The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny

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.

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

“…The highest similarity of repeats within the groups of M. beccarii / M. textilis and M. acuminata / M. ornata or M. acuminata / M. ornata / M. balbisiana are in agreement with previous results that showed close phylogenetic relationships of these species [6], [8], [46] and support the new taxonomy of Musaceae [9]. In general, sequence and quantitative differences were proportional to diversification of species of the Musaceae family (compare Fig.…”

DArT whole genome profiling provides insights on the evolution and taxonomy of edible Banana (Musaspp.)

“…Some authors have claimed the occurrence of parthenocarpic BBB cultivars (Valmayor et al , 2000). Ribosomal DNA analysed for one of these accessions, ITC0652 ‘Kluaï Tiparot’, indeed revealed a B genome component only (Boonruangrod et al , 2008) while internal transcribed spacer (ITS) sequence and cytogenetic analyses of satellite DNA unambiguously confirmed the presence of rDNA loci specific to the B as well as to the A genome in the second accessions, ITC0473 ‘Balonkawe’ (Hřibová et al , 2011; Čížková et al , 2013). Therefore, the potential occurrence of an incomplete A genome within this subgroup needs to be investigated.…”

Molecular and cytological characterization of the global Musa germplasm collection provides insights into the treasure of banana diversity

“…The recent revision of the sectional classification (Häkkinen 2013), supported by the results obtained using DNA markers and phylogenetic analyses (e.g. Bartoš et al 2005;Risterucci et al 2009;Li et al 2010;Christelová et al 2011;Hřibová et al 2011) suggested a merger between Eumusa and Rhodochlamys into the newly established Musa section and, similarly, all Australimusa species are covered by the section Callimusa.…”