CoChat
Sign Up
Cited by 105

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

A call for benchmarking transposable element annotation methods

Hoen, Douglas R., Hickey, Glenn, Bourque, Guillaume, Casacuberta, Josep, Cordaux, Richard, Feschotte, Cédric, Fiston-Lavier, Anna-Sophie, Hua-Van, Aurélie, Hubley, Robert, Kapusta, Aurélie, Lerat, Emmanuelle, Maumus, Florian, Pollock, David D., Quesneville, Hadi, Smit, Arian, Wheeler, Travis J., Bureau, Thomas E., Blanchette, Mathieu·2015·Mobile DNA
DOI 10.1186/s13100-015-0044-6PMC PMC4524446
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/s13100-015-0044-6

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Figures

Fig. 1 Variation among TE annotation tools. a TE coverage in the Arabidopsis thaliana genome resulting from three commonly used repetitiveness-based de novo tools, compared to a reference set of TEs [8]. The total amount of TE coverage differs between the three, as does the fraction of the reference TEs that were found or missed and the amount of non-reference putative TEs. b Full-length LTR TEs in the Drosophila melanogaster X chromosome found by five different LTR-specific de novo tools, compared to a reference set of TEs [24]. Similar to a but even more pronounced, the number of TEs found by the tools and their agreement with the reference set vary widely. c A 100-kbp segment of the Arabidopsis lyrata genome (scaffold_1:14,957,501-15,057,500) displayed on a custom UCSC genome browser [76, 77], illustrating differences among TE annotations resulting from several approaches, as well as additional genomic data useful in identifying bona fide TEs. From top to bottom, the tracks represent: RepeatMasker annotations using libraries from Repbase [37], RepeatModeler [30], REPET [44], or de la Chaux et al. [78]; full-length LTR TE predictions by LTR_Finder [33] or LTRharvest [79]; tandem repeat predictions by TRF [29]; gene models predictions by FGenesH [80]; a set of TE-specific domains [13]; mapped mRNA and small RNA short reads [77]; inter-species conservation (alignment percent identity plots) to other Brassicaceae species [77]; and genome self-alignment depth (generated with LASTZ)
Fig. 1 Variation among TE annotation tools. a TE coverage in the Arabidopsis thaliana genome resulting from three commonly used repetitiveness-based de novo tools, compared to a reference set of TEs [8]. The total amount of TE coverage differs between the three, as does the fraction of the reference TEs that were found or missed and the amount of non-reference putative TEs. b Full-length LTR TEs in the Drosophila melanogaster X chromosome found by five different LTR-specific de novo tools, compared to a reference set of TEs [24]. Similar to a but even more pronounced, the number of TEs found by the tools and their agreement with the reference set vary widely. c A 100-kbp segment of the Arabidopsis lyrata genome (scaffold_1:14,957,501-15,057,500) displayed on a custom UCSC genome browser [76, 77], illustrating differences among TE annotations resulting from several approaches, as well as additional genomic data useful in identifying bona fide TEs. From top to bottom, the tracks represent: RepeatMasker annotations using libraries from Repbase [37], RepeatModeler [30], REPET [44], or de la Chaux et al. [78]; full-length LTR TE predictions by LTR_Finder [33] or LTRharvest [79]; tandem repeat predictions by TRF [29]; gene models predictions by FGenesH [80]; a set of TE-specific domains [13]; mapped mRNA and small RNA short reads [77]; inter-species conservation (alignment percent identity plots) to other Brassicaceae species [77]; and genome self-alignment depth (generated with LASTZ)CC BY · PubMed Central

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Research works printed but not linked: 89

  1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921. · DOI · Paper page
  2. de Koning APJ, Gu W, Castoe TA, Batzer MA, Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011;7, e1002384.
  3. Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, et al. Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res. 2013;41(Database issue):D70–82. · DOI
  4. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009;326:1112–1115. · DOI
  5. Solyom S, Kazazian HH. Mobile elements in the human genome: implications for disease. Genome Med. 2012;4:12. · DOI
  6. Kazazian HH. Mobile elements: drivers of genome evolution. Science. 2004;303:1626–32. · DOI · Paper page
  7. Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nat Rev Genet. 2009;10:691–703. · DOI
  8. Maumus F, Quesneville H. Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter. PLoS One. 2014;9, e94101. · DOI
  9. Gifford WD, Pfaff SL, Macfarlan TS. Transposable elements as genetic regulatory substrates in early development. Trends Cell Biol. 2013; doi: 10.1016/j.tcb.2013.01.001 · DOI
  10. Lisch DR, Bennetzen JL. Transposable element origins of epigenetic gene regulation. Curr Opin Plant Biol. 2011;14:156–61. · DOI
  11. Hoen DR, Bureau TE. in Plant transposable elements. Springer Berlin Heidelberg; 2012. 24, p. 219–251. · DOI
  12. Volff J-N. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays. 2006;28:913–22. · DOI
  13. Hoen DR, Bureau TE. Discovery of novel genes derived from transposable elements using integrative genomic analysis. Mol Biol Evol. 2015;32:1487–1506. · DOI
  14. Li Y, Li C, Xia J, Jin Y. Domestication of transposable elements into MicroRNA genes in plants. PLoS One. 2011;6, e19212.
  15. Jacques P-É, Jeyakani J, Bourque G. The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet. 2013;9, e1003504.
  16. Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, et al. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res. 2014;24:1963–76. · DOI · Paper page
  17. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007;8:973–82. · DOI
  18. Kapitonov VV, Jurka J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet. 2008;9:411–2. author reply 414. · DOI
  19. Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, et al. Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol. 2005;1:166–75. · DOI
  20. Hu TT, Pattyn P, Bakker EG, Cao J, Cheng J-F, Clark RM, et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet. 2011;43:476–81. · DOI
  21. Bergman CM, Quesneville H. Discovering and detecting transposable elements in genome sequences. Brief Bioinformatics. 2007;8:382–92. · DOI
  22. Lerat E. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity. 2010;104:520–33. · DOI
  23. Flutre T, Permal E, Quesneville H. in Plant transposable elements. Springer Berlin Heidelberg; 2012. 24, p. 17–39. · DOI
  24. Saha S, Bridges S, Magbanua ZV, Peterson DG. Computational approaches and tools used in identification of dispersed repetitive DNA sequences. Tropical Plant Biol. 2008;1:85–96. · DOI
  25. Caspi A, Pachter L. Identification of transposable elements using multiple alignments of related genomes. Genome Res. 2006;16:260–70. · DOI
  26. El-Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, et al. A new approach for annotation of transposable elements using small RNA mapping. Nucleic Acids Res. 2015;gkv257. · DOI
  27. Bao Z, Eddy SR. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002;12:1269–76. · DOI
  28. Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21 Suppl 1:i351–8. · DOI
  29. Xu Z, Wang H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007;35:W265–8. · DOI
  30. McCarthy EM, McDonald JF. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics. 2003;19:362–7. · DOI · Paper page
  31. Han Y, Wessler SR. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res. 2010;38:e199–9. · DOI
  32. Feschotte C, Keswani U, Ranganathan N, Guibotsy ML, Levine D. Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes. Genome Biol Evol. 2009;1:205–20. · DOI
  33. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7. · DOI
  34. Kohany O, Gentles AJ, Hankus L, Jurka J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics. 2006;7:474. · DOI
  35. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10. · DOI · Paper page
  36. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10(1):421. http://doi.org/10.1186/1471-2105-10-421 . · DOI · Paper page
  37. Wheeler TJ, Eddy SR. nhmmer: DNA homology search with profile HMMs. Bioinformatics. 2013;29:2487–9. · DOI
  38. Flutre T, Duprat E, Feuillet C, Quesneville H. Considering transposable element diversification in de novo annotation approaches. PLoS One. 2011;6, e16526. · DOI
  39. Li R, Ye J, Li S, Wang J, Han Y, Ye C, et al. ReAS: recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol. 2005;1:313–21.
  40. DeBarry JD, Liu R, Bennetzen JL. Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the assisted automated assembler of repeat families (AAARF) algorithm. BMC Bioinformatics. 2008;9:235. · DOI
  41. Keane TM, Wong K, Adams DJ. RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics. 2013;29:389–90. · DOI
  42. Zytnicki M, Akhunov E, Quesneville H. Tedna: a transposable element de novo assembler. Bioinformatics. 2014;30:2656–8. · DOI
  43. Koch P, Platzer M, Downie BR. RepARK—de novo creation of repeat libraries from whole-genome NGS reads. Nucleic Acids Res. 2014;42:gku210–e80. · DOI
  44. Fiston-Lavier A-S, Barrón MG, Petrov DA, González J. T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data. Nucleic Acids Res. 2015;43:e22–2. · DOI
  45. Ouyang S, Buell C. The TIGR plant repeat databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 2004;32:D360–3. · DOI
  46. Saha S, Bridges S, Magbanua ZV, Peterson DG. Empirical comparison of ab initio repeat finding programs. Nucleic Acids Res. 2008;36:2284–94. · DOI
  47. Ragupathy R, You FM, Cloutier S. Arguments for standardizing transposable element annotation in plant genomes. Trends Plant Sci. 2013; doi: 10.1016/j.tplants.2013.03.005 . · DOI
  48. Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013;2:10. · DOI
  49. Balaji S, Sujatha S, Kumar SS, Srinivasan N. PALI—a database of Phylogeny and ALIgnment of homologous protein structures. Nucleic Acids Res. 2001;29:61–5. · DOI
  50. Van Walle I, Lasters I, Wyns L. SABmark—a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics. 2005;21:1267–8. · DOI
  51. Thompson JD, Koehl P, Ripp R, Poch O. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins. 2005;61:127–36. · DOI
  52. Talwalkar A, Liptrap J, Newcomb J, Hartl C, Terhorst J, Curtis K, et al. SMaSH: a benchmarking toolkit for human genome variant calling. Bioinformatics. 2014;30:2787–2795. · DOI
  53. Kim SY, Speed TP. Comparing somatic mutation-callers: beyond Venn diagrams. BMC Bioinformatics. 2013;14:189. · DOI
  54. Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G. Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biol. 2014;15:462. · DOI
  55. Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol. 2005;15:285–9. · DOI
  56. Doolittle WF, Sapienza C. Selfish genes, the phenotype paradigm and genome evolution. Nature. 1980;284:601–3. · DOI
  57. Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996;6:743–8. · DOI
  58. Kapitonov VV, Jurka J. Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci U S A. 2001;98:8714–9. · DOI
  59. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR. Pack-MULE transposable elements mediate gene evolution in plants. Nature. 2004;431:569–73. · DOI
  60. Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE. The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res. 2005;15:1292–7. · DOI
  61. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet. 2005;37:997–1002. · DOI
  62. Pritham EJ, Feschotte C. Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci U S A. 2007;104:1895–900. · DOI
  63. Yang L, Bennetzen JL. Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci U S A. 2009;106:19922–7. · DOI
  64. Thomas J, Vadnagara K, Pritham. DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (helentrons). Mob DNA. 2014;5:18. · DOI
  65. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, et al. Human-mouse alignments with BLASTZ. Genome Res. 2003;13(1):103–7. http://doi.org/10.1101/gr.809403 . · DOI
  66. Frith MC, Park Y, Sheetlin SL, Spouge JL. The whole alignment and nothing but the alignment: the problem of spurious alignment flanks. Nucleic Acids Res. 2008;36:5863–71. · DOI
  67. Caballero J, Smit AFA, Hood L, Glusman G. Realistic artificial DNA sequences as negative controls for computational genomics. Nucleic Acids Res. 2014;42:e99–9. · DOI · Paper page
  68. Levin HL, Moran JV. Dynamic interactions between transposable elements and their hosts. Nat Rev Genet. 2011;12:615–27. · DOI · Paper page
  69. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12(6):996–1006. http://doi.org/10.1101/gr.229102 · DOI · Paper page
  70. Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, et al. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet. 2013;45:891–8. · DOI
  71. de-la-Chaux N, Tsuchimatsu T, Shimizu KK, Wagner A. The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata. Mob DNA. 2012;3:2. · DOI
  72. Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008;9:18. · DOI
  73. Salamov AA, Solovyev VV. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 2000;10:516–22. · DOI
  74. Cai J, Liu X, Vanneste K, Proost S, Tsai W-C, Liu K-W, et al. The genome sequence of the orchid Phalaenopsis equestris. Nat Genet. 2015;47(1):65–72. http://doi.org/10.1038/ng.3149 . · DOI
  75. Xu P, Zhang X, Wang X, Li J, Liu G, Kuang Y, et al. Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet. 2014;46:1212–9. http://doi.org/10.1038/ng.3098 . · DOI
  76. Rondeau EB, Minkley DR, Leong JS, Messmer AM, Jantzen JR, Schalburg von KR, et al. The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. PLoS One. 2014;9(7), e102089. http://doi.org/10.1371/journal.pone.01020 . · DOI
  77. Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet. 2014;46(9):982–8. http://doi.org/10.1038/ng.3044 . · DOI
  78. Marmoset Genome Sequencing and Analysis Consortium. The common marmoset genome provides insight into primate biology and evolution. Nat Genet. 2014;46:850–7. · DOI
  79. Li F, Fan G, Wang K, Sun F, Yuan Y, Song G, et al. Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet. 2014;46(6):567–72. http://doi.org/10.1038/ng.2987 . · DOI
  80. Sierro N, Battey JND, Ouadi S, Bakaher N, Bovet L, Willig A, et al. The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun. 2014;5:3833. http://doi.org/10.1038/ncomms4833 . · DOI
  81. International Glossina Genome Initiative. Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science. 2014;344:380–386. · DOI
  82. Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noel B, et al. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun. 2014;5:3657. http://doi.org/10.1038/ncomms4657 . · DOI
  83. Wang B, Ekblom R, Bunikis I, Siitari H, Höglund J. Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution. BMC Genomics. 2014;15:180. · DOI
  84. Wegrzyn JL, Liechty JD, Stevens KA, Wu L-S, Loopstra CA, Vasquez-Gross HA, et al. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics. 2014;196(3):891–909. http://doi.org/10.1534/genetics.113.159996 . · DOI
  85. Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, et al. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun. 2014;5. http://doi.org/10.1038/ncomms4311 . · DOI
  86. Chen S, Zhang G, Shao C, Huang Q, Liu G, Zhang P, et al. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet. 2014;46(3):253–60. http://doi.org/10.1038/ng.2890 . · DOI
  87. Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, et al. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Pnas. 2014;111(14):5135–40. http://doi.org/10.1073/pnas.1400975111 . · DOI
  88. Kim S, Park M, Yeom S-I, Kim Y-M, Lee JM, Lee H-A, et al. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet. 2014;46(3):270–8. http://doi.org/10.1038/ng.2877 . · DOI
  89. Zhou D, Zhang D, Ding G, Shi L, Hou Q, Ye Y, et al. Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites. BMC Genomics. 2014;15(1):42. http://doi.org/10.1186/1471-2164-15-42 . · DOI

Cited by

Sorted by citations

See all 105

Metadata

Authors
Hoen, D. R., Hickey, G., Bourque, G., Casacuberta, J., Cordaux, R., Feschotte, C., Fiston-Lavier, A.-S., Hua-Van, A., Hubley, R., Kapusta, A., Lerat, E., Maumus, F., Pollock, D. D., Quesneville, H., Smit, A., Wheeler, T. J., Bureau, T. E., & Blanchette, M.
Venue
Mobile DNA
Publisher
Springer Science and Business Media LLC
Published
2015-08-04
Volume
6
Issue
1
ISSN
1759-8753
DOI
10.1186/s13100-015-0044-6
PMC
PMC4524446
Cited by
105
References
3
Language
en
Licence
creativecommons.org/licenses/by/4.0 (unspecified)
Funders
Genome Canada, Genome Quebec, and the Canadian Institutes for Health Research (ID0ELOAE14)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review