Article

High coding density on the largest Paramecium tetraurelia somatic chromosome.

Institute of Biochemistry and Biophysics, DNA Sequencing Laboratory, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
Current Biology (impact factor: 9.65). 09/2004; 14(15):1397-404. DOI:10.1016/j.cub.2004.07.029 pp.1397-404
Source: PubMed

ABSTRACT Paramecium, like other ciliates, remodels its entire germline genome at each sexual generation to produce a somatic genome stripped of transposons and other multicopy elements. The germline chromosomes are fragmented by a DNA elimination process that targets heterochromatin to give a reproducible set of some 200 linear molecules 50 kb to 1 Mb in size. These chromosomes are maintained at a ploidy of 800n in the somatic macronucleus and assure all gene expression. We isolated and sequenced the largest megabase somatic chromosome in order to explore its organization and gene content. The AT-rich (72%) chromosome is compact, with very small introns (average size 25 nt), short intergenic regions (median size 202 nt), and a coding density of at least 74%, higher than that reported for budding yeast (70%) or any other free-living eukaryote. Similarity to known proteins could be detected for 57% of the 460 potential protein coding genes. Thirty-two of the proteins are shared with vertebrates but absent from yeast, consistent with the morphogenetic complexity of Paramecium, a long-standing model for differentiated functions shared with metazoans but often absent from simpler eukaryotes. Extrapolation to the whole genome suggests that Paramecium has at least 30,000 genes.

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Keywords

460 potential protein coding genes
 
average size 25 nt
 
coding density
 
differentiated functions
 
entire germline genome
 
free-living eukaryote
 
gene content
 
gene expression
 
germline chromosomes
 
largest megabase somatic chromosome
 
long-standing model
 
median size 202 nt
 
multicopy elements
 
sexual generation
 
short intergenic regions
 
simpler eukaryotes
 
small introns
 
somatic genome
 
targets heterochromatin
 
whole genome