High coding density on the largest Paramecium tetraurelia somatic chromosome.
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.
Zagulski
Marek
M
Institute of Biochemistry and Biophysics, DNA Sequencing Laboratory, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
Nowak
Jacek K
JK
Le Mouël
Anne
A
Nowacki
Mariusz
M
Migdalski
Andrzej
A
Gromadka
Robert
R
Noël
Benjamin
B
Blanc
Isabelle
I
Dessen
Philippe
P
Wincker
Patrick
P
Keller
Anne-Marie
AM
Cohen
Jean
J
Meyer
Eric
E
Sperling
Linda
L
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics*; D040461:Gene Components; D015723:Gene Library; D017125:Genes, Protozoan / Q000235:genetics*; D018503:Genome, Protozoan; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D016805:Paramecium tetraurelia / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology