Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States

Toward kingdom-wide analyses of gene expression

Gene expression data for Archaeplastida are accumulating exponentially, with more than 300 000 RNA-sequencing (RNA-seq) experiments available for hundreds of species. The gene expression data stem from thousands of experiments that capture gene expression in various organs, tissues, cell types, (a)biotic perturbations, and genotypes. Advances in software tools make it possible to process all these data in a matter of weeks on modern office computers, giving us the possibility to study gene expression in a kingdom-wide manner for the first time. We discuss how the expression data can be accessed and processed and outline analyses that take advantage of cross-species analyses, allowing us to generate powerful and robust hypotheses about gene function and evolution.

Transcriptome profiling reveals that foliar water uptake occurs with C3 and crassulacean acid metabolism facultative photosynthesis in Tamarix ramosissima under extreme drought

Tamarix ramosissima is a typical desert plant species that is widely distributed in the desert areas of Northwest China. It plays a significant role in sand fixation and soil water conservation. In particular, how it uses water to survive in the desert plays an important role in plant growth and ecosystem function. Previous studies have revealed that T. ramosissima can alleviate drought by absorbing water from its leaves under extreme drought conditions. To date, there is no clear molecular regulation mechanism to explain foliar water uptake (FWU). In the present study, we correlated diurnal meteorological data, sap flow and photosynthetic parameters to determine the physical and biological characteristics of FWU. Our results suggested that the lesser the groundwater, the easier it is for T. ramosissima to absorb water via the leaves. Gene ontology annotation and Kyoto Encyclopaedia of Genes and Genomes pathway analysis of the transcriptome profile of plants subjected to high humidity suggested that FWU was highly correlated to carbohydrate metabolism, energy transfer, pyruvate metabolism, hormone signal transduction and plant-pathogen interaction. Interestingly, as a C₃ plant, genes such as PEPC, PPDK, MDH and RuBP, which are involved in crassulacean acid metabolism (CAM) photosynthesis, were highly upregulated and accompanied by FWU. Therefore, we proposed that in the case of sufficient water supply, C₃ photosynthesis is used in T. ramosissima, whereas in cases of extreme drought, starch is degraded to provide CO₂ for CAM photosynthesis to make full use of the water obtained via FWU and the water that was transported or stored to assimilating branches and stems. This study may provide not only an important theoretical foundation for FWU and conversion from C₃ plants to CAM plants but also for engineering improved photosynthesis in high-yield drought-tolerant plants and mitigation of climate change-driven drought.

Population Genomics Reveals Gene Flow and Adaptive Signature in Invasive Weed Mikania micrantha

A long-standing and unresolved issue in invasion biology concerns the rapid adaptation of invaders to nonindigenous environments. Mikania micrantha is a notorious invasive weed that causes substantial economic losses and negative ecological consequences in southern China. However, the contributions of gene flow, environmental variables, and functional genes, all generally recognized as important factors driving invasive success, to its successful invasion of southern China are not fully understood. Here, we utilized a genotyping-by-sequencing approach to sequence 306 M. micrantha individuals from 21 invasive populations. Based on the obtained genome-wide single nucleotide polymorphism (SNP) data, we observed that all the populations possessed similar high levels of genetic diversity that were not constrained by longitude and latitude. Mikania micrantha was introduced multiple times and subsequently experienced rapid-range expansion with recurrent high gene flow. Using FST outliers, a latent factor mixed model, and the Bayesian method, we identified 38 outlier SNPs associated with environmental variables. The analysis of these outlier SNPs revealed that soil composition, temperature, precipitation, and ecological variables were important determinants affecting the invasive adaptation of M. micrantha. Candidate genes with outlier signatures were related to abiotic stress response. Gene family clustering analysis revealed 683 gene families unique to M. micrantha which may have significant implications for the growth, metabolism, and defense responses of M. micrantha. Forty-one genes showing significant positive selection signatures were identified. These genes mainly function in binding, DNA replication and repair, signature transduction, transcription, and cellular components. Collectively, these findings highlight the contribution of gene flow to the invasion and spread of M. micrantha and indicate the roles of adaptive loci and functional genes in invasive adaptation.

Optimal Irrigation Regime for Woody Species Potentially Suitable for Effective and Sustainable Afforestation in the Desert Region of Mongolia

Long-term studies on plant response mechanisms to different irrigation regimes will provide a better understanding of the survivability and establishment of plant communities in a desert environment. Thus, across 10 years, we regularly investigated the effects of the rainfall (control), rainfall + 4 L h−1, rainfall + 8 L h−1, and rainfall + 12 L h−1 irrigation regimes on the growth and leaf morpho-physiology of Tamarix ramosissima Ledeb., Ulmus pumila L., Elaeagnus moorcroftii Wall. ex Schltdl., and Hippophae rhamnoides L. to suggest an optimal irrigation regime for each woody species for effective and sustainable afforestation in Mongolia. We measured the root collar diameter (RCD), annual height growth, survivability, leaf area (LA), specific leaf area (SLA), leaf biomass (LB), total chlorophyll concentration, and predawn (ψp) and midday (ψm) leaf water potentials across the treatments and species. Results showed that trees grown at 12 L h−1 grew taller per year and generally resulted in a higher SLA, but generally resulted in a lower survival rate compared with those in the other treatments in all species. Total chlorophyll content was higher in trees grown under 4 and/or 8 L h−1, particularly for T. ramosissima and E. moorcroftii. Lastly, leaf water potentials were found more negative for trees subjected to 4 L h−1, especially in T. ramosissima and U. pumila, but still resulted in a higher survival rate and LB compared with 12 L h−1. H. rhamnoides showed higher survivability at 8 and/or 12 L h−1 than at 4 L h−1. Therefore, we suggest 4 L h−1 to be the optimal irrigation regime for irrigating T. ramosissima, U. pumila and E. moorcroftii, and 8 and/or 12 L h−1 for H. rhamnoides. Our findings are relevant to ensuring the sustainability of afforestation programs in arid and semiarid landscapes in Mongolia.