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Characterization of pseudogenes in members of the order Frankineae

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Abstract

Pseudogenes are defined as non-functional relatives of genes whose protein-coding abilities are lost and are no longer expressed within cells. They are an outcome of accumulation of mutations within a gene whose end product is not essential for survival. Proper investigation of the procedure of pseudogenization is relevant for estimating occurrence of duplications in genomes. Frankineae houses an interesting group of microorganisms, carving a niche in the microbial world. This study was undertaken with the objective of determining the abundance of pseudogenes, understanding strength of purifying selection, investigating evidence of pseudogene expression, and analysing their molecular nature, their origin, evolution and deterioration patterns amongst domain families. Investigation revealed the occurrence of 956 core pFAM families sharing common characteristics indicating co-evolution. WD40, Rve_3, DDE_Tnp_IS240 and phage integrase core domains are larger families, having more pseudogenes, signifying a probability of harmful foreign genes being disabled within transposable elements. High selective pressure depicted that gene families rapidly duplicating and evolving undoubtedly facilitated creation of a number of pseudogenes in Frankineae. Codon usage analysis between protein-coding genes and pseudogenes indicated a wide degree of variation with respect to different factors. Moreover, the majority of pseudogenes were under the effect of purifying selection. Frankineae pseudogenes were under stronger selective constraints, indicating that they were functional for a very long time and became pseudogenes abruptly. The origin and deterioration of pseudogenes has been attributed to selection and mutational pressure acting upon sequences for adapting to stressed soil environments.

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Acknowledgements

The authors thank the Bioinformatics Division of the Department of Biotechnology (DBT), India, for providing financial assistance in setting up Bioinformatics Facility in the University of North Bengal. SS acknowledges DBT for providing fellowship. The work is partially funded by UGC project on Frankia awarded to AS. AS also acknowledges the receipt of DBT-CREST award.

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Authors and Affiliations

  1. Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, 734 013, India

    Saubashya Sur, Sangita Saha & Arnab Sen

  2. Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA

    Louis S Tisa

  3. Raiganj University College, Raiganj, India

    Asim K Bothra

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  1. Saubashya Sur
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  2. Sangita Saha
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  3. Louis S Tisa
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  4. Asim K Bothra
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  5. Arnab Sen
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Correspondence to Saubashya Sur.

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[Sur S, Saha S, Tisa LS, Bothra AK and Sen A 2013 Characterization of pseudogenes in members of the order Frankineae. J. Biosci. 38 1–6] DOI 10.1007/s12038-013-9356-1

Supplementary materials pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/nov2013/supp/Sur.pdf

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Sur, S., Saha, S., Tisa, L.S. et al. Characterization of pseudogenes in members of the order Frankineae. J Biosci 38, 727–732 (2013). https://doi.org/10.1007/s12038-013-9356-1

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  • DOI: https://doi.org/10.1007/s12038-013-9356-1

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