NEW YORK (GenomeWeb News) – By sequencing the genome of the Arabidopsis lyrata plant, investigators have learned more about the sorts of changes that contribute to genome size differences in flowering plants.
The international research team, led by investigators at the Max Planck Institute for Developmental Biology, compared the newly sequenced genome to the much smaller genome of the model organism A. thaliana. Their findings suggest that the pared down version of the genome found in A. thaliana reflects a spate of small deletions — many affecting transposons and non-protein coding sequences. The study appeared in the early, online version of Nature Genetics yesterday.
"The high-quality reference genome for A. lyrata will be an important resource for functional evolutionary and ecological studies in the genus Arabidopsis," co-corresponding author Ya-Long Guo, a Max Planck molecular biology researcher, and co-authors wrote.
Genome sizes vary dramatically from one flowering plant to the next, the authors explained, ranging from around 64 million to nearly 150 billion bases. But teasing apart the reasons for this variability has been tough, they explained, given the long divergence times between most of the plants whose genomes are best characterized so far.
With that in mind, the team decided to look at this process within the Arabidopsis genus, which contains plants whose genomes have undergone relatively rapid changes.
"An exciting opportunity to understand what drives differences in genome size over shorter time scales is offered by the genus Arabidopsis in the Brassicaceae family," they wrote, noting that the A. thaliana genome is among the more diminutive in the family, while the A. lyrata genome is larger than average.
Using Sanger sequencing, the researchers sequenced the 207 million base genome of an A. lyrata strain from North America known as MN47 to roughly 8.3 times coverage.
Their subsequent analyses of the genome indicate that it contains an estimated 32,670 genes — just a few thousand more genes than reported for the 125 million base A. thaliana genome.
When they compared the two genomes in more detail, the researchers found that A. lyrata and A. thaliana remain similar in sequence identity, gene arrangement, gene ontology distributions, and more, despite having diverged from one another about 10 million years ago.
Although they detected millions of rearrangements between the two genomes, their analyses hint that the reductions in genome size seen in A. thaliana are likely a consequence of a slew of deletions affecting non-coding regions and transposable element sequences.
Still, they noted, more research is needed to explore whether genome expansions in the A. lyrata lineage have also contributed to genome size differences — and to better understand genome evolution within Arabidopsis species and other plants.
"A complete understanding of the processes behind genome contraction and expansion over short time scales will … require better knowledge of mutational events and a deeper understanding of the distribution of, and selection on, non-coding regulatory sequences," they concluded.