Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics

Annals of Botany

Volumn 113, Issue 5, 2014, Pages 753-761

  Sveinsson, Saemundur ^a   McDill, Joshua ^b   Wong, Gane K S ^b   Li, Juanjuan ^c   Li, Xia ^c   Deyholos, Michael K ^b   Cronk, Quentin C B ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

^c BGI SHENZHEN   (China)

Author keywords

flax; gene trees; genomic phylogenetics; Linum usitatissimum; paleopolyploidy; paralogue age distribution; species phylogeny; transcriptomics; whole genome duplication

Indexed keywords

AGE STRUCTURE; CLADISTICS; CULTIVAR; DICOTYLEDON; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; GENOMICS; PHYLOGENY; POLYPLOIDY;

TRANSCRIPTOME;

EVOLUTION; FLAX; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PLANT GENOME; POLYPLOIDY; SEQUENCE ANALYSIS;

BIOLOGICAL EVOLUTION; FLAX; GENOME, PLANT; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYPLOIDY; SEQUENCE ANALYSIS, PROTEIN; TRANSCRIPTOME;

EID: 84896919317     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mct306     Document Type: Article

References (62)

1. Adams KL, Wendel JF. 2005. Polyploidy and genome evolution in plants. Current Opinion in Plant Biology 8: 135-41.
2. Altschul SF, Madden TL, Schäffer AA, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
3. Barker MS, Kane NC, Matvienko M, et al. 2008. Multiple paleopolyploidiza-tions during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Molecular Biology and Evolution 25: 2445-2455.
4. Barker MS, Vogel H, Schranz ME. 2009. Paleopolyploidy in the Brassicales: analyses of the cleome transcriptome elucidate the historyof genome dupli-cationsinarabidopsis and other Brassicales. Genome Biologyand Evolution 1: 391-399.
5. Birney E, Clamp M, Durbin R. 2004. Gene Wise and Genomewise. Genome Research 14: 988-995.
6. Blanc G, Wolfe KH. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678.
7. Capella-Gutiérrez S, Silla-Mart́inez JM, Gabaldón T. 2009. trimAl:atool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973.
8. Chaudhuri P, Marron JS. 1999. SiZer for exploration of structures in curves. Journal of the American Statistical Association 94: 807-823.
9. Cui L, Wall PK, Leebens-Mack JH, et al. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Research 16: 738-749.
10. Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772.
11. Doyle JJ, Egan AN. 2010. Dating the origins of polyploidy events. New Phytologist 186: 73-85.
12. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113. doi:10.1186/1471-2105-5- 113.
13. Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Seattle: Department of Genome Sciences, University of Washington.
14. Goldman N, Yang ZH. 1994. Codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11: 725-736.
15. Goodstein DM, Shu S, Howson R, et al. 2012. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40: D1178-D1186.
16. Grabherr MG, Haas BJ, Yassour M, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29: 644-652.
17. Green AG. 1986. Genetic control of polyunsaturated fatty acid biosynthesis in flax (Linum usitatissimum) seed oil. Theoretical and Applied Genetics 72: 654-661.
18. Guerra M. 2008. Chromosome numbers in plant cytotaxonomy: concepts and implications. Cytogenetic and Genome Research 120: 339-350
19. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
20. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methodstoestimate maximum-likelihood phylo-genies: assessing the performance of PhyML 3.0. Systematic Biology 59: 307-21.
21. Harper AL, Trick M, Higgins J, et al. 2012. Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nature Biotechnology 30: 798-802.
22. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylo-genetic trees. Bioinformatics 17: 754-755.
23. Huson DH, Scornavacca C. 2012. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Systematic Biology 61: 1061-1067.
24. Ihaka R, Gentleman R. 1996. R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics 5: 299-314.
25. Jiao Y, Wickett NJ, Ayyampalayam S, et al. 2011. Ancestral polyploidyinseed plants and angiosperms. Nature 473: 97-100.
26. Jiao Y, Leebens-Mack J, Ayyampalayam S, et al. 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biology 13: R3. doi:10.1186/gb-2012-13-1-r3.
27. Johnson MTJ, Carpenter EJ, Tian Z, et al. 2012. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PloS One 7: e50226. doi:10.1371/journal.-pone. 0050226
28. Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772-780.
29. Koch MA, Haubold B, Mitchell-Olds T. 2000. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Molecular Biology and Evolution 17: 1483-1498.
30. Li L, Stoeckert CJ, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research 13: 2178-2189.
31. Li W, Godzik A. 2006. Cd-hit: afast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
32. Li W, Jaroszewski L, Godzik A. 2001. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17: 282-283.
33. Liu L, Yu L. 2010. Phybase: an R package for species tree analysis. Bioinformatics 26: 962-963.
34. Liu L, Yu L, Pearl DK, Edwards SV. 2009. Estimating species phylogenies using coalescence times among sequences. Systematic Biology 58: 468-477.
35. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
36. Ma B, Tromp J, Li M. 2002. Pattern Hunter: fasterand more sensitive homology search. Bioinformatics 18: 440-445.
37. McDill J, Simpson BB. 2011. Molecular phylogenetics of Linaceae with complete generic sampling and data from two plastid genes. Botanical Journal of the Linnean Society 165: 64-83.
38. McDill J, Repplinger M, Simpson BB, Kadereit JW. 2009. The phylogeny of Linum and Linaceae subfamily Linoideae, with implications for their sys-tematics, biogeography, and evolution of heterostyly. Systematic Botany 34: 386-405.
39. McLachlanGJ, Peel D, Basford KE, Adams P. 1999. The EMMIX software for the fitting of mixtures of normal and t-components. Journal of Statistical Software 4: 1-14.
40. Mohanty AK, Misra M, Hinrichsen G. 2000. Biofibres, biodegradable polymers and biocomposites: an overview. Macromolecular Materials and Engineering 276: 1-24.
41. Otto SP, Whitton J. 2000. Polyploid incidence and evolution. Annual Review of Genetics 34: 401-437.
42. Rannala B, Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.
43. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
44. Schlueter JA, Dixon P, Granger C, et al. 2004. Mining EST data bases to resolve evolutionary events in major crop species. Genome 47: 868-876.
45. Schubert I, Lysak M. 2011. Interpretation of karyotype evolution should consider chromosome structural constraints. Trends in Genetics 27: 207-216.
46. Seo T-K. 2008. Calculating bootstrap probabilities of phylogeny using multilo-cus sequence data. Molecular Biology and Evolution 25: 960-971.
47. Shi T, Huang H, Barker MS. 2010. Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Annals of Botany 106: 497-504.
48. Singh KK, Mridula D, Rehal J, Barnwal P. 2011. Flaxseed: a potential source of food, feed and fiber. Critical Reviews in Food Science and Nutrition 51: 210-222.
49. Soltis DE, Albert VA, Leebens-Mack J, et al. 2009. Polyploidyand angiosperm diversification. American Journal of Botany 96: 336-348.
50. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogen-etic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
51. Vamosi JC, Dickinson TA. 2006. Polyploidy and diversification: aphylogenetic investigation in Rosaceae. International Journal of Plant Sciences 167: 349-358.
52. Van de Peer Y. 2011. A mystery unveiled. Genome Biology 12: 113.
53. Vanneste K, Van de Peer Y, Maere S. 2013. Inference of genome duplications from age distributions revisited. Molecular Biology and Evolution 30: 177-190.
54. Wang Z, Hobson N, Galindo L, et al. 2012. The genome of flax (Linum usita-tissimum) assembled de novo from short shotgun sequence reads. Plant Journal 72: 461-473.
55. Wasmuth JD, Blaxter ML. 2004. prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics 5: 187. doi:10.1186/1471-2105-5- 187.
56. Wernersson R, Pedersen AG. 2003. RevTrans-Constructing alignments of coding DNA from aligned amino acid sequences. Nucleic Acids Research 31: 3537-3539.
57. Wheeler DL, Barrett T, Benson DA, et al. 2007. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 35: D5-D12.
58. Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH. 2009. The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences of the USA 106: 13875-13879.
59. Xi Z, Ruhfel BR, Schaefer H, et al. 2012. Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proceedings of the National Academy of Sciences of the USA 109: 17519-17524
60. Yang Z. 1997. PAML:aprogram packagefor phylogeneticanalysisbymaximum likelihood. Computer Applications in the Biosciences 13: 555-556.
61. Zhang Z, Schwartz S, Wagner L, Miller W. 2000. Agreedyalgorithm foralign-ing DNA sequences. Journal of Computational Biology 7: 203-214.
62. Zwickl DJ. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD Thesis, University of Texas at Austin, USA.