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Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project

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Abstract

The macronuclear genomes of spirotrichous ciliates are almost entirely polyploid, single-gene chromosomes (“nanochromosomes”). We recently performed a pilot genome project for a member of this group, Oxytricha trifallax (Sterkiella histriomuscorum), in which ∼2000 nanochromosomes were cloned at random and end-sequenced. Here we describe the global properties of the coding regions predicted for these molecules, including nucleotide composition, codon usage, and intron properties. In identifying splice donor, acceptor and branch sites, we found that longer introns in Oxytricha have a stronger signal at the donor site than do smaller introns, as has been found for Caenorhabditis elegans and Drosophila, despite the overall small size of the introns. A systematic search for multi-gene chromosomes identified 11 candidate nanochromosomes. We compare the results from this large dataset with those obtained from earlier studies and with statistics recorded from ciliates and other eukaryotes.

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Acknowledgements

We would like to thank Diane Dunn and Robert Weiss from the Utah Genome Depot, and Glenn Herrick from the University of Utah. L.F.L. acknowledges support from NIGMS grant GM59708 and NSF grant EIA0121422.

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Authors and Affiliations

  1. Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA

    Andre R. O. Cavalcanti, Nicholas A. Stover, Lorenzo Orecchia, Thomas G. Doak & Laura F. Landweber

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  1. Andre R. O. Cavalcanti
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  2. Nicholas A. Stover
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  3. Lorenzo Orecchia
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  4. Thomas G. Doak
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  5. Laura F. Landweber
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Correspondence to Laura F. Landweber.

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Communicated by E.A. Nigg

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Cavalcanti, A.R.O., Stover, N.A., Orecchia, L. et al. Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma 113, 69–76 (2004). https://doi.org/10.1007/s00412-004-0295-3

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  • DOI: https://doi.org/10.1007/s00412-004-0295-3

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