Can genomics replace electron microscopy?
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next-generation sequencing |
However, electron microscopy provides information on virion structure. At the same time, genomics does not show the whole virus, gives no single
dimension, provides no information on virus structure and physicochemical properties, identifies unusual bases such as 5-hydroxymethylcytosine, and predicts only some biological properties, such as a lysogenic
nature. No sequence can indicate simple things such as the size of phage
capsids, their geometry, or the number of capsomers. If, as likely, the
length of phage tails depends on the length of ruler protein genes
(Katsura and Hendrix, 1984; Pedulla et al., 2003), this must be ascertained
by measuring many phage tails under strict magnification control. Unfortunately, this has not been the case. If, as pretended, a genome
contains all information on a virus, we have not yet found the instruction
manual to read it.
Concerning virus identification, genomics generally does not indicate to which virus family a tailed phage belongs; for example, there are
no sequences specific to Myo-, Sipho-, or Podoviridae. Only in the case of
small polyhedral or filamentous phages (Micro-, Levi, and Inoviridae)
does genomics allow for identifying virus families (Ackermann
and Kropinski, 2007). Similarly, a Bacillus tectivirus from the earthworm
gut was identified by genomics alone without the benefit of electron
microscopy (Schuch et al., 2010). However, in general, investigation
of a complete virus sequence may take months and is infinitely slower
and more labor-intensive than electron microscopy.
Can metagenomics replace electron microscopy?
The answer is ‘‘no’’
again. For virus identification, metagenomics relies totally on known and
identified genes and genomes, which, in turn, belong to viruses known
and characterized by electron microscopy. In other terms, the vast majority of numerous genes detected by metagenomics can be identified only to
the extent as they belong to known sequences from known viruses.
Further, metagenomics will not tell whether any detected lines
belong to complete, infectious virions or not.
Can electron microscopy replace genomics?
The answer is ‘‘yes,’’ but only when it comes to identifying high-level taxonomic categories. Clearly, electron microscopy and genomics (or metagenomics) are not alternatives but complementary. Both of them answer different questions and appear as other
fingers of the same hand.
(Read more about bacteriophage here)
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MICROSCOPY