEDURES;

ANIMALS; BACTERIA; BEETLES; DNA; DNA, PLANT; GENE LIBRARY; GENOMICS; HISTONES; METAGENOME; METAGENOMICS; MULTIGENE FAMILY; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 84979862124     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv086     Document Type: Article

References (63)

1. Amnuaykanjanasin A, Phonghanpot S, Sengpanich N, Cheevadhanarak S, Tanticharoen M. 2009. Insect-specific polyketide synthases (PKSs), potential PKS-nonribosomal peptide synthetase hybrids, and novel PKS clades in tropical fungi. Appl Environ Microbiol. 75:3721-3732.
2. Andújar C, et al. 2015. Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Mol Ecol.
3. Barberán A, Fernández-Guerra A, Bohannan BJM, Casamayor EO. 2012. Exploration of community traits as ecological markers in microbial metagenomes. Mol Ecol. 21:1909-1917.
4. Basset Y, et al. 2012. Arthropod diversity in a tropical forest. Science 338:1481-1484.
5. Benson DA, et al. 2013. GenBank. Nucleic Acids Res. 41:36-42.
6. Bentley DR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59.
7. Bock DG, Kane NC, Ebert DP, Rieseberg LH. 2014. Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol. 201:1021-1030.
8. Bruvo-MadarićB, Plohl M, UgarkovićD. 2007. Wide distribution of related satellite DNA families within the genus Pimelia (Tenebrionidae). Genetica 130:35-42.
9. Chan SK, et al. 2012. Transcriptome and full-length cDNA resources for themountain pine beetle, Dendroctonus ponderosae Hopkins, amajor insect pest of pine forests. Insect Biochem Mol Biol. 42:525-536.
10. Chen L, et al. 2013. Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis. BMC Genomics 14:339.
11. Crampton-Platt A, Timmermans MJTN, Gimmel ML, Narayanan Kutty S, Cockerill TD, Vun Khen C, Vogler AP. 2015. Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample. Mol Biol Evol. Advance Access publication May 8, 2015, doi:10.1093/molbev/msv111.
12. Duron O, Hurst GD. 2013. Arthropods and inherited bacteria: from counting the symbionts to understanding how symbionts count. BMC Biol. 11:45.
13. Ferrari J, Vavre F. 2011. Bacterial symbionts in insects or the story of communities affecting communities. Philos Trans R Soc Lond B Biol Sci. 366:1389-1400.
14. Ficetola GF, Miaud C, Pompanon F, Taberlet P. 2008. Species detection using environmental DNA from water samples. Biol Lett. 4:423-425.
15. Forêt S, Wanner KW, Maleszka R. 2007. Chemosensory proteins in the honey bee: insights from the annotated genome, comparative analyses and expressional profiling. Insect Biochem Mol Biol. 37:19-28.
16. Frago E, Dicke M, Godfray HCJ. 2012. Insect symbionts as hidden players in insect-plant interactions. Trends Ecol Evol. 27:705-711.
17. Friedrich M, Muqim N. 2003. Sequence and phylogenetic analysis of the complete mitochondrial genome of the flour beetle Tribolium castanaeum. Mol Phylogenet Evol. 26:502-512.
18. Gillett CPDT, et al. 2014. Bulk de novomitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Mol Biol Evol. 31:2223-2237.
19. Gómez-Rodríguez C, Crampton-Platt A, Timmermans MJTN, Baselga A, Vogler AP. 2015. Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages. Methods Ecol Evol.
20. Grasela JJ, McIntosh AH. 2003. Application of inter-simple sequence repeats to insect cell lines: identification at the clonal and tissue-specific level. In Vitro Cell Dev Biol Anim. 39:353-363.
21. Huttenhower C, Hofmann O. 2010. A quick guide to large-scale genomic data mining. PLoS Comput Biol. 6:e1000779.
22. i5K Consortium. 2013. The i5K initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. J Hered. 104:595-600.
23. Ji Y, et al. 2013. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol Lett. 1245-1257.
24. Jurka J, et al. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110:462-467.
25. Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518.
26. Keeling CI, et al. 2013. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biol. 14:R27.
27. LeeMH, Lee S-W. 2013. Bioprospecting potential of the soilmetagenome: novel enzymes and bioactivities. Genomics Inform. 11:114-120.
28. Lohse M, et al. 2012. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 40:W622-W627.
29. MaléPJG, et al. 2014. Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Mol Ecol Resour. 14:966-975.
30. Marchler-Bauer A, et al. 2011. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 39:D225-D229.
31. Mavromatis K, et al. 2007. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 4:495-500.
32. May RM. 2010. Ecology Tropical arthropod species, more or less? Science 329:41-42.
33. McMeniman CJ, et al. 2009. Stable introduction of a life-shortening Wolbachia infection into the mosquito Aedes aegypti. Science 323:141-144.
34. Metzker ML. 2010. Sequencing technologies - the next generation. Nat Rev Genet. 11:31-46.
35. Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for nextgeneration sequencing data. Genomics 95:315-327.
36. Misof B, et al. 2014. Phylogenomics resolves the timing and pattern of insect evolution. Science 346:763-767.
37. Nakabachi A. 2015. Horizontal gene transfers in insects. Curr Opin Insect Sci. 24-29.
38. Okonechnikov K, Golosova O, Fursov M. 2012. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166-1167.
39. Paula DP, et al. 2014. Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. Mol Ecol Resour.
40. Peng Y, Kou G, Shi Y, Chen Z. 2008. A descriptive framework for the field of data mining and knowledge discovery. Int J Inf Technol Decis Mak. 7:639-682.
41. Quast C, et al. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41:D590-D596.
42. Raven JA. 2012. Algal biogeography: metagenomics shows distribution of a picoplanktonic pelagophyte. Curr Biol. 22:R682-R683.
43. Roehrdanz R, Heilmann L, Senechal P, Sears S, Evenson P. 2010. Histone and ribosomal RNA repetitive gene clusters of the bollweevil are linked in a tandem array. Insect Mol Biol. 19:463-471.
44. Straub SCK, et al. 2012. Navigating the tip of the genomic iceberg: nextgeneration sequencing for plant systematics. Am J Bot. 99:349-364.
45. Sucher NJ, Hennell JR, CarlesMC. 2012. DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants. Methods Mol Biol. 862:13-22.
46. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH. 2012. Environmental DNA. Mol Ecol. 21:1789-1793.
47. Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E. 2012. Towards next-generation biodiversity assessment using DNAmetabarcoding. Mol Ecol. 21:2045-2050.
48. Tang M, et al. 2014. Multiplex sequencing of pooled mitochondrial genomes - a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Res. 42:e166.
49. Tarailo-Graovac M, Chen N. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. Chapter 4:Unit 4.10.
50. Trivedi P, Anderson IC, Singh BK. 2013. Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction. Trends Microbiol. 641-651.
51. Valentini A, et al. 2009. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Mol Ecol Resour. 9:51-60.
52. Wallinger C, et al. 2013. The effect of plant identity and the level of plant decay on molecular gut content analysis in a herbivorous soil insect. Mol Ecol Resour. 13:75-83.
53. Weitemier K, Straub SCK, Fishbein M, Liston A. 2015. Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae). PeerJ. 3:e718.
54. Werren JH, Baldo L, Clark ME. 2008. Wolbachia: master manipulators of invertebrate biology. Nat Rev Microbiol. 6:741-751.
55. Wheeler Q. 1982. The Biology of the Coleoptera. by R. A. Crowson. Review by: Quentin Wheeler. Syst Zool. 31:342-345.
56. Wheeler TJ, et al. 2013. Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucl. Acids Res. (1 January 2013) 41 (D1): D70-D82 first published online November 30, 2012 doi:10.1093/nar/gks1265
57. Wicker T, et al. 2007. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 8:973-982.
58. Wittkopp PJ, Kalay G. 2012. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet. 13:59-69.
59. Yang Y, et al. 2013. The microbial gene diversity along an elevation gradient of the Tibetan grassland. ISME J. 1-11.
60. Yoccoz NG. 2012. The future of environmental DNA in ecology. Mol Ecol. 21:2031-2038.
61. Zarraonaindia I, Smith DP, Gilbert JA. 2013. Beyond the genome: community-level analysis of the microbial world. Biol Philos. 28:261-282.
62. Zhang Z. 2011. Animal biodiversity: an introduction to higher-level classification and taxonomic richness. Zootaxa 12:7-12.
63. Zhou X, et al. 2013. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience 2:4.