Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps

G3: Genes, Genomes, Genetics

Volumn 4, Issue 7, 2014, Pages 1339-1346

  Burton, Joshua N ^a   Liachko, Ivan ^a   Dunham, Maitreya J ^a   Shendure, Jay ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Algorithms; Assembly; Clustering; Hi C; Metagenome; Metagenomics

Indexed keywords

ANIMAL CELL; ARCHEAN; ARTICLE; BACTERIAL GENOME; BACTERIUM; CELL LINE; CHROMATIN; CONTROLLED STUDY; EUKARYOTE; FUNGUS; GENE CLUSTER; GENE LIBRARY; GENE MAPPING; HI C METHOD; METAGENOME; METAPHASE; MICROBIAL COMMUNITY; NONHUMAN; PROBABILITY; SPECIES IDENTIFICATION;

EID: 84904548768     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.011825     Document Type: Article

References (39)

1. Albertsen, M., P. Hugenholtz, A. Skarshewski, K. L. Nielsen, G. W. Tyson et al., 2013 Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31: 533-538
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, 1990 Basic local alignment search tool. J. Mol. Biol. 215: 403-410
3. Baker, C. R., B. B. Tuch, and A. D. Johnson, 2011 Extensive DNA-binding specificity divergence of a conserved transcription regulator. Proc. Natl. Acad. Sci. USA 108: 7493-7498
4. Beitel C. W., Froenicke L., Lang J. M., Korf I. F., Michelmore R. W., et al., 2014. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ PrePrints 2:e260v1. https://peerj.com/preprints/260v1/
5. Beitel, C. W., L. Froenicke, J. M. Lang, I. F. Korf, R. W. Michelmore et al., 2014 Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2: e415
6. Belloch, C., E. Barrio, M. D. Garcia, and A. Querol, 1998 Inter- and intraspecific chromosome pattern variation in the yeast genus Kluyveromyces. Yeast 14: 1341-1354
7. Burton, J. N., A. Adey, R. P. Patwardhan, R. L. Qiu, J. O. Kitzman et al., 2013 Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31: 1119-1125
8. Carr, R., S. S. Shen-Orr, and E. Borenstein, 2013. Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PLoS Comp. Biol. 9
9. David, L. A., C. F. Maurice, R. N. Carmody, D. B. Gootenberg, J. E. Button et al., 2014 Diet rapidly and reproducibly alters the human gut microbiome. Nature 505: 559-563
10. Dekker, J., M. A. Marti-Renom, and L. A. Mirny, 2013 Exploring the threedimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 14: 390-403
11. Dick, G. J., A. F. Andersson, B. J. Baker, S. L. Simmons, A. P. Yelton et al., 2009 Community-wide analysis of microbial genome sequence signatures. Genome Biol. 10: R85
12. Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein, 1998 Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95: 14863-14868
13. Frias-Lopez, J., Y. Shi, G. W. Tyson, M. L. Coleman, S. C. Schuster et al., 2008 Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. USA 105: 3805-3810
14. Howe, A. C., J. K. Jansson, S. A. Malfatti, S. G. Tringe, J. M. Tiedje et al., 2014 Tackling soil diversity with the assembly of large, complex metagenomes. Proc. Natl. Acad. Sci. USA 111: 4904-4909
15. Hug, L. A., C. J. Castelle, K. C. Wrighton, B. C. Thomas, I. Sharon et al., 2013 Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome 1: 22
16. Huttenhower, C. D. Human Microbiome Project Consortium, et al., 2012 Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214
17. Iverson, V., R. M. Morris, C. D. Frazar, C. T. Berthiaume, R. L. Morales et al., 2012 Untangling genomes from metagenomes: revealing an uncultured class of marine euryarchaeota. Science 335: 587-590
18. Jarvis, R. A., and E. A. Patrick, 1973 Clustering using a similarity measure based on shared near neighbors. IEEE Trans. Comput. C-22: 1025-1034
19. Jeffries, T. W., I. V. Grigoriev, J. Grimwood, J. M. Laplaza, A. Aerts et al., 2007 Genome sequence of the lignocellulose-bioconverting and xylosefermenting yeast Pichia stipitis. Nat. Biotechnol. 25: 319-326
20. Kaplan, N., and J. Dekker, 2013 High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat. Biotechnol. 31: 1143-1147
21. Le, T. B. K., M. V. Imakaev, L. A. Mirny, and M. T. Laub, 2013 Highresolution mapping of the spatial organization of a bacterial chromosome. Science 342: 731-734
22. Li, H., and R. Durbin, 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760
23. Lieberman-Aiden, E., N. L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy et al., 2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293
24. Mitra, S., K. Forster-Fromme, A. Damms-Machado, T. Scheurenbrand, S. Biskup et al., 2013 Analysis of the intestinal microbiota using SOLiD16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics 14 (Suppl 5): S16
25. Moustafa, A., A. N. Evans, D. M. Kulis, J. D. Hackett, D. L. Erdner et al., 2010 Transcriptome profiling of a toxic dinoflagellate reveals a generich protist and a potential impact on gene expression due to bacterial presence. PLoS ONE 5: e9688
26. Namiki, T., T. Hachiya, H. Tanaka, and Y. Sakakibara, 2012 MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 40: e155
27. Narasingarao, P., S. Podell, J. A. Ugalde, C. Brochier-Armanet, J. B. Emerson et al., 2012 De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 6: 81-93
28. Peng, Y., H. C. M. Leung, S. M. Yiu, and F. Y. L. Chin, 2012 IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: 1420-1428
29. Qin, J. J., R. Li, J. Raes, M. Arumugam, K. S. Burgdorf et al., 2010 A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65
30. Renouf, V., O. Claisse, and A. Lonvaud-Funel, 2007 Inventory and monitoring of wine microbial consortia. Appl. Microbiol. Biotechnol. 75: 149-164
31. Rinke, C., P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson et al., 2013 Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437
32. Saeed, I., S. L. Tang, and S. K. Halgamuge, 2012 Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition. Nucleic Acids Res. 40: e34
33. Sharon, I., M. J. Morowitz, B. C. Thomas, E. K. Costello, D. A. Relman et al., 2013 Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 23: 111-120
34. Umbarger, M. A., E. Toro, M. A. Wright, G. J. Porreca, D. Bau et al., 2011 The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol. Cell 44: 252-264
35. van Berkum, N. L., Lieberman-Aiden E., Williams L., Imakaev M., Gnirke A., et al., 2010 Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp. 39. pii: 1869
36. Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch et al., 2004 Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74
37. Wood, D. E., and S. L. Salzberg, 2014 Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15: R46
38. Xin, G., D. Glawe, and S. L. Doty, 2009 Characterization of three endophytic, indole-3-acetic acid-producing yeasts occurring in Populus trees. Mycol. Res. 113: 973-980
39. Yaffe, E., and A. Tanay, 2011 Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet. 43: 1059-1065