Skip to main content
SpringerLink
Log in
SpringerLink
Log in

Comparative Genome Annotation

  • Protocol
  • First Online:
Comparative Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1704))

Abstract

Newly sequenced genomes are being added to the tree of life at an unprecedented fast pace. Increasingly, such new genomes are phylogenetically close to previously sequenced and annotated genomes. In other cases, whole clades of closely related species or strains ought to be annotated simultaneously. Often, in subsequent studies differences between the closely related species or strains are in the focus of research when the shared gene structures prevail. We here review methods for comparative structural genome annotation. The reviewed methods include classical approaches such as the alignment of protein sequences or protein profiles against the genome and comparative gene prediction methods that exploit a genome alignment to annotate a target genome. Newer approaches such as the simultaneous annotation of multiple genomes are also reviewed. We discuss how the methods depend on the phylogenetic placement of genomes, give advice on the choice of methods, and examine the consistency between gene structure annotations in an example. Further, we provide practical advice on genome annotation in general.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  1. Salzberg SL, Angiuoli SV, Dunning Hotopp JC, Tettelin H (2011) Improving pan-genome annotation using whole genome multiple alignment. BMC Bioinf 12(1):272

    Article  Google Scholar 

  2. Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV (2012) OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res 41:D358–D365

    Article  PubMed  PubMed Central  Google Scholar 

  3. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E (2009) EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19(2):327–335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Schmitt-Engel C, Schultheis D, Schwirz J, Ströhlein N, Troelenberg N, Majumdar U, Grossmann D, Richter T, Tech M, Dönitz J, Gerischer L, Theis M, Schild I, Trauner J, Koniszewski NDB, Küster E, Kittelmann S, Hu Y, Lehmann S, Siemanowski J, Ulrich J, Panfilio KA, Schröder R, Morgenstern B, Stanke M, Buchhholz F, Frasch M, Roth S, Wimmer EA, Schoppmeier M, Klingler M, Bucher G (2015) The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology. Nat Commun 6:7822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Avila-Herrera A, Pollard KS (2015) Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. BMC Bioinf 16(1):1–18

    Article  Google Scholar 

  6. Zhang G (2015) Genomics: bird sequencing project takes off. Nature 522(7554):34–34

    Article  CAS  PubMed  Google Scholar 

  7. Smit AFA, Hubley R (2008–2015) RepeatModeler Open-1.0. http://www.repeatmasker.org

  8. Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D (2011) Cactus: algorithms for genome multiple sequence alignment. Genome Res 21(9):1512–1528

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21

    Article  CAS  PubMed  Google Scholar 

  10. Wu TD, Nacu S (2010) Fast and snp-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26:873–881

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Daehwan K, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36

    Article  Google Scholar 

  12. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotech 33:290–295. StringTie transcript assembler. http://ccb.jhu.edu/software/stringtie. Accessed 28 Oct 2014

  13. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Behr J, Kahles A, Zhong Y, Sreedharan VT, Drewe P, Rätsch G (2013) MITIE: simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics 29(20):2529–2538

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28(8):1086–1092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Brian Couger M, Eccles D, Li B, Lieber M, et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8(8):1494–1512

    Article  CAS  PubMed  Google Scholar 

  17. Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24(5):637–644

    Article  CAS  PubMed  Google Scholar 

  18. Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7(Suppl 1):S10

    Article  PubMed  PubMed Central  Google Scholar 

  19. Behr J, Bohnert R, Zeller G, Schweikert G, Hartmann L, Rätsch G (2010) Next generation genome annotation with mGene.ngs. BMC Bioinf 11(S10):O8

    Google Scholar 

  20. Steijger T, Abril JF, Engstrom PG, Kokocinski F, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bohnert R, et al (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10(12):1177–1184

    Article  CAS  PubMed  Google Scholar 

  21. Schweikert G, Zien A, Zeller G, Behr J, Dietrich C, Ong GS, Philips P, De Bona F, Hartmann L, Bohlen A, et al (2009) mGene: accurate SVM-based gene findng with an application to nematode genomes. Genome Res 19:2133–2143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Seledtsov I, Molodtsov V, Kosarev P, Solovyev V (2014) Transomics transcript assembly pipeline. http://www.softberry.com. Accessed 28 Oct 2014

  23. Slater GSC, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinf 6(1):31

    Article  Google Scholar 

  24. Korf I (2013) Genomics: the state of the art in RNA-seq analysis. Nat Methods 10(12):1165–1166

    Article  CAS  PubMed  Google Scholar 

  25. Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299:682–686

    Article  CAS  PubMed  Google Scholar 

  26. Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei C-L, Kaeppler S, Chen F, Wang Z (2014) A near complete snapshot of the zea mays seedling transcriptome revealed from ultra-deep sequencing. Sci Rep 4:4519

    Article  PubMed  PubMed Central  Google Scholar 

  27. Gremme G (2013) Computational Gene Structure Prediction. PhD thesis, Universität Hamburg

    Google Scholar 

  28. Iwata H, Gotoh O (2012) Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Res 40(20):e161

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. ProSplign (2014). http://www.ncbi.nlm.nih.gov/sutils/static/prosplign/prosplign.html. Accessed 17 Oct 2014

  30. Usuka J, Brendel V (2000) Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring. J Mol Biol 297(5):1075–1085

    Article  CAS  PubMed  Google Scholar 

  31. Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Genome Res 14:988–995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Keller O, Kollmar M, Stanke M, Waack S (2011) A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics 27(6):757–763

    Article  CAS  PubMed  Google Scholar 

  33. Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F (2016) Using intron position conservation for homology-based gene prediction. Nucleic Acids Res 44(9):e89

    Article  PubMed  PubMed Central  Google Scholar 

  34. Korf I, Flicek P, Duan D, Brent MR (2001) Integrating genomic homology into gene structure prediction. Bioinformatics 1 Suppl. 1:S1–S9

    Google Scholar 

  35. Alexandersson M, Cawley S, Pachter L (2003) SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res 13:496–502

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, et al (2005) Comparative genome sequencing of drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res 15(1):1–18

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Gross SS, Brent MR (2005) Using multiple alignments to improve gene prediction. In: Proceedings of RECOMB 2005

    Google Scholar 

  38. Gross S, Do C, Sirota M, Batzoglou S (2007) CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol 8(12):R269

    Article  PubMed  PubMed Central  Google Scholar 

  39. Brent MR (2008) Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet 9:62–73

    Article  CAS  PubMed  Google Scholar 

  40. Elsik C, Worley K, Bennett A, Beye M, Camara F, Childers C, de Graaf D, Debyser G, Deng J, Devreese B, et al (2014) Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics 15(1):86

    Article  PubMed  PubMed Central  Google Scholar 

  41. Csuros M, Rogozin IB, Koonin EV (2011) A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comput Biol 7(9):e1002150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Gotoh O, Morita M, Nelson DR (2014) Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment. BMC Bioinf 15(1):189

    Article  Google Scholar 

  43. König S, Romoth LW, Gerischer L, Stanke M (2016) Simultaneous gene finding in multiple genomes. Bioinformatics 32:3388–3395

    PubMed  Google Scholar 

  44. König S, Romoth L, Gerischer L, Stanke M (2015) Simultaneous gene finding in multiple genomes. PeerJ PrePrints 3:e1296v1

    Google Scholar 

  45. Hickey G, Paten B, Earl D, Zerbino D, Haussler D (2013). HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics 29(10):1341–1342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B (2014) Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics 30:3293–3301

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Hiller M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, Bejerano G (2012) A “forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species. Cell Rep 2(4):817–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Goodswen SJ, Kennedy PJ, Ellis JT (2012) Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques. PloS One 7(11):e50609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Lomsadze A, Burns PD, Borodovsky M (2014) Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic Acids Res 42(15):e119

    Article  PubMed  PubMed Central  Google Scholar 

  50. Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M (2015) BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32(5):767–769

    Article  PubMed  Google Scholar 

  51. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) Busco: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31(19):3210–3212

    Article  PubMed  Google Scholar 

  52. Keller O, Odronitz F, Stanke M, Kollmar M, Waack S (2008) Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. BMC Bioinf 9(1):278

    Article  Google Scholar 

  53. Haas B, Salzberg S, Zhu W, Pertea M, Allen J, Orvis J, White O, Buell CR, Wortman J (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 9(1):R7

    Article  PubMed  PubMed Central  Google Scholar 

  54. Holt C, Yandell M (2011) MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinf 12:491

    Article  Google Scholar 

  55. Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M (2005) Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res 33(20):6494–6506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Hoff KJ, Stanke M (2013) WebAUGUSTUS – a web service for training AUGUSTUS and predicting genes in eukaryotes. Nucleic Acids Res 41:W123–W1238

    Article  PubMed  PubMed Central  Google Scholar 

  57. Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ (2013) Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30(7):1003–1005

    Article  PubMed  PubMed Central  Google Scholar 

  58. McKay SJ, Vergara IA, Stajich JE (2010) Using the generic synteny browser (gbrowse_syn). Curr Protoc Bioinformatics UNIT 9.12

    Google Scholar 

  59. Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10(3):155–159

    Article  CAS  PubMed  Google Scholar 

  60. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15(Suppl 1):R17–R29

    Article  CAS  PubMed  Google Scholar 

  61. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775–1789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Lin MF, Jungreis I, Kellis M (2011) PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27(13):i275–i282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Ulitsky I, Bartel DP (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154(1):26–46

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Rivas E, Eddy SR (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2(1):1

    Article  Google Scholar 

  65. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH (2009) JBrowse: a next-generation genome browser. Genome Res 19:1630–1638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Pirovano W, Boetzer M, Derks MF, Smit S (2015) NCBI-compliant genome submissions: tips and tricks to save time and money. Brief Bioinform 18(2):179–182

    Google Scholar 

Download references

Acknowledgement

The research was supported by the German National Academic Foundation (to S.K.) and the German Research Foundation (DFG RTG 1870).

Author information

Authors and Affiliations

  1. Institut für Mathematik und Informatik, Ernst Moritz Arndt Universität Greifswald, Greifswald, Germany

    Stefanie König, Lars Romoth & Mario Stanke

Authors
  1. Stefanie König
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lars Romoth
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mario Stanke
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mario Stanke .

Editor information

Editors and Affiliations

  1. Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil

    João C. Setubal

  2. Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Jens Stoye

  3. Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    Peter F. Stadler

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

König, S., Romoth, L., Stanke, M. (2018). Comparative Genome Annotation. In: Setubal, J., Stoye, J., Stadler, P. (eds) Comparative Genomics. Methods in Molecular Biology, vol 1704. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7463-4_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7463-4_6

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7461-0

  • Online ISBN: 978-1-4939-7463-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation