Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

Abstract

BackgroundIn flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in ~200 species representing the family diversity and other closely related groups.ResultsDominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes.ConclusionsOur results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units, their copy number and chromosomal organisation may occur within relatively short evolutionary time. We hypothesize that the 5S gene integration within the 35S unit might have repeatedly occurred during plant evolution, and probably once in Asteraceae.

Detection of genetic diversity among some species of Anthemis L. (Asteraceae) in Saudi Arabia by using RAPD-PCR analysis

“…Results of monomorphism and polymorphism of Anthemis using RAPD-analysis might be precise findings for the genetic diversity of genus Anthemis, to specify each species with the appearance of specific markers and definitive bands. Many studies conducted on other genus revealed similar results with insufficient molecular studies of Anthemideae (Matousek et al, 2007;Garcia et al, 2010;Riggins and Seigler, 2012). Similar results were obtained by other authors (Riggins and Seigler, 2012;Patil et al, 2016;Higgins et al, 2016;Kumar et al, 2016).…”

Early evolutionary colocalization of the nuclear ribosomal 5S and 45S gene families in seed plants: evidence from the living fossil gymnosperm Ginkgo biloba

“…Their results implied that unlinked 45S-5S rDNA arrays were identified for all seed plants checked, including the 10 gymnosperms and the single basal angiosperm lineage experimentally analyzed (Nympheales), and the scrutiny of 10 ribosomal 45S IGS sequences available in public databases (Wicke et al, 2011). These results suggest that in seed plants linked 45S-5S units were exclusive of the Asteraceae family, a derived angiosperm lineage, and that the linkage of both ribosomal gene families likely occurred 7-10 million years ago (Mya) (García et al, 2010).…”

“…Recently, however, it has been unequivocally shown for the first time, using molecular cytogenetics, Southern blot hybridization, PCR-based techniques and DNA sequencing, that 5S genes can be embedded within the 45S multigene family in angiosperms (Asteraceae; García et al, 2009;García et al, 2010). The detailed survey within Asteraceae has revealed that in about 25% of the species in this family, the two ribosomal gene families have been combined into a single, linked 45S-5S unit (García et al, 2010). These authors suggested that the 5S gene integration within the 45S multigene family probably occurred once in Asteraceae, but might have repeatedly occurred elsewhere during plant evolution.…”

“…The juxtaposition of 45S and 5S fluorescent-based signals in dividing cells or interphase nuclei, as observed by FISH, has traditionally been used as putative evidence for the linkage of 45S and 5S rRNA genes in plants. In seed plants, FISH colocalization of both multigene families has been observed not only in the Asteraceae (García et al, 2010), but also in other unrelated angiosperm lineages such as Tulipa (Mizuochi et al, 2007), Rhoeo (Golczyk et al, 2005), Linum (Muravenko et al, 2004), Silene (Široký et al, 2001), Brassica (Snowdon et al, 2000;Hasterok et al, 2001), as well as in a couple of gymnosperm genera: Ginkgo (Nakao et al, 2005) and Podocarpus (Murray et al, 2002). However, given the shortcomings of the axialresolution detection limits of classical FISH (between 2000 and 10 000 kb; Figueroa and Bass, 2010), such molecular cytogenetic methods could generate crude estimates or visual artifacts concerning the organization of the 45S and 5S rDNA families in plants.…”

Karyotype analysis in Allium roseum L. (Alliaceae) using fluorescent in situhybridization of rDNA sites and conventional stainings

“…This technique is very useful for the physical mapping of DNA sequences due to the possibility of simultaneous detection of several probes on the same metaphase chromosomal spread. FISH has been used in many plants to identify chromosomes using species-specific repetitive DNA sequences, ribosomal genes, and even unique DNA sequences (Maluszynska and Heslop-Harrison, 1991;Garcia et al, 2010). Many authors have reported the physical mapping of multigene families, such as 5S and 18S-5.8S-26S rDNA and highly repeated DNA sequences (Rao and Guerra, 2012;Gong et al, 2013).…”