As mentioned in the first calendar door of our advents calendar this year, genomics of small animals is challenging. Yesterday, Nhu Dinh successfully finished her Master thesis but she also experienced some of the challenges related to the small animals and genomics. The problem is that some of them are so small and so few cells, that it is not possible to get enough DNA out of them even for the most sophisticated methods available to date for the modern sequencing technologies. Hence, what shall we do about them. Shall we just forget about it?
This is not a solution as a substantial part of animal biodiversity is small, often very small. Neglecting these animals would mean we neglect a substantial part of what it means to be an animal and their evolution. They are crucial part of their ecosystems bridging between the very small like bacteria to the very large like fish. Hence, we need to get as much information as possible. Nowadays, this entails genomic information. However, some of us are up for this challenge. As we say in Germany: “Einfach kann jeder”.
A PhD student, Nick Roberts, of the lab of our collaborator on the InvertOmics project took up the challenge and he explored the options of whole genome amplification. In the end, he settled in his project on the RepliG method, which proved to be quite successful. He conducted a proof-of-principle study, where he used a single individual of the model organism Caenorhabitis elegans, a nematode. It has its genome already published using thousands of inbred individuals instead of just one and hence he could test the performance of the new protocol. These analyses showed that the new protocol is as good and sometimes slightly than a procedure using hundreds of specimens. Hence, it showed that it is possible to get high quality genomes out of a single individual even if it is tiny.
Then he went even further and applied to an single individual even smaller, one of the gastrotrich Lepidodermella squamata (see image above). More astonishingly, he dared to use only half of that tiny organism and guess what; it worked out. We got the first high-quality genome for a gastrotrich ever. The resulting assembly was 122 Mbp contained in 157 contigs with an N50 of 3.9 Mbp and an L50 of 13. This is just amazingly good quality given the amount of starting material. A few years ago, this would have even been considered marvelous for much larger animals.
That this is a very valuable resource for future studies, we could also show. We used the genome of Lepidodermella squamata together with genomic data of other taxa to determine the closer relatives of the phylum Gastrotricha. It confirmed previous studies by placing them as the sister to the flatworms (Platyhelminthes). This group has been named Rouphozoa before as in contrast to all other phyla in Lophotrochozoa the animals in these two groups can take up food only be sucking it up.
If you want to learn about our study, it has been published yesterday in Genome Biology and Evolution. It is a very interesting, ground-breaking paper and a great accomplishment by Nick.
Featured image modified from picture by Giuseppe Vago (Flickr.com) used with CC BY 2.0
