Evolutionary trends in animal ribosomal DNA loci: introduction to a new online database

Jana Sochorová,Aleš Kovařík,Sònia Garcia,Francisco Gálvez,Radka Symonová

doi:10.1007/s00412-017-0651-8

Abstract

Ribosomal DNA (rDNA) loci encoding 5S and 45S (18S-5.8S-28S) rRNAs are important components of eukaryotic chromosomes. Here, we set up the animal rDNA database containing cytogenetic information about these loci in 1343 animal species (264 families) collected from 542 publications. The data are based on in situ hybridisation studies (both radioactive and fluorescent) carried out in major groups of vertebrates (fish, reptiles, amphibians, birds, and mammals) and invertebrates (mostly insects and mollusks). The database is accessible online at www.animalrdnadatabase.com. The median number of 45S and 5S sites was close to two per diploid chromosome set for both rDNAs despite large variation (1–74 for 5S and 1–54 for 45S sites). No significant correlation between the number of 5S and 45S rDNA loci was observed, suggesting that their distribution and amplification across the chromosomes follow independent evolutionary trajectories. Each group, irrespective of taxonomic classification, contained rDNA sites at any chromosome location. However, the distal and pericentromeric positions were the most prevalent (> 75% karyotypes) for 45S loci, while the position of 5S loci was more variable. We also examined potential relationships between molecular attributes of rDNA (homogenisation and expression) and cytogenetic parameters such as rDNA positions, chromosome number, and morphology.

Highlights

Ribosomal DNA encodes the four essential genes needed for ribosome function: the 5S, 5.8S, 18S, and 28S rRNAs
The database comprises information about the number and position of Ribosomal DNA (rDNA) in animal species collected until the end of 2016, coming from 541 publications
The tabular database structure comprising the information on number and position of rDNA loci and the source publications was created in SQL tables on a MySQL server

Summary

Introduction

Ribosomal DNA (rDNA) encodes the four essential genes needed for ribosome function: the 5S, 5.8S, 18S, and 28S rRNAs. They have been intensively studied at the cytogenetic and molecular levels Probes derived from their conserved regions hybridise to chromosomes of diverged biological taxa, Jana Sochorová and Sònia Garcia contributed to this work. Studies have detected changes in the chromosomal location and size of specific rDNA arrays (loci). The amount of literature containing cytogenetic rDNA data has been steadily increasing in the last years (Fig. 1). With the purpose of providing a tool allowing a better and easier use of animal rDNA cytogenetic information on the number and position of loci available, we have constructed the animal rDNA database. We have analysed the database searching for relationships between the number of 5S and 45S (nucleolus organiser regions (NOR)) loci and for their preferential position (if any) on chromosomes

Methods

Results and discussion

Compliance with ethical standards