, Volume 280, Issue 3-4, pp 187-206
Date: 20 May 2009

Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications

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Abstract

The evolution of 5S rRNA gene unit (5S gene unit) was studied among the ten species belonging to Vigna subgenus Ceratotropis by sequencing and analyzing the intra- and inter-specific sequence heterogeneity. The 5S unit from these species ranged from 214 to 342 bp in length as a result of several indels in the intergenic spacer (IGS) region. A large deletion (>100 bp) was found specifically in the IGS of V. radiata accessions. IGS showed high sequence variation with more than 50% polymorphic and 35.4% parsimony informative sites. However, the coding region (5S gene) was highly conserved, both in length and in sequence. Intra-genomic and intra-specific divergence was observed among some species, which indicated that the 5S unit is evolving at different rates among the Vigna species. Most Vigna species harbored one type of 5S unit indicating complete homogenization among them. Vigna glabrescens, a tetraploid species, also showed single type of 5S rDNA from only one of the diploid progenitor indicating loss or homogenization of the other type. However, V. nakashimae and V. riukiuensis harbored multiple, diverse, ‘intra-genomic 5S types’ indicating that 5S rDNA is not completely homogenized by concerted evolution and is still evolving. In general, the phylogeny based on IGS sequences was in agreement with many of the earlier reports except some surprising observations such as, V. glabrescens clustered with V. mungo in section Ceratotropis and unlike most of the species, wild and cultivated types of V. umbellata were present in different subclusters. Presence of divergent 5S sequences in V. nakashimae and V. riukiuensis caused errors in phylogeny reconstruction at species level and suggested a horizontal ‘gene transfer’ as a result of inter-species hybridization. The comparative analysis showed that 5S IGS sequences have better phylogenetic utility than chloroplast DNA sequences, such as atpB-rbcL and is comparable to ITS1 and ITS2 in this respect.