Conference Report - Surviving the extremes: Abiotic stress tolerance in extremophile plants

At the Jacob Blaustein Institutes for Desert Research (BIDR), February 2-5, 2015.

Although the conference has now come and gone, it was a great success and a more complete report will appear here in a matter of a few more days. Please check back.

Featured topics included:

► The genus Thellungiella is closely related to Arabidopsis thaliana but its species are endemic to saline, resource-poor habitats, making them good models for the evolution of plant adaptation to extreme environments. A draft genome for Thellungiella parvula was published in 2011 and updated in March, 2012*;. Subsequently, the draft genome for T. salsuginea was also published, and together they (and were highlighted in the August 16th edition of Genome Biology (thanks to Simon Dittami and Thierry Tonon). The sequencing of both genomes was done entirely with "next generation" techniques (Roche 454 and Illumina Solexa). T. parvula assembled into 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. The genome of T. salsuginea is about 70% larger. In both cases, the sequences were anchored to seven pseudo-chromosomes. Particularly noteworthy was that the T. parvula sequences identified a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for its extremophile lifestyle. T. salsuginea, in contrast, is characterized by many more transposable element derived repetitive sequences. The sequences themselves and an associated BLAST tool are available directly under the "Resources" menu to the left.

A second version of the T. salsuginea genome, under the name Eutrema salsugineum has also been published. The interim sequences, useable subject to the Ft. Lauderdale Protocol, are available here. The complete reference and abstract are in the Literature section, but it does not yet seem to have appeared in databases such as Web of Science. For more details, readers can contact the authors directly: Karen S. Schumaker or Xiangfeng Wang at the University of Arizona. It will be very interesting to see how the final assemblies of the two drafts differ both in sequences and in placement of the genes within the chromosomes.

A note on Thellungiella nomenclature: Recently, Koch and German (2013) noted that while the sequencing of the two Thellungiella genomes has been important, older studies on taxonomic diversity, phylogeny and geographic distribution of the species have been neglected. At the same time, a good deal of confusion has arisen over the names and existence of Thellungiella species as names in the molecular literature have been misapplied. In particular, this relates to T. salsuginea and T. halophila, with both transient confusion and propagating errors regarding (1) if they are the same species (they are not), and (2) which one was actually being used in any given study. For those wishing to sequence something novel, neither the species known as T. halophila nor the one known as T. botschantzevii has been done. The latter has apparently received no attention other than in a few taxonomic studies.

In 2005, Al-Shehbaz and Warwick re-classified the Thellungiellas, putting them in the genus Eutrema (see the Koch and German article for references). In 2010, German and Al-Shehbaz, analyzed the group again, and moved T. parvula (or E. parvulum) back out of Eutrema, putting it in a new genus, Schrenkiella, all by itself. Koch and German (2013) have noted that this is one of 20 Brassicaceae genera "who's precise position and tribal affiliation still remains uncertain".

While the confusion summarized by Koch and German is certainly germane and it behooves anyone working with a species to know which one it is, it is a bit depressing that, even given resources available before the genome sequences, there has been (apparently) no use of molecular data in the systematics publications. To those who are not systematists, it appears rather pointless to keep changing names in molecular genetics papers to keep up with the latest guesses at the "precise positions" of the species. This simply adds to the confusion; it doesn't clarify anything. Nevertheless, anyone publishing on the Thellungiellas should read this article before submitting their manuscripts.

For now, therefore, the name of the website will remain, rather than Perhaps a meeting of the Thellungiella research community in conjunction with some larger international gathering is called for to come to an agreement on how to publish while the systematics are being deconvoluted. Papers addressing any of these monikers will continue to be included in the bibliography.

* The sequencing and annotation of T. parvula were carried out with the support of the Next-Generation BioGreen 21 Program (SSACProject No. PJ009030: Studies on plant stress systems using comparative genomics approaches),Rural Development Administration, Republic of Korea.
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