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    Class-specific evolution and transcriptional differentiation of 14-3-3 family members in mesohexaploid Brassica rapa
    (Frontiers Media S.A., 2016) Chandna, Ruby; Augustine, Rehna; Kanchupati, Praveena; Kumar, Roshan; Kumar, Pawan; Arya, Gulab C.; Bisht, Naveen C.
    14-3-3s are highly conserved, multigene family proteins that have been implicated in modulating various biological processes. The presence of inherent polyploidy and genome complexity has limited the identification and characterization of 14-3-3 proteins from globally important Brassica crops. Through data mining of Brassica rapa, the model Brassica genome, we identified 21 members encoding 14-3-3 proteins namely, BraA.GRF14.a to BraA.GRF14.u. Phylogenetic analysis indicated that B. rapa contains both ε (epsilon) and non-ε 14-3-3 isoforms, having distinct intron-exon structural organization patterns. The non-ε isoforms showed lower divergence rate (Ks < 0.45) compared to ε protein isoforms (Ks > 0.48), suggesting class-specific divergence pattern. Synteny analysis revealed that mesohexaploid B. rapa genome has retained 1–5 orthologs of each Arabidopsis 14-3-3 gene, interspersed across its three fragmented sub-genomes. qRT-PCR analysis showed that 14 of the 21 BraA.GRF14 were expressed, wherein a higher abundance of non-ε transcripts was observed compared to the ε genes, indicating class-specific transcriptional bias. The BraA.GRF14 genes showed distinct expression pattern during plant developmental stages and in response to abiotic stress, phytohormone treatments, and nutrient deprivation conditions. Together, the distinct expression pattern and differential regulation of BraA.GRF14 genes indicated the occurrence of functional divergence of B. rapa 14-3-3 proteins during plant development and stress responses.
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    Origin, structure and function of millions of chromosomes present in the macronucleus of unicellular eukaryotic ciliate, Oxytricha trifallax: a model organism for transgenerationally programmed genome rearrangements
    (Indian Academy of Sciences, 2015) Kumar, Sushil; Kumari, Renu
    The unicellular eukaryotic ciliate protists characteristically contain a germline micronucleus (MIC) and a somatic macronucleus (MAC) in their cytoplasm. The MAC, which is crucial for the pursuit of cellular growth and mitotic divisions, is derived from a postzygotic MIC. The transition from MIC to MAC involves extensive editing of the MIC genome, followed by massive amplification of the residual MAC genome. The spirotrichous ciliate, Oxytricha trifallax, has been most extensively deployed as the model system to reveal the mechanism(s) of origin of the architectural complexities of MAC. This has been possible by the application of genome sequencing, synthetic RNA transgenesis and a variety of other genetic techniques. Here, we summarize and discuss the current observations of MAC genome derived from MIC genome, properties of MAC genome structure, function and significance of the novel features described in O. trifallax. The differences in the genome organization of O. trifallax and its relative alveolate species Paramecium tetraurelia and Plasmodium falciparum have been described. Aspects of programmed genome rearrangements, MAC genome structure and function requiring further analyses in different ciliate protest have been pointed out.