A high-quality genome sequence helps pinpoint the genetic basis for trait diversity.
October 31, 2016
A recent publication in Nature Plants reports the genome sequence of hairy bittercress (Cardamine hirsuta). The authors describe how they assembled a high-quality genome sequence using a scaffolding algorithm called BAMLINK. The close relationship of hairy bittercress to thale cress (Arabidopsis thaliana) means that the hairy bittercress genome will be extremely useful to plant scientists researching comparative questions. For example, the authors used comparative transcriptomics to identify the transcription factors PLETHORA5/7 as regulators of leaf shape diversity between hairy bittercress and thale cress.
A small international consortium, led by scientists at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, produced a high-quality genome sequence of Cardamine hirsuta, the garden weed more commonly known as hairy bittercress.
Genome sequencing is figuring out the order of nucleotides in a genome — the order of As, Cs, Gs, and Ts that make up an organism's DNA. The hairy bittercress genome was sequenced by a "whole-genome shotgun" method, which involves breaking the genome up into small pieces, sequencing the pieces, and reassembling the pieces into the full genome sequence. Much of the work involved in genome sequencing lies in putting together this giant biological jigsaw puzzle. Lead author and computer scientist, Xiangchao Gan, explains how he did this by designing a novel scaffolding algorithm called BAMLINK. Gan, who originally joined the project when he was a post-doc in Richard Mott’s lab at the Wellcome Trust Centre for Human Genetics, University of Oxford, explains that BAMLINK “efficiently exploits the statistical information of raw data generated on different sequencing platforms that produce different lengths of DNA sequence, and can exploit fuzzy information”.
Sequencing the hairy bittercress genome is an important step towards understanding it. As author Michiel Kwantes says, “Having a genome lets you test the generality of ideas that come from studying one gene at a time”. At the very least, the genome sequence represents a valuable shortcut, helping scientists find genes much more easily and quickly. For instance, the authors identified the genes PLETHORA5 and 7 for the first time as transcription factors that control the difference in leaf shape between hairy bittercress and thale cress. As well, they have begun to identify some of the genes associated with the differences between the seed pods of these two plant species.
Having a high-quality genome of hairy bittercress means that scientists can use this as a reference to compare with the genomes of thale cress and other species in the crucifer family. Author Angela Hay explains that the high quality of their genome “allows very meaningful comparisons to be drawn between C. hirsuta and its close relative A. thaliana.” What’s more, scientists can easily manipulate the genetic make-up of both plants and transfer genes between them. Genes that are critical for species-specific traits are expected to make one species look a bit more like the other when transferred between them. This type of “gene transfer” experiment can help identify sequences that underlie trait differences between species.
This genome promises to be a useful tool for scientists in the years to come as they work to answer fundamental questions about the role of genes in causing the diversity of traits across species.