The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. Swart, E., C., Bracht, J., R., Magrini, V., Minx, P., Chen, X., Zhou, Y., Khurana, J., S., Goldman, A., D., Nowacki, M., Schotanus, K., Jung, S., Fulton, R., S., Ly, A., McGrath, S., Haub, K., Wiggins, J., L., Storton, D., Matese, J., C., Parsons, L., Chang, W., Bowen, M., S., Stover, N., A., Jones, T., A., Eddy, S., R., Herrick, G., A., Doak, T., G., Wilson, R., K., Mardis, E., R., & Landweber, L., F. PLoS Biology, 2013.

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The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (~5%) of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10%, encode 2-8 genes), have minimal noncoding regions, and are differentially amplified to an average of ~2,000 copies. We report the high-quality genome assembly of ~16,000 complete nanochromosomes (~50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ~3.2 kb) and encode ~18,500 genes. Alternative DNA fragmentation processes ~10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ~4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease. © 2013 Swart et al.

@article{
 title = {The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes},
 type = {article},
 year = {2013},
 keywords = {Base Sequence,DNA,DNA Copy Number Variations,DNA Fr,Gene Amplification,Gene Rearrangement,Genetic Variation,Genome,Macronucleus,Messenger,Molecular Sequence Data,Protozoan,Sequence Analysis,Telomere,article,bacterial strain,cell expansion,contro,transposase},
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 abstract = {The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (~5%) of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10%, encode 2-8 genes), have minimal noncoding regions, and are differentially amplified to an average of ~2,000 copies. We report the high-quality genome assembly of ~16,000 complete nanochromosomes (~50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ~3.2 kb) and encode ~18,500 genes. Alternative DNA fragmentation processes ~10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ~4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease. © 2013 Swart et al.},
 bibtype = {article},
 author = {Swart, E C and Bracht, J R and Magrini, V and Minx, P and Chen, X and Zhou, Y and Khurana, J S and Goldman, A D and Nowacki, M and Schotanus, K and Jung, S and Fulton, R S and Ly, A and McGrath, S and Haub, K and Wiggins, J L and Storton, D and Matese, J C and Parsons, L and Chang, W.-J. and Bowen, M S and Stover, N A and Jones, T A and Eddy, S R and Herrick, G A and Doak, T G and Wilson, R K and Mardis, E R and Landweber, L F},
 doi = {10.1371/journal.pbio.1001473},
 journal = {PLoS Biology},
 number = {1}
}

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