viruses (Wolf et al. 2018). Viruses with a +ssRNA genome have the advantage that
their genome functions as a coding strand equivalent to mRNA which can be
translated directly by the host’s ribosomes. DNA viruses however, particularly the
circular, replication protein (Rep)-encoding ssDNA (CRESS-DNA) viruses, could
have evolved in a very different way, namely from bacterial and archaeal plasmids
using cDNA copies of capsid genes of eukaryotic +RNA viruses on three independent occasions as proposed by Kazlauskas et al. (2019) suggesting polyphyletic
origins. In addition, viroids, which are basically pieces of RNA, can self-replicate
and at least fulfill some of the criteria of life (Ding 2010). All this information led to
the proposal of an RNA world to have existed before the DNA-protein world
evolved (Leslie 2004; Robertson and Joyce 2012) (Fig. 28.2).
We know and fear viruses as obligate parasites dependent on host cells and able to
cause devastating diseases affecting all branches of the tree of life. Interestingly,
scientists have discovered that some viruses have significantly contributed to the
evolution of some of their host species and were even named “editors of the
biological code” (Villarreal 1999, 2012). Amazingly, the development of the mammalian placenta is encoded partially by viral genes that these eukaryotic species
obtained from prior viral infections, established as so-called non-coding DNA
(nDNA) but important for regulatory functions (Villarreal 2016). A lot is still
unknown about the genetic information humans and mammals in general obtained
from viruses, which makes up a substantial amount of our chromosomal information. In this sense, even though viruses are responsible for infections, some of them
deadly, they should be considered as a driver of evolution for eukaryotes and
prokaryotes alike, in the past, now, and will certainly also shape evolution of future
life forms on our planet.
28.4 Diversity of Viruses
The development of modern next-generation sequencing allows us to detect viral
genes in the environment, as well as in hosts, without the need for cultivation of
those viruses. These sequences are then used to build databases that can help us to
identify novel viruses and compare the diversity of viruses between environments.
However, compared to nucleotide databases on the ribosomal gene that are used to
identify bacterial, archaeal, and microeukaryotic species, the viral databases are very
modest, comprising a fraction of the data deposited for prokaryotic species which
limits the ability of alignment-based classification of viral agents. With time, however, these databases will grow and become indispensable for viral researchers in the
medical field and environmental field alike. Unfortunately, viruses are so diverse that
they lack a universally conserved gene analogous to the ribosomal gene that we use
to compare prokaryotic and eukaryotic diversity. In addition, known members of
some viral families have segmented genomes, such as members of the
Polydnaviridae (10–11 segments), Orthomyxoviridae (6–8 segments), and
Reoviridae (8–12 segments) (Lucía-Sanz and Manrubia 2017), which provide a
28 Viruses, Underestimated Drivers of Ecology and Evolution of Life
619
their genome functions as a coding strand equivalent to mRNA which can be
translated directly by the host’s ribosomes. DNA viruses however, particularly the
circular, replication protein (Rep)-encoding ssDNA (CRESS-DNA) viruses, could
have evolved in a very different way, namely from bacterial and archaeal plasmids
using cDNA copies of capsid genes of eukaryotic +RNA viruses on three independent occasions as proposed by Kazlauskas et al. (2019) suggesting polyphyletic
origins. In addition, viroids, which are basically pieces of RNA, can self-replicate
and at least fulfill some of the criteria of life (Ding 2010). All this information led to
the proposal of an RNA world to have existed before the DNA-protein world
evolved (Leslie 2004; Robertson and Joyce 2012) (Fig. 28.2).
We know and fear viruses as obligate parasites dependent on host cells and able to
cause devastating diseases affecting all branches of the tree of life. Interestingly,
scientists have discovered that some viruses have significantly contributed to the
evolution of some of their host species and were even named “editors of the
biological code” (Villarreal 1999, 2012). Amazingly, the development of the mammalian placenta is encoded partially by viral genes that these eukaryotic species
obtained from prior viral infections, established as so-called non-coding DNA
(nDNA) but important for regulatory functions (Villarreal 2016). A lot is still
unknown about the genetic information humans and mammals in general obtained
from viruses, which makes up a substantial amount of our chromosomal information. In this sense, even though viruses are responsible for infections, some of them
deadly, they should be considered as a driver of evolution for eukaryotes and
prokaryotes alike, in the past, now, and will certainly also shape evolution of future
life forms on our planet.
28.4 Diversity of Viruses
The development of modern next-generation sequencing allows us to detect viral
genes in the environment, as well as in hosts, without the need for cultivation of
those viruses. These sequences are then used to build databases that can help us to
identify novel viruses and compare the diversity of viruses between environments.
However, compared to nucleotide databases on the ribosomal gene that are used to
identify bacterial, archaeal, and microeukaryotic species, the viral databases are very
modest, comprising a fraction of the data deposited for prokaryotic species which
limits the ability of alignment-based classification of viral agents. With time, however, these databases will grow and become indispensable for viral researchers in the
medical field and environmental field alike. Unfortunately, viruses are so diverse that
they lack a universally conserved gene analogous to the ribosomal gene that we use
to compare prokaryotic and eukaryotic diversity. In addition, known members of
some viral families have segmented genomes, such as members of the
Polydnaviridae (10–11 segments), Orthomyxoviridae (6–8 segments), and
Reoviridae (8–12 segments) (Lucía-Sanz and Manrubia 2017), which provide a
28 Viruses, Underestimated Drivers of Ecology and Evolution of Life
619