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    StAR-related lipid transfer (START) domains across the rice pangenome reveal how ontogeny recapitulated selection pressures during rice domestication
    (Frontiers Media S.A., 2021) Mahtha, Sanjeet Kumar; Purama, Ravi Kiran; Yadav, Gitanjali
    The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.
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    Sub-functionalization in rice gene families with regulatory roles in abiotic stress responses
    (Taylor & Francis Group, 2017) Sharma, G.; Giri, Jitender; Tyagi, Akhilesh K.
    Plants have developed intricate mechanisms to overcome abiotic stresses. The process of signal perception and activation of signaling cascades involves a large number of factors and molecules belonging to diverse classes of gene families. In comparison to animals, plants harbor larger multigene families along with the occurrence of plant-specific ones. Gene families with abiotic-stress-responsive members were analyzed and categorized into classes such as transcription factors, signal transduction components, transporters, epigenetic regulators, and other regulatory components. The number of members, phylogeny, family expansion, domain composition, subcellular localization, and expression profiling during varied abiotic stresses have been summarized. Candidate genes from families, functionally characterized for abiotic stress responses, have been described. Based on our compilation, the expansion of abiotic-stress-responsive gene families in rice has occurred via segmental and tandem duplication events to accommodate sub-functionalization needed for regulating diverse abiotic stress responses at expression, localization, and functional levels. The information documented here can be further utilized as a primer for selecting candidate genes for improvement of rice yield under abiotic stresses.
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    Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
    (Frontiers Media S.A., 2015) Singh, Vikash K.; Jain, Mukesh
    Auxin plays a central role in many aspects of plant growth and development. Auxin/Indole-3-Acetic Acid (Aux/IAA) genes cooperate with several other components in the perception and signaling of plant hormone auxin. An investigation of chickpea and soybean genomes revealed 22 and 63 putative Aux/IAA genes, respectively. These genes were classified into six subfamilies on the basis of phylogenetic analysis. Among 63 soybean Aux/IAA genes, 57 (90.5%) were found to be duplicated via whole genome duplication (WGD)/segmental events. Transposed duplication played a significant role in tandem arrangements between the members of different subfamilies. Analysis of Ka/Ks ratio of duplicated Aux/IAA genes revealed purifying selection pressure with restricted functional divergence. Promoter sequence analysis revealed several cis-regulatory elements related to auxin, abscisic acid, desiccation, salt, seed, and endosperm, indicating their role in development and stress responses. Expression analysis of chickpea and soybean Aux/IAA genes in various tissues and stages of development demonstrated tissue/stage specific differential expression. In soybean, at least 16 paralog pairs, duplicated via WGD/segmental events, showed almost indistinguishable expression pattern, but eight pairs exhibited significantly diverse expression patterns. Under abiotic stress conditions, such as desiccation, salinity and/or cold, many Aux/IAA genes of chickpea and soybean revealed differential expression. qRT-PCR analysis confirmed the differential expression patterns of selected Aux/IAA genes in chickpea. The analyses presented here provide insights on putative roles of chickpea and soybean Aux/IAA genes and will facilitate elucidation of their precise functions during development and abiotic stress responses.
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    Two divergent genes encoding L-myo-inositol 1-phosphate synthase1 (CaMIPS1) and 2 (CaMIPS2) are differentially expressed in chickpea
    (Wiley-Blackwell, 2008) Kaur, Harmeet; Shukla, Rakesh Kumar; Yadav, Gitanjali; Chattopadhyay, Debasis; Majee, Manoj
    L-myo-inositol 1-phosphate synthase (MIPS; EC5.5.1.4) catalyses the rate-limiting step in inositol biosynthetic pathway, and is extremely widespread in living organisms including plants. Several plants possess multiple copies of MIPS gene(s) indicating a possibility of differential expression of each gene to perform distinct physiological functions. To explore this, two MIPS genes (CaMIPS1 and CaMIPS2) were isolated from a drought-tolerant plant chickpea. Both genes are extremely divergent in respect to their introns, at the same time retaining 85% identity to their exons and functionally complementing inositol auxotroph Schizosaccharomyces pombe. Expression analysis showed both genes were expressed in all organs except seed, where only CaMIPS2 transcript was detected. Under environmental stresses, only CaMIPS2 was induced whereas CaMIPS1 expression remained same, which could be explained by the divergence of their 5' upstream regulatory sequences. Remarkably, both gene products exhibited similar biochemical characteristics; however, CaMIPS2 retained higher activity than CaMIPS1 at a high temperature and salt concentration. Furthermore, functional expression of CaMIPS2 in S. pombe results better growth response than CaMIPS1 under stress environment. Taken together, our results suggest that CaMIPS1 and CaMIPS2 are differentially expressed in chickpea to play discrete though overlapping roles in plant; however CaMIPS2 is likely to be evolved through gene duplication to function under environmental stresses.