Ajay Saini

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

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 approximately 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.

The BamHI site in the internal transcribed spacer region of mungbean ribosomal RNA gene is partially methylated.

The 18s-5.8s-25s ribosomal gene (18s-25s rDNA) in higher plants is present in multiple copies, on different chromosomes, as tandemly repeated units. Among the multiple BamHI sites that occur in the repeat unit, only the site in the middle of the 25s rRNA coding region is methylated in most cereals and pulses. BamHI restriction enzyme analyses of the mungbean 18s-25s rDNA showed the presence of two populations. Nearly 50% of the 18s-25s rDNA population had BamHI site situated in the internal transcribed spacer region (ITS-BamHI) resistant to cleavage by BamHI. The amplified ITS fragment was completely digestible by BamHI showing that partial cleavage by BamHI is not due to variation in the recognition sequence but most probably due to methylation. The complete cleavage of the ITS-BamHI site by BstYI that recognizes BamHI site but is insensitive to methylation confirms that the ITS-BamHI site is methylated. Methylation is probably due to the presence of a guanosine residue adjacent to the 3′ cytosine in the recognition sequence.

Genetic diversity assessment in Pandanus amaryllifolius Roxb. populations of India

Pandanus amaryllifolius is cultivated in home gardens in coastal regions of India. Leaves of P. amaryllifolius are scented and exploited commercially by flavour industry. In the present attempt, 40 clonal populations were used for genetic diversity assessment using ISSR and AFLP molecular marker. In ISSR based diversity analysis, out of 38 scorable primers, only one primer showed polymorphism and most of the polymorphic fragments were found in clonal populations from Thailand locality only. In AFLP based diversity analysis all clonal populations from India showed very low genetic distance except Kolkata and Amtala but these populations showed more similarity with Sri Lanka clones and these two localities showed more similarity with Thailand population. Present study confirms that the species has very low level of genetic variation even though it is exposed to a wide range of environmental conditions across peninsular India. Thus, the genome of P. amaryllifolius is said to be highly conserved and remained unaffected through its spread. As per previous report P. amaryllifolius has been introduced in Kolkata, India in 1798 from Indonesia, the similarity is shown by the populations of West Bengal with Thailand population which is close to Indonesia. The populations from Sri Lanka showed similarity with the populations from east and west coast of India suggests that Sri Lanka may be the another source of introduction of P. amaryllifolius in India.

Assessment of hybridization among wild and cultivated Vigna unguiculata subspecies revealed by arbitrarily primed polymerase chain reaction analysis.

This paper show that inter-subspecies hybridization among certain Vigna unguiculata subspecies, occurred during the course of evolution. This has affected several regions of the genome and is interfering with the dependable assessment of sub-species relationships using single (rRNA regions) or multilocus markers.

Heat-stress priming and alternative splicing-linked memory

This article comments on: Ling Y, Serrano N, Gao G, Atia M, Mokhtar M, Woo YH, Bazin J, Veluchamy A, Benhamed M, Crespi M, Gehring C, Reddy ASN, Mahfouz MM. 2018. Thermopriming triggers splicing memory in Arabidopsis. Journal of Experimental Botany 69, 2659–2675.