High Coding Density on the Largest Paramecium tetraurelia Somatic Chromosome

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.

An Ins(1,4,5)P3 receptor in Paramecium is associated with the osmoregulatory system

“…As shown in Fig. 4A, affinity-purified anti- (Yamauchi et al, 1995), accession number S60032, and downstream by a gene (PtSNF1 PK) homologous to a putative SNF1-related protein kinase [ (Zagulski et al, 2004) (Tatusova and Madden, 1999). Sequences are shown in single-letter code and are numbered on the left side.…”

Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number

“…Cold Spring Harbor Laboratory Press on May 10, 2018 -Published by genome.cshlp.org Downloaded from apparently high intron densities of early eukaryotes (Fedorov et al 2002;Rogozin et al 2003;Roy and Gilbert 2005a) or the large population size unicellular species Cryptococcus neoformans and Chlamydomonas reinhardtii (Lynch and Conery 2003;Lin and Zhang 2005;Loftus et al 2005), nor the persistence of a large number of introns in otherwise reduced genomes (Gilson andMcFadden 1996, 2002;Zagulski et al 2004).…”

Overview of gene structure in C. elegans

“…The modal length of Drosophila introns is only 59 bp (The International Human Genome Sequencing Consortium, 2001), as compared to 47 bp for the worm. The mean size of introns on the largest, somatic, macronuclear chromosome of Paramecium is only 25 bp (Zagulski et al, 2004). Fungal introns are also small; Neurospora introns average 134 bp (Galagan et al, 2003), Sordaria macrospora 106 bp (Nowrousian et al, 2004), and Cryptococcus neoformans 67 bp (Loftus et al, 2005).…”