1.8: Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence. Overall, this contributes to the phenomena that prokaryotic genomes tend to be smaller (i.e. contain fewer bases) on average than those of eukaryotes.

Unsurprisingly, given this observation, the smallest known genomes are mostly prokaryotes. Candidatus Carsonella rudii, for example, is a highly simplified proteobacterium which has a genome size of just 160 thousand base-pairs. Having lost many genes that it needed to synthesize life-essential proteins, it has evolved to be an obligate intracellular symbiont. At the opposite end of the spectrum, the eukaryote Japanese flowering plant Paris japonica is one of the largest known genomes, at around 150 billion base-pairs. Although the number of genes this encodes isn’t known, the genome shows vast amounts of duplication and non-coding sequence.

Within the genome of an average prokaryote there are roughly 3,000 genes. The average eukaryote has somewhere in the region of 20,000. But the genome size, especially in eukaryotes, is wildly variable - in large part due to the amount of non-coding sequence.

The Creation of New Genes

In order to evolve new genes, organisms have a few main options. The one thing most of these have in common is that they modify sequences that already exist.

Duplication plays an important role in creating new genes, and there are a few types of duplication that can result in these novel sequences. In gene duplication, a section of DNA containing a gene is duplicated. This second copy does not face the selection pressure which constrains the first, and so it can diverge. In time, this can lead to the evolution of novel genes, with new roles.

Another type of duplication - DNA shuffling - can result in just a section of a gene being duplicated and joining another gene. This can result in the creation of novel genes, with novel products.

Sometimes new genes simply evolve from accumulated mutations over time. This is known as intragenic mutation, and is most noticeable when comparing across species or divergent populations.

Finally, it is also possible to obtain new genes from external sources, in a process known as horizontal gene transfer. This means genetic material can be incorporated from other individuals, sometimes of the same species, but also potentially from another species entirely. This is a frequent source of novel genes in prokaryotes and archaea. It is less common in eukaryotes, but has been shown to occur, and eukaryotes can even pick up genetic information from sources as distant as bacteria or fungi.

Despite the simple nature of the genetic code, there is considerable variation in terms of genome size, from the smallest known genomes - including the proteobacterium Candidatus Carsonella ruddii at less than 160 thousand base pairs, to the largest, such as the Japanese flowering plant Paris japonica at around 150 billion.
 
Despite these extremes, bacteria and archaea generally have around 3,000 genes within their genomes. Because prokaryotes have almost no non-coding sequences, this means that their genomes can be relatively small compared to those of eukaryotes. Smaller genomes also mean less to replicate at each round of cell division - which makes logistical sense for fast reproduction.

Eukaryotes typically have somewhere in the region of 20,000 genes, but their genomes are punctuated by long stretches of non-coding sequence - meaning their genome size does not necessarily translate to complexity. 

Paris japonica’s genome may be over fifty times the size of the human genome - but this is due at least in part to vast amounts of non-coding sequence and probably high levels of duplication - not necessarily more novel genes.

So how do organisms evolve new genes? The answer is typically by modifying the sequence that already exists.

One of the primary resources for new genes to evolve is through gene duplication. Imagine a section of DNA containing a gene is accidentally duplicated. Now the organism has a second copy of an existing gene. 

Such new gene copies are free from the constraints placed on the original to maintain function, and so they can diverge - potentially evolving a novel role or a modified function of the original. 

Another way to create new genes is DNA shuffling - where segments of an existing gene or gene copy are separated and moved to join those of a different gene - making a hybrid gene that can take on a new function.

Intragenic mutation - the changes in a gene sequence introduced by mutations over time, accounts for many “new” genes. This divergence which is most noticeable when comparing species or lineages which are themselves diverging independently. Once this divergence is beyond a certain point, or one gene takes on a novel function, they may be classified as different genes entirely.

Finally, horizontal gene transfer brings in novel genes and sequences to the genome from external sources - such as other individuals and even other species. This type of novel gene acquisition is most common in prokaryotes and archaea, with the transfer of antibiotic resistance genes being a well-known example. 

While rare in eukaryotes, it is still considered to be an essential source of genetic novelty, and genetic material can even come from distantly related species, such as the bacteria and fungi in this example.