Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a ‘near-complete’ draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.
"Decades of research have suggested that AUXIN BINDING PROTEIN 1 (ABP1) is an essential membrane-associated auxin receptor, but recent findings directly contradict this view. Here we show that embryonic lethality observed in abp1-1, which has been a cornerstone of ABP1 studies, is caused by the deletion of the neighbouring BELAYA SMERT (BSM) gene, not by disruption of ABP1. On the basis of our results, we conclude that ABP1 is not essential for Arabidopsis development."
Mary Williams's insight:
The ABP1 story is so fascinating and important - you should put this paper and the associated literature onto your reading list for your next course or discussion group.
Imagine a typical industrial process – say the production of gasoline or polyethylene plastic. It starts with non-renewable petrochemical resource that is transformed to the desired product through a series of catalytic steps, many requiring high temperature and pressure or dangerous solvents.
A single lineage of Nicotiana benthamiana is widely used as a model plant1 and has been instrumental in making revolutionary discoveries about RNA interference (RNAi), viral defence and vaccine production. It is peerless in its susceptibility to viruses and its amenability in transiently expressing transgenes2,3. These unparalleled characteristics have been associated both positively and negatively with a disruptive insertion in the RNA-dependent RNA polymerase 1 gene, Rdr14–6. For a plant so routinely used in research, the origin, diversity and evolution of the species, and the basis of its unusual abilities, have been relatively unexplored. Here, by comparison with wild accessions from across the spectrum of the species’ natural distribution, we show that the laboratory strain of N. benthamiana is an extremophile originating from a population that has retained a mutation in Rdr1 for ∼0.8 Myr and thereby traded its defence capacity for early vigour and survival in the extreme habitat of central Australia. Reconstituting Rdr1 activity in this isolate provided protection. Silencing the functional allele in a wild strain rendered it hypersusceptible and was associated with a doubling of seed size and enhanced early growth rate. These findings open the way to a deeper understanding of the delicate balance between protection and vigour.
As I sat writing this ‘personal reflections’ manuscript in the spring of 2015, I was seeing press reports related to the use of tobacco to make an Ebola therapeutic called ZMapp. For several months newspaper articles, radio shows and hour-long TV documentaries have given the public unprecedented exposure to the fact that ‘plant-made pharmaceuticals’ (PMP) can be life-saving drugs. I have been asked by many nonspecialists – why tobacco? How can this work? After spending over twenty years doing research in this field and many, many hours in public policy meetings promoting PMPs as an important tool of public health, I do not tire of hearing the same questions. Although there is an increasing pipeline of new protein drugs that will come from plants for both human and animal health, the general public has little knowledge of these specialized tools and therefore limited support for the field. ZMapp has given us free advertising on an international scale that I could never have anticipated.
An American teacher tries to instill independent thinking under the resistant eye of China’s education system.
Mary Williams's insight:
This is very interesting and worth reading - it highlights the cultural differences in attitudes and expectations towards education that persist beyond high school. If you have Chinese-educated students in your lab or course this article might provide an opportunity for dialogue.
Normally, our Friday posts highlight plants featured in the news over the past week, but this week we take a short break to make an appeal for your thoughts on the most notable and newsworthy plant-related events, resources, breakthroughs and headline makers of the past year.
What do you consider the top stories, breakthroughs, headline makers and other highlights of plant science, 2015? You can reply to this blog, email email@example.com, or Tweet to @PlantTeaching. We’ll share our lists during the final week of the year.
The special Plant Physiology focus issue on Metabolism is truly an inspiring collection that doesn’t minimize the challenges of understanding plant metabolism, but at the same time inspires us to explore, seek out and boldly go towards the final frontier of metabolism. http://blog.aspb.org/2015/11/11/metabolism-the-final-frontier/
"Promoting microbiology education through the iGEM synthetic biology competition." I'm a huge fan of iGEM and this article summarizes all that it has achieved (so far). It's not just promoting microbiology, it's promoting enthusiasm in science more broadly and a really effective way to show undergraduates (and even high school students) what research is like. http://femsle.oxfordjournals.org/conte…/…/16/fnv129.abstract
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