Cockroaches scurry around with thousands of pieces of bacterial genomes
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It’s easy to see why horizontal gene transfer would be common among microbes.
They often live in complex communities that are likely awash in the DNA of dead and damaged cells. Plus, bacteria and archaea lack a membrane between their DNA and the rest of the cell, making it easier for environmental DNA to find its way to the genome. However, a new study this week shows that horizontal gene transfers are remarkably common even in multicellular animals.
And it does so by examining the genomes of multiple cockroach species, which have had bits of bacterial DNA for millions of years. Neither bacteria nor archaea keep their DNA in a structure like the nucleus. As a result, any DNA that finds its way inside the cell has the potential to become intermingled with the genome and be incorporated permanently.
That permanent incorporation is often aided by the DNA damage repair enzymes, which sometimes “fix” damage by inserting any DNA they come across in a cell. Another reason horizontal gene transfer is a big factor among microbes is that they lack dedicated germ cells. If foreign DNA gets incorporated into the genome of any cell, it will be inherited by any descendants of that cell.
In contrast, in multicellular animals, any foreign DNA incorporated into the genome of a liver cell will not be inherited by anything. So, you not only have to get the foreign DNA into the nucleus, but it also needs to get into the nucleus of the right cell. Horizontal gene transfer in complex, multicellular animals was expected to be rare.
When researchers started sequencing animal genomes, they found lots of bits of viruses scattered throughout most of them. But they didn’t find many pieces of bacterial DNA. That was partly because the software that assembled the genome from individual fragments of genome sequence was made to treat bacterial sequence as contamination.
That is not unreasonable, given that we were typically growing up lots of copies of the animal DNA by placing it in bacteria. Since then, we’ve developed techniques that allow us to sequence DNA without growing lots of copies in bacteria. We’ve also got the ability to obtain sequence-extended fragments of DNA, sometimes many thousands of bases long.
These “long read” DNA sequences will often cover both borders where the bacterial sequence meets the animal sequence, making clear that the bacterial version wasn’t the result of contamination. Over time, it has become clear that dozens of animal genes have originated from horizontal gene transfer—including a number in our own genome. If you consider areas of the genome that don’t encode genes, the contribution from other species gets considerably larger.
A team decided to gain perspective by making a comprehensive list of horizontally transferred DNA found in a group of related animal species. They chose cockroaches, and they had a good reason. Cockroaches are closely related to termites.
Termites don’t get a lot of nitrogen in their diet of wood, which is largely comprised of a polymer of sugar molecules. To make up for that, they rely on endosymbiotic bacteria called Blattabacterium that reside inside the termite’s body, and are very efficient at recycling the nitrogen that would be excreted as waste in other species. While the roaches’ diets have diversified considerably, they’ve held on to the Blattabacterium.
Since these bacteria live inside the animals’ bodies and are transferred to ensuing generations by being placed in their eggs, there are plenty of opportunities for horizontal gene transfer.
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