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Journal of Heredity Advance Access published online on October 27, 2009
Journal of Heredity, doi:10.1093/jhered/esp084
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© The American Genetic Association. 2009. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Phylogenetic Analysis of Subgenus Vigna Species Using Nuclear Ribosomal RNA ITS: Evidence of Hybridization among Vigna unguiculata Subspecies

Archana Vijaykumar, Ajay Saini, and Narendra Jawali

From the Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India

Address correspondence to Dr Narendra Jawali at the address above, or e-mail: enjay{at}barc.gov.in.

Molecular phylogeny among species belonging to subgenus Vigna (genus Vigna) was inferred based on internal transcribed spacer (ITS) sequences of 18S–5.8S–26S ribosomal RNA gene unit. Analysis showed a total of 356 polymorphic sites of which ~80% were parsimony informative. Phylogenetic reconstruction by neighbor joining and maximum parsimony methods placed the 57 Vigna accessions (belonging to 15 species) into 5 major clades. Five species viz. Vigna heterophylla, Vigna pubigera, Vigna parkeri, Vigna laurentii, and Vigna gracilis whose position in the subgenus was previously not known were placed in the section Vigna. A single accession (Vigna unguiculata ssp. tenuis, NI 1637) harbored 2 intragenomic ITS variants, indicative of 2 different types of ribosomal DNA (rDNA) repeat units. ITS variant type-I was close to ITS from V. unguiculata ssp. pubescens, whereas type-II was close to V. unguiculata ssp. tenuis. Transcript analysis clearly demonstrates that in accession NI 1637, rDNA repeat units with only type-II ITS variants are transcriptionally active. Evidence from sequence analysis (of 5.8S, ITS1, and ITS2) and secondary structure analysis (of ITS1 and ITS2) indicates that the type-I ITS variant probably does not belong to the pseudogenic rDNA repeat units. The results from phylogenetic and transcript analysis suggest that the rDNA units with the type-I ITS may have introgressed as a result of hybridization (between ssp. tenuis and ssp. pubescens); however, it has been epigenetically silenced. The results also demonstrate differential evolution of ITS sequence among wild and cultivated forms of V. unguiculata.

Key Words: epigenetic gene silencing • internal transcribed spacer • subgenus Vigna • Vigna unguiculata

Corresponding Editor: John Stommel

Received January 15, 2009
Revised August 18, 2009
Accepted September 14, 2009


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