During macronuclear development, ciliate genomes undergo a high level of chromosomal processing, the extent of which varies among ciliate groups. For example in Tetrahymena (class Oligo-hymenophorea), the five large zygotic chromosomes (totaling ~110Mb) are fragmented and DNA is eliminated to produce 200 distinct macronuclear chromosomes between 100 and 1500 kb long. Each of these chromosomes contains several hundred genes and is amplified an average of 45 times (Chalker and Yao 2001; Prescott 1994; Orias and Higashinakagawa 1990). In other species in Oligohymenophorea, such as Paramecium tetra-urelia, each macronuclear chromosome is amplified an average of 800 times (Jahn and Klobutcher 2002; Klobutcher and Herrick 1997; Yao et al. 2002). Some extensive fragmenters of the class Spiro-trichea fragment their approximately 120 zygotic chromosomes into as many as 24 000 macronuclear chromosomes, each less than 15 kb in length and most of which contain only a single gene; each chromosome may be amplified 950-15000 times (Klobutcher and Herrick 1997; Prescott 1994).
At least a portion of the genome, the ribosomal DNA locus, is thought to be highly processed in all ciliates. In all species studied to date, zygotic chromosomes are processed such that rDNA genes are found on macronuclear chromosomes ranging from 8 to 15 kb and containing either a single or pair of rDNA clusters with no other genes (Prescott 1994). In fact, extrasomal processing and amplification of rDNAs occurs in diverse lineages of eukaryotes (i.e. Euglena gracilis, Dictyostelium discoideum, Entamoeba histolytica, Xenopus laevis embryos; reviewed in Zufall et al. 2005). Perhaps the effect of this processing is to maintain high levels of homogeneous rDNAs that are necessary to meet the requirements of translation.
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