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Detection and Analysis of Non-retroviral RNA Virus-Like Elements in Plant, Fungal, and Insect Genomes

  • Hideki KondoEmail author
  • Sotaro Chiba
  • Nobuhiro Suzuki
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1236)

Abstract

Endogenous non-retroviral RNA like sequences (NRVSs) have been discovered in the genome of a wide range of eukaryotes. These are considered as fossil RNA viral elements integrated into host genomes by as-yet-known mechanisms, and in many cases, those fossils are estimated to be millions-of-years-old. It is likely that the number of NRVS records will increase rapidly due to the growing availability of whole-genome sequences for many kinds of eukaryotes. Discovery of the novel NRVSs and understanding of their phylogenetic relationship with modern viral relatives provide important information on deep evolutionary history of RNA virus–host interactions. In this chapter, therefore, the common strategies for the identification and characterization of endogenous NRVSs from plants, insects, and fungi are described.

Key words

Paleovirology Molecular fossil record Non-retrovirus-like sequence Database search Whole-genome shotgun Genomic PCR Southern blotting Phylogenetic analysis Maximum-likelihood 

Notes

Acknowledgment

This work was supported in part by a Grant-in-Aid for Scientific Research from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (KAKENHI 40263628, 25252011) (H.K. and N.S.).

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Institute of Plant Science and Resources (IPSR)Okayama UniversityKurashikiJapan

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