Extensive length variation in the ribosomal DNA intergenic spacer of yellow perch (Perca flavescens)

Introduction The multicopy genes encoding ribosomal RNA (rRNA) are arranged as tandem head-to-tail repeats in ribosomal DNA (rDNA). Each copy is composed of three coding genes (18S, 5.8S, and 28S) [...]
The intergenic spacer (IGS) is located between ribosomal RNA (rRNA) gene copies. Within the IGS, regulatory elements for rRNA gene transcription are found, as well as a varying number of other repetitive elements that are at the root of IGS length heterogeneity. This heterogeneity has been shown to have a functional significance through its effect on growth rate. Here, we present the structural organization of yellow perch (Perca flavescens) IGS based on its entire sequence, as well as the IGS length variation within a natural population. Yellow perch IGS structure has four discrete regions containing tandem repeat elements. For three of these regions, no specific length class was detected as allele size was seemingly normally distributed. However, for one repeat region, PCR amplification uncovered the presence of two distinctive IGS variants representing a length difference of 1116 bp. This repeat region was also devoid of any CpG sites despite a high GC content. Balanced selection may be holding the alleles in the population and would account for the high diversity of length variants observed for adjacent regions. Our study is an important precursor for further work aiming to assess the role of IGS length variation in influencing growth rate in fish. Keywords: IGS, spacer length variants, rRNA genes, repetitive elements, Perca flavescens. L'espaceur intergenique (IGS) est situe entre chaque copie des genes de l'ADN ribosomique (ADNr). Le nombre d'elements regulateurs de la transcription des genes ADNr ainsi qu'un nombre variable d'autres elements repetes sont a la base de la variation en taille de l'IGS. Il a ete demontre que cette heterogeneite a un role fonctionnel de par son effet sur le taux de croissance. Dans cette etude, nous presentons l'organisation de l'IGS de la perchaude (Perca flavescens) a partir de la sequence complete ainsi que la variation en taille de l'IGS dans une population naturelle. L'IGS de la perchaude contient quatre regions differentes contenant des elements repetes en tandem. Pour trois de ces regions, il n'y a pas de categories distinctives et la taille des alleles est normalement distribuee. Cependant, pour la region restante, les amplifications par PCR revelent la presence de deux alleles distinctifs, presentant une difference de 1116 pb. Cette region repetee est egalement depourvue de CpG malgre un fort contenu en GC. La selection balancee pourrait maintenir ces deux alleles depuis longtemps dans la population et expliquer la diversite elevee d'alleles de tailles differentes observee dans les regions adjacentes. Cette etude est un important precurseur aux futurs travaux portant sur le role de la variation en taille des IGS et de son influence sur la croissance des poissons. Mots-cles : IGS, variants de longueur de l'espaceur, genes d'ARNr, elements repetes, Perca flavescens.