Demographic patterns of two related desert shrubs with overlapping distributions in response to past climate changes

Numerous studies have revealed that past geological events and climatic fluctuations had profoundly affected the genetic structure and demographic patterns of species. However, related species with overlapping ranges may have responded to such environmental changes in different ways. In this study, we compared the genetic structure and population dynamics of two typical desert shrubs with overlapping distributions in northern China, Nitraria tangutorum and Nitraria sphaerocarpa, based on chloroplast DNA (cpDNA) variations and species distribution models. We sequenced two cpDNA fragments (trnH-trnA and atpH-atpI) in 633 individuals sampled from 52 natural populations. Twenty-four chlorotypes, including eight rare chlorotypes, were identified, and a single dominant haplotype (H4) widely occurred in the entire geographical ranges of the two species. There were also a few distinctive chlorotypes fixed in different geographical regions. Population structure analyses suggested that the two species had significantly different levels of total genetic diversity and interpopulation differentiation, which was highly likely correlated with the special habitat preferences of the two species. A clear phylogeographic structure was identified to exist among populations of N. sphaerocarpa, but not exist for N. tangutorum. The neutral tests, together with the distribution of pairwise differences revealed that N. tangutorum experienced a sudden demographic expansion, and its expansion approximately occurred between 21 and 7 Kya before present, while a rapid range expansion was not identified for N. sphaerocarpa. The ecological niche modeling (ENM) analysis indicated that the potential ranges of two species apparently fluctuated during the past and present periods, with obvious contraction in the Last Glacial Maximum (LGM) and recolonization in the present, respectively, comparing to the Last Interglacial (LIG). These findings suggest that the two species extensively occurred in the Northwest of China before the Quaternary, and the current populations of them originated from a few separated glacial refugia following their habitat fragmentation in the Quarternary. Our results provide new insights on the impact of past geological and climatic fluctuations on the population dynamics of desert plants in northwestern China, and further enforce the hypothesis that there were several independent glacial refugia for these species during the Quaternary glaciations.

Transcriptome Profiling and Chlorophyll Metabolic Pathway Analysis Reveal the Response of Nitraria tangutorum to Increased Nitrogen

To identify genes that respond to increased nitrogen and assess the involvement of the chlorophyll metabolic pathway and associated regulatory mechanisms in these responses, Nitraria tangutorum seedlings were subjected to four nitrogen concentrations (N0, N6, N36, and N60: 0, 6, 36, and 60 mmol·L^-1 nitrogen, respectively). The N. tangutorum seedling leaf transcriptome was analyzed by high-throughput sequencing (Illumina HiSeq 4000), and 332,420 transcripts and 276,423 unigenes were identified. The numbers of differentially expressed genes (DEGs) were 4052 in N0 vs. N6, 6181 in N0 vs. N36, and 3937 in N0 vs. N60. Comparing N0 and N6, N0 and N36, and N0 and N60, we found 1101, 2222, and 1234 annotated DEGs in 113, 121, and 114 metabolic pathways, respectively, classified in the Kyoto Encyclopedia of Genes and Genomes database. Metabolic pathways with considerable accumulation were involved mainly in anthocyanin biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, flavonoid biosynthesis, and amino acid metabolism. N36 increased δ-amino levulinic acid synthesis and upregulated expression of the magnesium chelatase H subunit, which promoted chlorophyll a synthesis. Hence, N36 stimulated chlorophyll synthesis rather than heme synthesis. These findings enrich our understanding of the N. tangutorum transcriptome and help us to research desert xerophytes' responses to increased nitrogen in the future.

Integrated metabolome and transcriptome analysis unveils novel pathway involved in the fruit coloration of Nitraria tangutorum Bobr

BACKGROUND

The desert shrub Nitraria tangutorum Bobr. is important for its resistance to salt and alkali in Northwest China. It is an ecologically important species in this region and provides edible and medicinal berries. This study showed a mutant of N. tangutorum (named Jincan, JC) that has a strong yellow pericarp vs red in a wild type (represented by NT).

RESULTS

In this study, the secondary metabolic and molecular mechanisms responsible for Nitraria fruit coloration were investigated using LC-MS-based widely targeted metabolomics and transcriptomics data. As a result of our study, 122 and 104 flavonoid metabolites were differentially expressed throughout the mature and transition stages between JC and NT, respectively. Furthermore, two cyanidin derivatives (cyanidin 3-O-glucoside and cyanidin-3-O-(2''-O-glucosyl) glucoside) and one pelargonidin derivative (pelargonidin-3-O-glucoside) were identified only in the NT phenotype. The functional genes F3H (flavanone 3-hydroxylase), F3'H (flavonoid 3'-hydroxylase) and UFGT (flavonoid 3-O-glucosyltransferase) and the transcription factors MYB, bHLH, NAC and bZIP were significantly downregulated in JC. Meanwhile, the activity of UFGT was extremely low in both periods of JC, with a five-fold higher enzymatic activity of UFGT in RT than in YT. In summary, due to the lack of catalysis of UGFT, yellow fruit of JC could not accumulate sufficient cyanidin and pelargonidin derivatives during fruit ripening.

CONCLUSION

Taken together, our data provide insights into the mechanism for the regulation of anthocyanin synthesis and N. tangutorum fruit coloration and provide a theoretical basis to develop new strategies for developing bioactive compounds from N. tangutorum fruits.

Allometry of bud dynamic pattern and linkage between bud traits and ecological stoichiometry of Nitraria tangutorum under fertilizer addition

Affected by the pressure and constraints of available resources, plant growth and development, as well as plant life history strategies, usually vary with environmental conditions. Plant buds play a crucial role in the life history of woody plants. Nitraria tangutorum is a common dominant woody species in desertified areas of northern China and its growth is critical to the desert ecosystem. Revealing the allometry of N. tangutorum aboveground bud fates and the linkage between bud traits and plant nutrient contents and stoichiometric ratios can be useful in understanding plant adaptation strategy. We applied seven nitrogen and phosphorus fertilizer addition treatments to natural N. tangutorum ramets in Ulan Buh Desert in three consecutive years. We surveyed three types of aboveground buds (dormant buds, vegetative buds, and reproductive buds) in each N. tangutorum ramet, then measured the plant carbon (C), nitrogen (N), and phosphorus (P) contents and ratios during three consecutive years. We specified that reserve growth potential (RGP), vegetative growth intensity (VGI) and sexual reproduction effort (SRE) are the three indices of bud dynamic pattern. The results showed that the bud dynamic pattern of N. tangutorum ramets differed significantly among different fertilizer addition treatments and sampling years. The allometry of RGP, VGI, and SRE was obvious, showing size dependence. The allometric growth relationship fluctuated among the sampling years. The linkage between bud traits and plant stoichiometric characteristics of N. tangutorum ramets showed close correlation with plant P content, C:P and N:P ratios, no significant correlation with plant C content, N content and C:N ratio. These results contribute to an improved understanding of the adaptive strategies of woody plants growing in desert ecosystems and provide insights for adoption of effective measures to restore and conserve plant communities in arid and semi-arid regions.

Pollen Morphology of Some Species from Genus Nitraria

An analysis of pollen grains (in Nitraria sibirica Pall., N. schoberi L., N. komarovii Iljin & Lava ex Bobrov, and N. pamirica L. Vassil.) was performed on natural material collected in Russia, Kazakhstan, and Tajikistan. Herbarium specimens from the collection at Komarov Botanical Institute, Russian Academy of Sciences (N. tangutorum Bobrov and N. praevisa Bobrov) were examined, too. Pollen grains of two species-N. pamirica and N. praevisa-were studied for the first time. N. tangutorum and N. praevisa were found to have the perprolate pollen shape, whereas N. pamirica was found to have the subprolate shape. An intraspecific differentiation of N. sibirica was noted. Populations of N. sibirica (Taskarasu, Karatal, and Basshi) possess pollen grains of the subprolate or prolate shape, striate and perforate exine ornamentation, and a longer equatorial axis and a shorter polar axis than other specimens of N. sibirica. N. schoberi in all populations had anomalous shapes of some pollen grains. Overall, we demonstrated that the length ratio of the polar axis to the equatorial axis, characteristics of pollen in polar view, colpus morphology, and surface ornamentation of pollen grains in the genus Nitraria are of great taxonomic importance for the identification of species.

Root exudates and rhizosphere soil bacterial relationships of Nitraria tangutorum are linked to k-strategists bacterial community under salt stress

When plants are subjected to various biotic and abiotic stresses, the root system responds actively by secreting different types and amounts of bioactive compounds, while affects the structure of rhizosphere soil bacterial community. Therefore, understanding plant-soil-microbial interactions, especially the strength of microbial interactions, mediated by root exudates is essential. A short-term experiment was conducted under drought and salt stress to investigate the interaction between root exudates and Nitraria tangutorum rhizosphere bacterial communities. We found that drought and salt stress increased rhizosphere soil pH (9.32 and 20.6%) and electrical conductivity (1.38 and 11 times), respectively, while decreased organic matter (27.48 and 31.38%), total carbon (34.55 and 29.95%), and total phosphorus (20 and 28.57%) content of N. tangutorum rhizosphere soil. Organic acids, growth hormones, and sugars were the main differential metabolites of N. tangutorum under drought and salt stress. Salt stress further changed the N. tangutorum rhizosphere soil bacterial community structure, markedly decreasing the relative abundance of Bacteroidota as r-strategist while increasing that of Alphaproteobacteria as k-strategists. The co-occurrence network analysis showed that drought and salt stress reduced the connectivity and complexity of the rhizosphere bacterial network. Soil physicochemical properties and root exudates in combination with salt stress affect bacterial strategies and interactions. Our study revealed the mechanism of plant-soil-microbial interactions under the influence of root exudates and provided new insights into the responses of bacterial communities to stressful environments.

The Full-Length Transcriptome Sequencing and Identification of Na+/H+ Antiporter Genes in Halophyte Nitraria tangutorum Bobrov

Nitraria tangutorum Bobrov is a halophyte that is resistant to salt and alkali and is widely distributed in northwestern China. However, its genome has not been sequenced, thereby limiting studies on this particular species. For species without a reference genome, the full-length transcriptome is a convenient and rapid way to obtain reference gene information. To better study N. tangutorum, we used PacBio single-molecule real-time technology to perform full-length transcriptome analysis of this halophyte. In this study, a total of 21.83 Gb of data were obtained, and 198,300 transcripts, 51,875 SSRs (simple sequence repeats), 55,574 CDS (coding sequence), and 74,913 lncRNAs (long non-coding RNA) were identified. In addition, using this full-length transcriptome, we identified the key Na⁺/H⁺ antiporter (NHX) genes that maintain ion balance in plants and found that these are induced to express under salt stress. The results indicate that the full-length transcriptome of N. tangutorum can be used as a database and be utilized in elucidating the salt tolerance mechanism of N. tangutorum.

CIPK11: a calcineurin B-like protein-interacting protein kinase from Nitraria tangutorum, confers tolerance to salt and drought in Arabidopsis

BACKGROUND

The CIPKs are a group of plant-specific Ser/Thr protein kinases acting in response to calcium signaling, which plays an important role in the physiological and developmental adaptation of plants to adverse environments. However, the functions of halophyte-derived CIPKs are still poorly understood, that limits a potential application of CIPKs from halophytes for improving the tolerance of glycophytes to abiotic stresses.

RESULTS

In this study, we characterized the NtCIPK11 gene from the halophyte Nitraria tangutorum and subsequently analyzed its role in salt and drought stress tolerance, using Arabidopsis as a transgenic model system. NtCIPK11 expression was upregulated in N. tangutorum root, stem and blade tissues after salt or drought treatment. Overexpressing NtCIPK11 in Arabidopsis improved seed germination on medium containing different levels of NaCl. Moreover, the transgenic plants grew more vigorously under salt stress and developed longer roots under salt or drought conditions than the WT plants. Furthermore, NtCIPK11 overexpression altered the transcription of genes encoding key enzymes involved in proline metabolism in Arabidopsis exposed to salinity, however, which genes showed a relatively weak expression in the transgenic Arabidopsis undergoing mannitol treatment, a situation that mimics drought stress. Besides, the proline significantly accumulated in NtCIPK11-overexpressing plants compared with WT under NaCl treatment, but that was not observed in the transgenic plants under drought stress caused by mannitol application.

CONCLUSIONS

We conclude that NtCIPK11 promotes plant growth and mitigates damage associated with salt stress by regulating the expression of genes controlling proline accumulation. These results extend our understanding on the function of halophyte-derived CIPK genes and suggest that NtCIPK11 can serve as a candidate gene for improving the salt and drought tolerance of glycophytes through genetic engineering.

Overexpression of NtSOS2 From Halophyte Plant N. tangutorum Enhances Tolerance to Salt Stress in Arabidopsis

The Salt Overly Sensitive (SOS) signaling pathway is key in responding to salt stress in plants. SOS2, a central factor in this pathway, has been studied in non-halophytes such as Arabidopsis and rice, but has so far not been reported in the halophyte Nitraria tangutorum. In order to better understand how Nitraria tangutorum acquires its tolerance for a high salt environment, here, the NtSOS2 was cloned from Nitraria tangutorum, phylogenetic analyses showed that NtSOS2 is homologous to the SOS2 of Arabidopsis and rice. Gene expression profile analysis showed that NtSOS2 localizes to the cytoplasm and cell membrane and it can be induced by salt stress. Transgenesis experiments showed that exogenous expression of NtSOS2 reduces leaf mortality and improves the germination rate, biomass and root growth of Arabidopsis under salt stress. Also, exogenous expression of NtSOS2 affected the expression of ion transporter-related genes and can rescue the phenotype of sos2-1 under salt stress. All these results revealed that NtSOS2 plays an important role in plant salt stress tolerance. Our findings will be of great significance to further understand the mechanism of salt tolerance and to develop and utilize molecular knowledge gained from halophytes to improve the ecological environment.

The East Asian Winter Monsoon Acts as a Major Selective Factor in the Intraspecific Differentiation of Drought-Tolerant Nitraria tangutorum in Northwest China

The influence of Quaternary climate fluctuation on the geographical structure and genetic diversity of species distributed in the regions of the Qinghai–Tibet Plateau (QTP) has been well established. However, the underlying role of the East Asian monsoon system (EAMS) in shaping the genetic structure of the population and the demography of plants located in the arid northwest of China has not been explored. In the present study, Nitraria tangutorum, a drought-tolerant desert shrub that is distributed in the EAMS zone and has substantial ecological and economic value, was profiled to better understand the influence of EAMS evolution on its biogeographical patterns and demographic history. Thus, the phylogeographical structure and historical dynamics of this plant species were elucidated using its five chloroplast DNA (cpDNA) fragments. Hierarchical structure analysis revealed three distinct, divergent lineages: West, East-A, and East-B. The molecular dating was carried out using a Bayesian approach to estimate the time of intraspecies divergence. Notably, the eastern region, which included East-A and East-B lineages, was revealed to be the original center of distribution and was characterized by a high level of genetic diversity, with the intraspecific divergence time dated to be around 2.53 million years ago (Ma). These findings, combined with the data obtained by ecological niche modeling analysis, indicated that the East lineages have undergone population expansion and differentiation, which were closely correlated with the development of the EAMS, especially the East Asian winter monsoon (EAWM). The West lineage appears to have originated from the migration of N. tangutorum across the Hexi corridor at around 1.85 Ma, and subsequent colonization of the western region. These results suggest that the EAWM accelerated the population expansion of N. tangutorum and subsequent intraspecific differentiation. These findings collectively provide new information on the impact of the evolution of the EAMS on intraspecific diversification and population demography of drought-tolerant plant species in northwest China.

NtCIPK9: A Calcineurin B-Like Protein-Interacting Protein Kinase From the Halophyte Nitraria tangutorum, Enhances Arabidopsis Salt Tolerance

Calcineurin B-like protein-interacting protein kinases (CIPKs) play essential roles in plant abiotic stress response. In order to better understand salt tolerance, we cloned and analyzed the NtCIPK9 gene from the halophyte Nitraria tangutorum. Phylogenetic analysis shows that NtCIPK9 belongs to a sister clade with the Arabidopsis AtCIPK9 gene and is thought to localize to the plasma membrane. NtCIPK9 shows the highest expression level in the Nitraria tangutorum root under normal growth conditions, whereas after NaCl treatment, the highest expression was found in the blade. NtCIPK9-overexpressing Arabidopsis plants have a higher seed germination rate, longer root length, and displayed higher salt tolerance than wild type seedlings under salt stress conditions. Furthermore, NtCIPK9 overexpression might enhance the expression of genes related to K+ transportation after NaCl treatment. Thus, we conclude that NtCIPK9 increases transgenic plant salt tolerance and reduces damage associated with salt stress by promoting the expression of genes controlling ion homeostasis. Our results suggest that NtCIPK9 could serve as an ideal candidate gene to genetically engineer salt-tolerant plants.

[An ecological stoichiometry model based on the size of Nitraria tangutorum]

Ecological stoichiometry provides a new method for understanding the characteristics, driving forces and mechanisms of C, N and P coupled cycles. However, there are few reports on the variation in ecological stoichiometry of plants during their growth. In this study, we fitted the total elemental mass of different module based on the size of Nitraria tangutorum, and derived the ecological stoichiometry models of different module and whole ramet by measuring the biomass and nutrient concentrations of the current-year stems in 2017, 2-year-old stems, more than 2-year-old stems, leaves, roots and layerings of N. tangutorum ramet. Our results showed that the derivation model could well reflect the changes in ecological stoichiometry during plant growth. The old stems and the layering had higher N:P and C:P, while leaves,current-year stems, and roots had lower N:P and C:P. The whole plant nutrient elements cumulative rate was P:N:C during the growth process. These results were consistent with the growth rate hypothesis and allometric theory, and provide evidence for nutrient reabsorption. This model could be used as an effective way to analyze the dynamic characteristics of elements in plant growth.

A rapid high-performance liquid chromatography separation of a new anthocyanin from Nitraria tangutorum

In this work, a rapid high-performance liquid chromatography method was developed to efficiently purify anthocyanin from Nitraria tangutorum based on reversed-phase column. A new anthocyanin was purified from N. tangutorum and elucidated on the basis of extensive spectroscopic analysis, including one- and two-dimensional nuclear magnetic resonance, as well as high-resolution mass spectrometry (HR-MS) data. The new anthocyanin was elucidated as cyanidin 3-[2″-(6‴-coumaroyl)-glucosyl]-glucoside.

Gene transcript profiles in the desert plant Nitraria tangutorum during fruit development and ripening

Nitraria tangutorum Bobr., a valuable wild shrub distributed in Northwest China, produces edible and medicinal berries. However, little is known about the molecular mechanisms of its fruit development and ripening. We performed de novo transcriptome sequencing of N. tangutorum fruit using the Illumina HiSeq™ 2000 sequencing platform. More than 62.94 million reads were obtained and assembled into 69,306 unigenes (average length, 587 bp). These unigenes were annotated by querying against five databases (Nr, Swiss-Prot, GO, COG, and KEGG); 42,929 and 26,809 unigenes were found in the Nr and Swiss-Prot databases, respectively. In ortholog analyses, 33,363 unigenes were assigned with one or more GO terms, 15,537 hits were aligned to 25 COG classes, and 24,592 unigenes were classified into 128 KEGG pathways. Digital gene expression analyses were conducted on N. tangutorum fruit at the green (S1), yellow (S2), and red (S3) developmental stages. In total, 8240, 5985, and 4994 differentially expressed genes (DEGs) were detected for S1 vs. S2, S1 vs. S3, and S2 vs. S3, respectively. Cluster analyses showed that a large proportion of DEGs related to plant hormones and transcription factors (TFs) showed high expression in S1, down-regulated expression in S2, and up-regulated expression in S3. We analyzed the expression patterns of 23 genes encoding 12 putative enzymes involved in flavonoid biosynthesis. The expression profiles of 10 DEGs involved in flavonoid biosynthesis were validated by Q-PCR analysis. The assembled and annotated transcriptome sequences and gene expression profile analyses provide valuable genetic resources for research on N. tangutorum.