Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: Improving accuracy and matrix occupancy for phylogenomics

Molecular Biology and Evolution

Volumn 31, Issue 11, 2014, Pages 3081-3092

  Yang, Ya ^a   Smith, Stephen A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Diplopoda; phylotranscriptomics; RNA seq; Vitaceae

Indexed keywords

TRANSCRIPTOME;

ACCURACY; ALGORITHM; ARTICLE; EVOLUTIONARY HOMOLOGY; GENE DUPLICATION; GENETIC CODE; GENETIC VARIABILITY; GENOME; HORIZONTAL GENE TRANSFER; HYMENOPTERA; MAXIMUM LIKELIHOOD METHOD; MILLIPEDE; MULTIGENE FAMILY; NONHUMAN; ORTHOLOGY; PARALOGY; PHYLOGENETIC TREE; PHYLOGENOMICS; SEQUENCE ALIGNMENT; ANIMAL; ARTHROPOD; CLASSIFICATION; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY; VITACEAE;

DIPLOPODA; VITACEAE;

ANIMALS; ARTHROPODS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENOME; HYMENOPTERA; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; TRANSCRIPTOME; VITACEAE;

EID: 84910656190     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu245     Document Type: Article

References (58)

1. Altenhoff AM, Gil M, Gonnet GH, Dessimoz C. 2013. Inferring hierarchical orthologous groups from orthologous gene pairs. PLoS One 8(1):e53786.
2. Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. 2011. OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res. 39:D289-D294.
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403-410.
4. An-e C, Larget B, Baum DA, Smith SD, Rokas A. 2007. Bayesian estimation of concordance among gene trees. Mol Biol Evol. 24(2):412-426.
5. Bonasio R, Zhang G, Ye C, Mutti NS, Fang X, Qin N, Dona hue G, Yang P, Li Q, Li C. 2010. Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science 329(5995):1068-1071.
6. Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23:323-330.
7. Brewer MS, Bond JE. 2013. Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses. PLoS One 8(11):e79935.
8. Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R. 2006. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 22(6):699-707.
9. Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, et al. 2011. The ecoresponsive genome of Daphnia pulex. Science 331(6017):555-561.
10. Cui R, Schumer M, Kruesi K, Walter R, Andolfatto P, Rosenthal GG. 2013. Phylogenomics reviews extensive reticulate evolution in Xiphophorus fishes. Evolution 67(8):2166-2179.
11. De Smet R , Adams KL, Vandepoele K, VanMontagu MCE, Maere S, Van de Peer Y. 2013. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Natl Acad Sci USA. 110(8):289 8-2903.
12. Dunn C, Howison M, Zapata F. 2013. Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14(1):330.
13. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smit h SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, et al. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452(7188):745-749.
14. Ebersberger I, Strauss S, von Haeseler A. 2009. HaMStR: profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol. 9(1):157.
15. Enright A, van Dongen S, Ouzounis C. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30: 1575-1584.
16. Fitch WM. 1970. Distinguishing homologous from analogous proteins. Syst Biol. 19(2):99-113.
17. Fi tch WM. 2000. Homology: a personal view on some of the problems. Trends Genet. 16(5):227-231.
18. Fu L, Niu B, Zhu Z, Wu S, Li W. 2012. CD-HIT: accelerated for clustering the next generation sequencing data. Bioinformatics 28(23):3150-3152.
19. Gabaldón T. 2008. Large-scale assignment of orthology: back to phylogenetics? Genome Biol. 9(10):235.
20. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al. 2011. Fulllength transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 29( 7):644-654.
21. Goodstein DM, Shu SQ, Howson R, Neupane R, Hayes RD, Fazo J,Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS. 2012. Phytozome: a comparative platform for green plant genomics. Nu cleic Acids Res. 40:D1178-D1186.
22. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, et al. 2013. De novo transcript sequence reco nstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 8(8):1494-1512.
23. Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467.
24. Johnson BR, Borowiec ML, Chiu JC, Lee EK, Atallah J, Ward PS. 2013. Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Curr Biol. 23(20):2058-2062.
25. Katoh K, Stand ley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772-780.
26. Kocher S, Li C, Yang W, Tan H, Yi S, Yang X, Hoekstra H, Zhang G, Pierce N, Yu D. 2013. The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biol. 14(12):R142.
27. Larget BR, Kotha SK, Dewey CN, An-e C. 2010. BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26(22):2910-2911.
28. Li H, Coghlan A, Ruan J, Coin L, Heriche J, Osmotherly L, Li R, Liu T, Zhang Z, Bo lund L, et al. 2006. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34: 572-580.
29. Li L, Stoeckert CJ J, Roos D. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189.
30. Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T. 2009. Rapid and accurate large-scale coestimation of sequence alignments and phylo genetic trees. Science 324(5934):1561-1564.
31. Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR. 2012. SAT-e-II: very fast and accurate simultaneous estimation of multip le sequence alignments and phylogenetic trees. Syst Biol. 61: 90-106.
32. Liu L, Yu L, Edwards S. 2010. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol. 10(1):302.
33. Liu L, Yu L, Pearl DK, Edwards SV. 2009. Estimating species phylogenies using coalescence times among sequences. Syst Biol. 58(5):468-477.
34. Marcet-Houben M, Gaba ldón T. 2011. TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees. Nucleic Acids Res. 39(10):e66.
35. Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, MacCallum RM, Redmond SN. 2012. VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res. 40(D1):D729-D734.
36. Meusemann K,von Reumont BM,Simon S,Roeding F Strauss S,Kuck P Ebersberger I,Walzl M,Pass Gn,Breuers S,et al., 2010. A phylogenomic approach to resolve the arthropod tree of life.Mol Biol Evol. 27, 11):2451-2464.
37. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2, approximately maximum-likelihood trees for large alignments. PLoS One 5(3):e9490.
38. Ranwez V, Harispe S, Delsuc F, Douzery E. 2011. MACSE: multiple alignment of coding sequences accounting for frameshifts and stop codons. PLoS One 6(9):e22594.
39. Roth A, Gonnet G, Dessim oz C. 2008. Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics 9(1):518.
40. Roure B, Rodriguez-Ezpeleta N, Philippe H. 2007. SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics. BMC Evol Biol. 7(Suppl. 1), S2.
41. Salichos L, Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497(7449):327-331.
42. Sanderson M, McMahon M. 2007. Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evol Biol. 7(Suppl 1), S3.
43. Schreiber F, Pick K, Erpenbeck D, Worheide G, Morgenstern B. 2009. OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. BMC Bioinformatics 10:219.
44. Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cas h E, Croset V, Currie CR, Elhaik E, Elsik CG. 2011. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci USA. 108(14):5673-5678.
45. Smith CR, Smith C D, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, et al. 2011. Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci USA. 108(14):5667-567 2.
46. Smith SA, Dunn CW. 2008. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24(5):715-716.
47. Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SCS, Rouse GW, Giribet G, Dunn CW. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480(7377):364-369.
48. Soria-Carrasco V, Castresana J. 2008 . Estimation of phylogenetic inconsistencies in the three domains of life. Mol Biol Evol. 25(11):2319-2329.
49. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-2690.
50. Stamatakis A, Aberer AJ, Goll C, Smith SA, Berger SA, Izquierdo-Carrasco F. 2012. RAxML-Light: a tool for computing terabyte phylogenies. Bioinformatics 28:2064-2066.
51. Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564-577.
52. van Dongen S. 2000. Graph clustering by flow simulation. [Ph.D thesis]. [Utrecht, Netherlands]: University of Utrecht.
53. van Dongen S, Abreu-Goodger C. 2012. Using MCL to extract clusters from networks. In: Helden JV, Toussaint A, Thieffry D, editors. Bacterial molecular networks: methods and protocols. Methods in molecular biology. Vol. 804. New York: Springer. p. 281-295.
54. Weinstock GM, Robinson GE, Gibbs RA, Worley KC, Evans JD, Maleszka R, Robertson HM, Weaver DB, Beye M, Bork P. 2006. Insights into social in sects from the genome of the honeybee Apis mellifera. Nature 443(7114):931-949.
55. Wen J, Xiong Z, Nie Z-L, Mao L, Zhu Y, Kan X-Z, Ickert-Bond SM, Gerrath J, Zimmer EA, Fang X-D. 2 013. Transcriptome sequences resolve deep relationships of the grape family. PLoS One 8(9):e74394.
56. Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Group TNGW. 2010. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327(5963):343-348.
57. Wilson JS, von Dohlen CD, Forister ML, Pitts JP. 2013. Family-level divergences in the stinging wasps (Hymenoptera: Aculeata), with correlations to angiosperm diversification. Evol Biol. 40(1):101-107.
58. Yang Y, Smith SA. 2013. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics 14(1):328.