Data from: The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

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.