Abstract
Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades – Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes.
Highlights
Ribosomal ribonucleic acid is the central component of ribosomes - small intracellular particles, which convert the information carried in the genetic code into protein molecules [1]
The present study provides the first insights into the nucleotide structure and diversity of the ITS1-5.8S-ITS2 region in Musaceae and reveal the presence of more than one type of the ITS sequence within some Musa species and hybrid banana clones
We show that it is necessary to use clone-based sequencing strategy for most of the species within Musaceae and identify putative pseudogenic ITS sequences that may have negative effect on phylogenetic reconstruction
Summary
Ribosomal ribonucleic acid (rRNA) is the central component of ribosomes - small intracellular particles, which convert the information carried in the genetic code into protein molecules [1]. The 18S, 5.8S and 26S rRNA genes are separated by internal transcribed spacers ITS1 and ITS2, and the 45S transcription units themselves are separated from each other by non-transcribed intergenic spacers (IGS), extending from the 39 end of 26S rRNA to 59 end of the 18S rRNA coding regions [2]. The ITS are not incorporated into the mature rRNA, they encode signals for proper processing of the rRNA transcripts, which itself depends on the secondary structure of ITS RNA [3]. In contrast to the ITS1 spacer, secondary structures of functional ITS2 spacer as well as 5.8S rDNA sequences are highly conserved within plants [4,5]. The conserved secondary structure of ITS2 and 5.8S sequences makes it possible to identify divergent ITS paralogs with non-functional pseudogenes [10,11,12]
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