Skip to main content
SpringerLink
Log in
Book cover

Brachypodium Genomics pp 149–171Cite as

Identification of Pseudogenes in Brachypodium distachyon Chromosomes

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1667))

Abstract

Pseudogenes are gene copies that have lost the capability to encode a functional protein. Based on their structure, pseudogenes are classified in two types. Processed pseudogenes arise by a process of retrotranscription from a spliced mRNA and subsequent integration into the genome. Nonprocessed (or duplicated) pseudogenes are generated by genomic duplication and subsequent mutations that disable their functionality so that they cannot longer encode a functional protein. Differently from processed pseudogenes, duplicated pseudogenes are expected to conserve the exon–intron structure of their functional paralogs.

Here, we describe a computational pipeline for identifying pseudogenes of both types in B. distachyon chromosomes. Our pipeline (1) identifies pseudogenes based on tBLASTn searches of B. distachyon proteins against the noncoding genomic complement of the same species, (2) identifies the most homologous pseudogenes functionally paralogous as the pseudogene paternal locus, (3) uses the intron–exon structure of paternal genes to distinguish between pseudogene types.

The pipeline is presented in its composing steps and tested on the Brachypodium distachyon Bd1 scaffold.

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

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768

    Article  Google Scholar 

  2. Wicker T, Mayer KFX, Gundlach H et al (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23:1706–1718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Wang W, Zheng H, Fan C et al (2006) High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18:1791–1802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Guo X, Zhang Z, Gerstein MB et al (2009) Small RNAs originated from pseudogenes: cis- or trans-acting? PLoS Comput Biol 5:e1000449

    Article  PubMed  PubMed Central  Google Scholar 

  5. Zhang Z, Carriero N, Zheng D et al (2006) PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (Oxford) 22:1437–1439

    Article  CAS  Google Scholar 

  6. Zhang ZD, Frankish A, Hunt T et al (2010) Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol 11:R26

    Article  PubMed  PubMed Central  Google Scholar 

  7. Harrison PM (2014) Pseudogenes: functions and protocols. Springer, New York, NY

    Google Scholar 

  8. Thibaud-Nissen F, Ouyang S, Buell CR (2009) Identification and characterization of pseudogenes in the rice gene complement. BMC Genomics 10:317

    Article  PubMed  PubMed Central  Google Scholar 

  9. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  10. Camiolo S, Porceddu A (2013) gff2sequence, a new user friendly tool for the generation of genomic sequences. BioData Mining 6:15

    Article  PubMed  PubMed Central  Google Scholar 

  11. Lipman DJ, Pearson WR (1985) Rapid and sensitive protein similarity searches. Science 227:1435–1441

    Article  CAS  PubMed  Google Scholar 

  12. Harris RS (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University

    Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Pearson WR, Wood T, Zhang Z et al (1997) Comparison of DNA sequences with protein sequences. Genomics 46:24–36

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dipartimento di Agraria, SACEG, Università degli studi di Sassari, Via Enrico De Nicola 1, Sassari, 07100, Italy

    Salvatore Camiolo & Andrea Porceddu

Authors
  1. Salvatore Camiolo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrea Porceddu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Salvatore Camiolo .

Editor information

Editors and Affiliations

  1. Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach IASMA, Trentino, Italy

    Gaurav Sablok

  2. Sabanci University, Istanbul, Turkey

    Hikmet Budak

  3. Climate Change Cluster (C3), University of Technology Sydney, Sydney, New South Wales, Australia

    Peter J. Ralph

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Camiolo, S., Porceddu, A. (2018). Identification of Pseudogenes in Brachypodium distachyon Chromosomes. In: Sablok, G., Budak, H., Ralph, P. (eds) Brachypodium Genomics. Methods in Molecular Biology, vol 1667. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7278-4_12

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7278-4_12

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7276-0

  • Online ISBN: 978-1-4939-7278-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation