Annotation of Plant Genome: A Case Study of Oryza sativa

  • Harpreet Kaur
  • Rajan Keshri
  • Tanzeel Tufail Mir
Keywords: senescence, interaction, signals, plant genome annotation, plant ontologies, plant gene family data bases, genome annotation pipelines, Functional annotation, Annotation Repetitive Sequence Functional Description


Rice! A perennial claim crop of the world. Besides satisfying the eager of energy rice, has also been known to support worlds trade economy. Hence, being a crop of such crucial importance its examinational study at genome level will serve in multiplying its production and quality to irrigate the burning crave of humanity.  Likewise, the senescence gene of rice is responsible for its age duration. Hence, understanding its property at 360° will help us to modify or to alter its function in positive portion.

Using Insilco analysis mode, the present study is an attempt to examine various characteristics conformation of senescence causing gene in rice. The two gene chosen were HCP and RR because, the interaction in between these two led to the onset of senescence in rice. Two gene that is HCP (Histidine-containing phosphotransfer protein 1) and RR (Two-component response regulator) are responsible for attaining the stage of senescence in rice. Understanding their molecular and structural property will be going to let us closer to perform successful adjustments. Moreover, their specific property is also responsible for their specific interaction which led to generation of such signals that triggers senescence. Therefore, this analysis was aimed to understand the features of the two genes as well as their interaction by the means of computational technique.

Understanding the features, function and flow of gene will lead us to stabilized effective measure in order to get a beneficiary outcome while going for alteration in its characters. As the pure data for the structure conformation of the selected genes are not available so, we have at first, searched the most similar homolog of the query sequence and the search was based on similar sequence homology on the platform of local alignment tool. And further analysis was carried out on the base conformation of the most relevant homologs (structure/sequence) found.

We have analyze the query gene sequence by various dry lab analysis tool to explore its structural and molecular features with the motive to contribute a little knowledge for the sake of further studies to delay senescence in rice plant in order to increase grain productivity.


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How to Cite
Harpreet Kaur, Rajan Keshri, & Tanzeel Tufail Mir. (2020). Annotation of Plant Genome: A Case Study of Oryza sativa. International Journal for Research in Applied Sciences and Biotechnology, 7(5), 12-41.