Schrenkiella parvula

Thellungiella parvula in situ
Schrenkiella parvula growing in situ at Tuz Gol (Anatolia, Turkey). Note siliques at the ends of most branches. Photo courtesy of Ismail Türkan.

Prime among the extremophyte crucifers for genomic resources are available are two species which were moved to the genus Thellungiella, only to be moved again (and again): Schrenkiella parvulum (T. parvula) and Eutrema salsugineum (T. salsuginea).  Both are in the diploid branch of the Brassicaceae (subclade Eutrema). Based on fossil evidence, A. thaliana and the Eutremeae diverged about 43 million years ago. Both species have 7 chromosomes and map comparisons with the arrangements on Arabidopsis chromosomes have been published.[1]  S. parvula has a genome size comparable to that of Arabidopsis while that of E. salsugineum is about twice as big.  The mapping and overall sequence similarities of the three species provide unique opportunities for tracing evolutionary rearrangements and, perhaps, identifying sources of their differing environmental tolerances.

Lake Tuz (Tuz Gölü), Anatolia, Turkey is one of the world’s largest inland hypersaline lakes, with an area more than 1600 sq. km.

S. parvula was originally selected as a model organism because of its ability, in the natural world, to function in the hypersaline conditions in central Anatolia, Turkey. [2]

A comparative study of 11 Brassicas suggested that S. parvula may perform slightly better under salt and drought conditions than E. salsugineum. [3] It is otherwise notable for its tolerance of high levels of other cations, especially Li+ and Mg2+.[4] These extreme adaptations were central to the initial decision to sequence the genome of this species.

At this point, a serious caveat is in order. Folklore has it that all of the S. parvula used in research derives from a seed (or seeds) of a single herbarium specimen, the herbarium being unknown to the author.  There is no ecological and not more than 1 or 2 physiological papers on the species. Although the photo at the top of the page was taken in situ at Lake Tuz, and although the overall conditions of the soil around the lake have been published[5] and there is a list of species with the zones in which they are found around the lake indeed, there is even a list of endemic species in the area, this promising model is not on any of them.[5]  It is not mentioned in the major phytosociological study of the area.[6] There is apparently no documentation of the soil conditions, the soil solution composition, the phenology or seasonality of this plant.

Despite this lack of background, Schrenkiella is considered a promising model for understanding adaptive responses to salinity. In hydroponic culture, it continues to grow at salinities up to 500 mM NaCl, even if the salinization is done rapidly. Moreover, if after a period of growth, it is given a down-shock, even from 500 mM NaCl to 0 mM, the plants resume more rapid growth immediately. For reasons that are unclear, however, like Eutrema salsuginea and most other halophytes, it doesn’t germinate well in the presence of salt, probably indicating adaptation to the fluctuating and seasonal salinity environments of their its habitat.

Genomic/transcriptomic resources

S. parvula shares many of the characteristics that make Arabidopsis a good model system. including its short life cycle and its ability to grow in Petri dishes or on simple light benches. Flower and silique structures are also very similar in the two species although S. parvula lacks petals and continues to branch and flower throughout its life cycle and it will not flower in the absence of Na+.  It also has the required genetic features for generation and rapid screening of mutants, and sufficient similarity to Arabidopsis that microarray tools have at least limited usefulness. With the ever decreasing costs of sequencing and assembling transcriptomes, however, this latter feature is rapidly losing significance.

The nuclear and chloroplast genomes of S. parvula has been sequenced and the data are available at NCBI, as are basal nuclear gene expressions with a comparison to Arabidopsis. [4]   A paper on the mitochondrial genome has been published, but the sequences seem to be not yet available. [8] Gene models and genomic data are available here and a BLAST tool has been developed to compare sequences to those. A CoGe syntenic dotplot with Arabidopsis thaliana is also available. For additional resources, consult thelluniella.org or NCBI.

[For a table of the lake composition and an artificial medium recipe, click here.]

References for the backstory

1.
Dassanayake M, Oh D-H, Haas JS, Hernandez A, Hong H, Ali S, et al. The genome of the extremophile crucifer Thellungiella parvula [Internet]. Vol. 43, Nature Genetics. Springer Nature; 2011. p. 913–8. Available from: http://dx.doi.org/10.1038/ng.889
2.
Inan G. Salt Cress. A Halophyte and Cryophyte Arabidopsis Relative Model System and Its Applicability to Molecular Genetic Analyses of Growth and Development of Extremophiles [Internet]. Vol. 135, PLANT PHYSIOLOGY. American Society of Plant Biologists (ASPB); 2004. p. 1718–37. Available from: http://dx.doi.org/10.1104/pp.104.041723
3.
Orsini F, D’Urzo MP, Inan G, Serra S, Oh D-H, Mickelbart MV, et al. A comparative study of salt tolerance parameters in 11 wild relatives of Arabidopsis thaliana [Internet]. Vol. 61, Journal of Experimental Botany. Oxford University Press (OUP); 2010. p. 3787–98. Available from: http://dx.doi.org/10.1093/jxb/erq188
4.
Oh D-H, Hong H, Lee SY, Yun D-J, Bohnert HJ, Dassanayake M. Genome Structures and Transcriptomes Signify Niche Adaptation for the Multiple-Ion-Tolerant Extremophyte Schrenkiella parvula [Internet]. Vol. 164, PLANT PHYSIOLOGY. American Society of Plant Biologists (ASPB); 2014. p. 2123–38. Available from: http://dx.doi.org/10.1104/pp.113.233551
5.
Ozfidan-Konakci C, Uzilday B, Ozgur R, Yildiztugay E, Sekmen AH, Turkan I. Halophytes as a source of salt tolerance genes and mechanisms: a case study for the Salt Lake area, Turkey. Functional Plant Biology [Internet]. 2016;43(7):575. Available from: http://dx.doi.org/10.1071/FP15288 [Source]
6.
HAMZAOÐLU1 E. Phytosociological Studies on the Halophytic Communities of Central Anatolia. Ekoloji [Internet]. 2009;18:1–14. Available from: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.537.469&rep=rep1&type=pdf [Source]
7.
Nilhan TG, Emre YA, Osman K. Soil Detenninants for Distribution of Halocnemum strobilaceum Bieb. (Chenopodiaceae) Around Lake Tuz, Turkey. Pak J Biol Sci. 2008;11:565–70. [Source]