TPJ article: A hitchhikers’ guide to foreign genomes

16 Mar 2021 - By: Leonie Verhage

A hitchhikers’ guide to foreign genomes


A Panicum‐derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress‐related genes

Mahelka, V., Krak, K., Fehrer, J., Caklová, P., Nagy Nejedlá, M., Čegan, R., Kopecký, D. and Šafář, J.

onlinelibrary.wiley.com/doi/10.1111/tpj.15167

TPJ - Leonie article Mars 2021

In 1928, bacteriologist Frederick Griffith performed experiments with pneumococcal bacteria in mice. He found that avirulent pneumococci became virulent when they were in contact with a virulent strain. It was the first experiment that showed that genetic material can be transferred between organisms other than from parent to offspring. Nowadays, this mechanism – called horizontal gene transfer – is known as a major driver of evolution in bacteria. For a long time, horizontal gene transfer was thought to be limited to prokaryotes. However, it is gradually becoming evident that horizontal gene transfer does exist in eukaryotic organisms, including plants. Nevertheless, the reports in plants were limited.

Several years ago, plant researchers stumbled upon something peculiar. The genomes of wild barley (Hordeum) species contained alien DNA sequences that matched ribosomal DNA (rDNA) genes from Panicum. The researchers were intrigued because the lineages to which wild barley and Panicum belong (pooid and panicoid grasses) had split about 50 million years ago. Recently, they established that the foreign DNA was transferred by horizontal gene transfer. In issue 105:5 of The Plant Journal, they managed to characterize the complete DNA fragment and found that it contains more than rDNA genes.

To characterize the complete fragment, the authors used bacterial artificial chromosome (BAC) libraries from two wild barley species. By screening the libraries with probes that targeted Panicum-like DNA, they found several BAC clones that harbored panicoid DNA. Fluorescent in situ hybridization and sequencing of the BAC clones showed that the different positive hits represent a single chromosomal fragment in both species. This fragment consists of repeated blocks of DNA that showed high similarity between the two species, which indicates a common origin.

The researchers analyzed the sequence of the foreign DNA and discovered that besides rDNA genes, the fragment also contains transposable elements (TEs) (Figure). Most of these transposons belonged to the group of long terminal repeat (LTR) retrotransposons. This was a useful finding because the LTRs in these transposons can be used for molecular dating. By analyzing the divergence of the LTR elements, the researchers were able to estimate the insertion time of the retrotransposons between 2.9 and 1.7 million years ago. Keeping in mind that the retrotransposons could have remained active for some time after the transfer, this matches the estimation based on phylogeny that the fragment was inserted between 5 and 1.7 million years ago. This is long after the split of the pooid and panicoid lineages.

In addition to the rDNA genes and TEs, the authors identified five protein-coding genes on the foreign DNA fragment. At least one of these genes, an Ervatamin-C-like cysteine protease, showed signs of functionality: it has a complete set of exons, the open reading frame is intact, and expression analysis showed that the gene was consistently expressed. Interestingly, the Ervatamin-C-like gene does not have any native homologs in wild barley. Thus, when the foreign fragment was introduced, Ervatamin-C-like was a new gene for the gene pool.

It remains enigmatic how the panicoid fragment was transferred into wild barley. Therefore, the corresponding authors Václav Mahelka and Jan Šafář are trying to understand how genetic material is transferred in grasses. The outcomes might help us understand if horizontal gene transfer is more common in plants than we currently think. 

 

Leonie Verhage, Research Highlights Editor

 


Author: Leonie Verhage
Category: The Plant Journal
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Leonie Verhage

Leonie Verhage

Leonie Verhage is Research Highlights Editor at The Plant Journal. For every issue, she highlights one of the key articles with a commentary paper.
On Twitter, Leonie keeps the followers of The Plant Journal (@ThePlantJournal) updated on the latest articles.

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