Abstract
Grass genomes harbor a diverse and complex content of repeated sequences. Most of these repeats occur as abundant transposable elements (TEs), which present unique challenges to sequence, assemble, and annotate genomes. Multiple copies of Long Terminal Repeat (LTR) retrotransposons can hinder sequence assembly and also cause problems with gene annotation. TEs can also contain protein-encoding genes, the ancient remnants of which can mislead gene identification software if not correctly masked. Hence, accurate assembly is crucial for gene annotation. We present TEnest v2.0. TEnest computationally annotates and chronologically displays nested transposable elements. Utilizing organism-specific TE databases as a reference for reconstructing degraded TEs to their ancestral state, annotation of repeats is accomplished by iterative sequence alignment. Subsequently, an output consisting of a graphical display of the chronological nesting structure and coordinate positions of all TE insertions is the result. Both linux command line and Web versions of the TEnest software are available at www.wiselab.org and www.plantgdb.org/tool/, respectively.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
IRGSP (2005) The map-based sequence of the rice genome. Nature 436:793–800
Baucom RS et al (2009) Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet 5:e1000732
Kronmiller BA, Wise RP (2008) TEnest: automated chronological annotation and visualization of nested plant transposable elements. Plant Physiol 146:45–59
Sabot F et al (2005) Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol Genet Genomics 274:119–130
Rabinowicz PD, Bennetzen JL (2006) The maize genome as a model for efficient sequence analysis of large plant genomes. Curr Opin Plant Biol 9:149–156
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410
SanMiguel P et al (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45
SanMiguel P et al (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765–768
Kronmiller BA, Wise RP (2009) Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. Plant Physiol 151:483–495
Gish W (1996–2004) http://blast.wustl.edu
Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Duvick J et al (2008) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res 36:D959–D965
Lipman DJ, Pearson WR (1985) Rapid and sensitive protein similarity searches. Science 227:1435–1441
Huang X, Miller W (1991) A time-efficient, linear-space local similarity algorithm. Adv Appl Math 12:337–357
Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444–2448
Boeke JD, Corces VG (1989) Transcription and reverse transcription of retrotransposons. Annu Rev Microbiol 43:403–434
Smit AFA, Hubley R, Green P (1996–2004) RepeatMasker Open-3.0. http://www.repeatmasker.org
Stein LD et al (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12:1599–1610
Wei F et al (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet 5:e1000728
Schnable PS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115
Meyer J, Pei D, Wise RP (2011) Rf8-Mediated T-urf13 transcript accumulation coincides with a pentatricopeptide repeat cluster on maize chromosome 2L. Plant Genome 4(3):283–299
Acknowledgments
The authors thank Regina Baucom, James Estill, and Jeff Bennetzen for access to uncharacterized maize LTR retrotransposons prior to publication. This research was supported in part by USDA-National Research Initiative (NRI) grant no. 2002-35301-12064. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, New York
About this protocol
Cite this protocol
Kronmiller, B.A., Wise, R.P. (2013). TEnest 2.0: Computational Annotation and Visualization of Nested Transposable Elements. In: Peterson, T. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 1057. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-568-2_22
Download citation
DOI: https://doi.org/10.1007/978-1-62703-568-2_22
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-567-5
Online ISBN: 978-1-62703-568-2
eBook Packages: Springer Protocols