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Contreras-Moreira B, Cantalapiedra CP, García-Pereira MJ, et al. Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. Front Plant Sci. 2017;8:184doi: 10.3389/fpls.2017.00184.
Contreras-Moreira, B., Cantalapiedra, C. P., García-Pereira, M. J., Gordon, S. P., Vogel, J. P., Igartua, E., Casas, A. M., & Vinuesa, P. (2017). Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. Frontiers in plant science, 8184. https://doi.org/10.3389/fpls.2017.00184
Contreras-Moreira, Bruno, et al. "Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species." Frontiers in plant science vol. 8 (2017): 184. doi: https://doi.org/10.3389/fpls.2017.00184
Contreras-Moreira B, Cantalapiedra CP, García-Pereira MJ, Gordon SP, Vogel JP, Igartua E, Casas AM, Vinuesa P. Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. Front Plant Sci. 2017 Feb 14;8:184. doi: 10.3389/fpls.2017.00184. eCollection 2017. PMID: 28261241; PMCID: PMC5306281.
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Front Plant Sci. 2017 Feb 14;8:184. doi: 10.3389/fpls.2017.00184. eCollection 2017.

Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species.

Frontiers in plant science

Bruno Contreras-Moreira, Carlos P Cantalapiedra, María J García-Pereira, Sean P Gordon, John P Vogel, Ernesto Igartua, Ana M Casas, Pablo Vinuesa

Affiliations

  1. Estación Experimental de Aula Dei - Consejo Superior de Investigaciones CientíficasZaragoza, Spain; Fundación ARAIDZaragoza, Spain.
  2. Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain.
  3. DOE Joint Genome Institute, Walnut Creek CA, USA.
  4. Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico.

PMID: 28261241 PMCID: PMC5306281 DOI: 10.3389/fpls.2017.00184

Abstract

The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19

Keywords: Arabidopsis thaliana; RNA-seq; accessory genome; barley; comparative genomics; core-genome; pan-genome

References

  1. Nature. 2011 Aug 28;477(7365):419-23 - PubMed
  2. Nat Genet. 2016 Mar;48(3):245-52 - PubMed
  3. Nature. 2012 Nov 29;491(7426):711-6 - PubMed
  4. DNA Res. 2016 Feb;23(1):21-8 - PubMed
  5. Genome Biol. 2013 Jun 12;14(6):R58 - PubMed
  6. Plant J. 2013 Nov;76(3):530-44 - PubMed
  7. Mol Syst Biol. 2011 Oct 11;7:539 - PubMed
  8. Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13403-8 - PubMed
  9. Bioinformatics. 2016 Jun 15;32(12):i192-i200 - PubMed
  10. Bioinformatics. 2016 Sep 1;32(17):i487-i493 - PubMed
  11. Genome Res. 1998 Nov;8(11):1113-30 - PubMed
  12. Funct Integr Genomics. 2006 Jul;6(3):202-11 - PubMed
  13. Methods Mol Biol. 2016;1482:279-95 - PubMed
  14. BMC Bioinformatics. 2015 Nov 02;16:352 - PubMed
  15. Trends Ecol Evol. 2000 Dec 1;15(12):496-503 - PubMed
  16. Plant Genome. 2016 Jul;9(2):null - PubMed
  17. Genome Biol. 2015 Sep 07;16:187 - PubMed
  18. Methods Mol Biol. 2015;1231:203-32 - PubMed
  19. Proc Natl Acad Sci U S A. 1998 Jan 6;95(1):370-5 - PubMed
  20. Curr Opin Plant Biol. 2014 Apr;18:31-6 - PubMed
  21. Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85 - PubMed
  22. Genome Res. 2003 Sep;13(9):2178-89 - PubMed
  23. Bioinformatics. 2009 May 1;25(9):1105-11 - PubMed
  24. Curr Opin Plant Biol. 2007 Apr;10(2):149-55 - PubMed
  25. Bioinformatics. 2006 Jul 1;22(13):1658-9 - PubMed
  26. Plant Physiol. 2012 Aug;159(4):1295-308 - PubMed
  27. Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):346-51 - PubMed
  28. Nat Biotechnol. 2010 May;28(5):511-5 - PubMed
  29. Nat Commun. 2015 Apr 16;6:6914 - PubMed
  30. Bioinformatics. 2014 Aug 1;30(15):2114-20 - PubMed
  31. Brief Bioinform. 2016 Oct 21;:null - PubMed
  32. Nature. 2006 Nov 16;444(7117):323-9 - PubMed
  33. Sci Rep. 2016 Jan 05;6:18936 - PubMed
  34. Nat Rev Genet. 2013 Jan;14(1):49-61 - PubMed
  35. Cell. 2016 Jul 14;166(2):481-91 - PubMed
  36. Nat Protoc. 2013 Aug;8(8):1494-512 - PubMed
  37. Mol Biol Evol. 2014 Jan;31(1):59-69 - PubMed
  38. PLoS Genet. 2009 Nov;5(11):e1000734 - PubMed
  39. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W95-W100 - PubMed
  40. Elife. 2016 Jun 03;5:null - PubMed
  41. BMC Bioinformatics. 2010 Sep 15;11:461 - PubMed
  42. Nat Biotechnol. 2010 Jan;28(1):57-63 - PubMed
  43. PLoS One. 2012;7(3):e33071 - PubMed
  44. Appl Environ Microbiol. 2013 Dec;79(24):7696-701 - PubMed
  45. Nat Genet. 2010 Nov;42(11):1027-30 - PubMed
  46. Nat Biotechnol. 2014 Oct;32(10):1045-52 - PubMed
  47. Comput Appl Biosci. 1997 Oct;13(5):555-6 - PubMed
  48. Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5 - PubMed
  49. Nat Commun. 2016 Nov 11;7:13390 - PubMed
  50. Nucleic Acids Res. 2008 Dec;36(21):6688-719 - PubMed
  51. BMC Bioinformatics. 2009 Dec 15;10:421 - PubMed
  52. Nat Methods. 2015 Jan;12(1):59-60 - PubMed
  53. Mol Genet Genomics. 2015 Apr;290(2):727-38 - PubMed
  54. Bioinformatics. 2013 Feb 1;29(3):308-15 - PubMed
  55. Plant Cell. 2014 Jan;26(1):121-35 - PubMed
  56. Genomics Proteomics Bioinformatics. 2015 Feb;13(1):73-6 - PubMed
  57. Mol Biol Evol. 2006 Feb;23(2):254-67 - PubMed
  58. Nat Genet. 2016 Aug;48(8):927-34 - PubMed
  59. Bioinformatics. 2003 Mar 22;19(5):651-2 - PubMed
  60. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 - PubMed
  61. Plant Biotechnol J. 2016 Apr;14 (4):1099-105 - PubMed
  62. Nat Genet. 2011 Aug 28;43(10):956-63 - PubMed

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