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Presumptive somatic cells of the copepod Cyclops kolensis specifically eliminate a large fraction of their genome by the process of chromatin diminution. The eliminated DNA (eDNA) remains only in the germline cells. Very little is known about the nature of the sequences eliminated from somatic cells. We cloned a fraction of the eDNA and sequenced 90 clones that total 32 kb. The following organizational patterns were demonstrated for the eDNA sequences. All do not contain open reading frames. Each fragment contains 1–3 families of short repeats (10–30 bp) highly homologous within families (87%–100%). Most repeats are separated by spacers up to 50 bp long. Homologous regions were found between fragments, motifs from 15–300 bp in length. Among fragments there occur groups in which the same motifs are ordered in the same fashion. However, spacers between the motifs differ in length and nucleotide composition. Ubiquitous motifs (those occurring in all fragments) were identified. Analysis of motifs revealed submotifs, each occurring within several motifs. Thus, motifs may be regarded as mosaic structures composed of submotifs (short repeats). Taken together, the results provide evidence of a high organizational ordering of the DNA sequences restricted to the germline. With this in mind, it appears incorrect to refer to this part of the genome as junk. Moreover, eDNA is redundant for only the somatic cells—its function is to be sought in germline cells

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.

This article provides an overview of research on chromatin diminution (CD) in copepods. The phenomenology, mechanisms and biological role of CD are discussed. A model of CD as an alternative means of regulating cell differentiation is presented. While the vast majority of eukaryotes inactivate genes that are no longer needed in development by heterochromatinization, copepods probably use CD for the same purpose. It is assumed that the copepods have exploited CD as a tool for adaptation to changing environmental conditions and as a mechanism for regulating the rate of evolutionary processes.

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Chromatin diminution (CD) is a phenomenon of programmed DNA elimination which takes place in early embryogenesis in some eukaryotes. The mechanism and biological role of CD remain largely unknown. During CD in the freshwater copepod Cyclops kolensis, the genome of cells of the somatic lineage is reorganized and reduced in size by more than 90% without affecting the genome of germline cells. Although the diploid chromosome number is unchanged, chromosome size is dramatically reduced by CD. The eliminated DNA consists primarily of repetitive sequences and localizes within granules during the elimination process. In this review, we provide an overview of CD in C. kolensis including both cytological and molecular studies.

The results of quantitative PCR (qPCR) presented in the paper clearly demonstrate that the sixteen-fold genome reduction inCyclops kolensisduring chromatin diminution (from 15.3 pg to 0.98 pg) results in a dramatic decrease in ribosomal RNA gene copy numbers in the genome of a somatic cell line by more than two orders of magnitude. The results presented allow for the consideration of the chromatin diminution as a mechanism of rDNA copy number regulation.