Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis

Genome-wide identification of five fern bHLH families and functional analysis of bHLHs in lignin biosynthesis in Alsophila spinulosa

BACKGROUND

The basic helix-loop-helix (bHLH) transcription factors are involved in the biosynthesis of various secondary metabolites. However, genome-wide studies on the bHLH gene family in ferns and their role in lignin biosynthesis remain limited. As the second largest group of vascular plants, ferns are of significant interest for understanding plant evolution and secondary metabolism. Among ferns, Alsophila spinulosa stands out as one of the few tree ferns with a distinctive trunk structure. Investigating the genes potentially regulating lignin biosynthesis in A. spinulosa offers valuable insights into the growth and development mechanisms of its trunk, which is pivotal for the overall architecture and function of the plant.

RESULTS

In this study, we conducted a systematic study of bHLH gene families in five ferns, including 186 in A. spinulosa, 130 in A. capillus, 107 in A. filiculoides, 71 in S. cucullata, and 67 in C. richardii. Based on phylogenetic analysis, all bHLH genes were classified into 28 subgroups. The number of bHLH members in different ferns was closely related to their growth patterns and life habits, with the number in tree ferns being much larger than in other ferns. In addition, we identified tandem duplication in C. richardii and A. capillus as a key driver of their bHLH gene diversity, whereas in A. spinulosa, segmental duplication contributed more to gene expansion and evolution. Most of the bHLH genes in ferns are in a state of purifying selection. Additionally, tissue-specific expression patterns of AspbHLH genes suggest diverse functional roles in plant growth, development, and metabolite synthesis. We further focused on three genes, AspbHLH80, AspbHLH120, and AspbHLH185, which are specifically highly expressed in xylem. Results from weighted gene co-expression network analysis (WGCNA) and downstream target gene prediction indicate their potential regulatory roles in lignin biosynthesis.

CONCLUSION

This study presents a comprehensive genomic analysis of the bHLH gene family in five fern species. We found a strong correlation between bHLH gene number and fern growth morphology, with tree ferns exhibiting a significantly higher number of bHLH genes. Tandem duplications were key to bHLH gene diversity in C. richardii, A. capillus, and A. spinulosa, while segmental duplications contributed more to bHLH gene expansion in A. spinulosa. Evolutionary analysis indicated most fern bHLH genes are under purifying selection. Tissue-specific expression patterns of AspbHLH genes suggest roles in growth, development, and secondary metabolism. Furthermore, WGCNA and target gene predictions highlight three genes (AspbHLH80, AspbHLH120, and AspbHLH185) potentially involved in lignin biosynthesis. Overall, this work provides key insights into the mechanisms of wood formation in ferns and advances our understanding of plant secondary metabolism.

Genome assembly of Stewartia sinensis reveals origin and evolution of orphan genes in Theaceae

Orphan genes play crucial roles in diverse biological processes, but the evolutionary trajectories and functional divergence remain largely unexplored. The Theaceae family, including the economically and culturally important tea plant, offers a distinctive model to examine these aspects. Here, we integrated Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods to decode a pseudo-chromosomal genome assembly of Stewartia sinensis, from the earliest-diverging tribe of Theaceae, spanning 2.95 Gb. Comparative genomic analysis revealed the absence of recent whole-genome duplication events in the Theaceae ancestor, highlighting tandem duplications as the predominant mechanism of gene expansion. We identified 31,331 orphan genes, some of which appear to have ancient origins, suggesting early emergence with frequent gains and losses, while others seem more specific and recent. Notably, orphan genes are distinguished by shorter lengths, fewer exons and functional domains compared to genes that originate much earlier, like transcription factors. Moreover, tandem duplication contributes significantly to the adaptive evolution and characteristic diversity of Theaceae, and it is also a major mechanism driving the origination of orphan genes. This study illuminates the evolutionary dynamics of orphan genes, providing a valuable resource for understanding the origin and evolution of tea plant flavor and enhancing genetic breeding efforts.

Pan-genome analyses of 11 Fraxinus species provide insights into salt adaptation in ash trees

Ash trees (Fraxinus) exhibit rich genetic diversity and wide adaptation to various ecological environments, and several species are highly salt tolerant. Dissecting the genomic basis of salt adaptation in Fraxinus is vital for its resistance breeding. Here, we present 11 high-quality chromosome-level genome assemblies for Fraxinus species, which reveal two unequal subgenome compositions and two recent whole-genome triplication events in their evolutionary history. A Fraxinus pan-genome was constructed on the basis of structural variations and revealed that presence-absence variations (PAVs) of transmembrane transport genes have likely contributed to salt adaptation in Fraxinus. Through whole-genome resequencing of an F1 population from an interspecies cross of F. velutina 'Lula 3' (salt tolerant) with F. pennsylvanica 'Lula 5' (salt sensitive), we mapped salt-tolerance PAV-based quantitative trait loci (QTLs) and pinpointed two PAV-QTLs and candidate genes associated with Fraxinus salt tolerance. Mechanistically, FvbHLH85 enhances salt tolerance by mediating reactive oxygen species and Na+/K+ homeostasis, whereas FvSWEET5 enhances salt tolerance by mediating osmotic homeostasis. Collectively, these findings provide valuable genomic resources for Fraxinus salt-resistance breeding and the research community.

A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation

BACKGROUND

Drought is a major limiting factor for plant survival and crop productivity. Stylosanthes angustifolia, a pioneer plant, exhibits remarkable drought tolerance, yet the molecular mechanisms driving its drought resistance remain largely unexplored.

RESULTS

We present a chromosome-scale reference genome of S. angustifolia, which provides insights into its genome evolution and drought tolerance mechanisms. The assembled genome is 645.88 Mb in size, containing 319.98 Mb of repetitive sequences and 36,857 protein-coding genes. The high quality of this genome assembly is demonstrated by the presence of 99.26% BUSCO and a 19.49 long terminal repeat assembly index. Evolutionary analyses revealed that S. angustifolia shares a whole-genome duplication (WGD) event with other legumes but lacks recent WGD. Additionally, S. angustifolia has undergone gene expansion through tandem duplication approximately 12.31 million years ago. Through integrative multiomics analyses, we identified 4 gene families-namely, xanthoxin dehydrogenase, 2-hydroxyisoflavanone dehydratase, patatin-related phospholipase A, and stachyose synthetase-that underwent tandem duplication and were significantly upregulated under drought stress. These gene families contribute to the biosynthesis of abscisic acid, genistein, daidzein, jasmonic acid, and stachyose, thereby enhancing drought tolerance.

CONCLUSIONS

The genome assembly of S. angustifolia represents a significant advancement in understanding the genetic mechanisms underlying drought tolerance in this pioneer plant species. This genomic resource provides critical insights into the evolution of drought resistance and offers valuable genetic information for breeding programs aimed at improving drought resistance in crops.

Population genetic diversity and environmental adaptation of Tamarix hispida in the Tarim Basin, arid Northwestern China

Arid ecosystems, characterized by severe water scarcity, play a crucial role in preserving Earth's biodiversity and resources. The Tarim Basin in Northwestern China, a typical arid region isolated by the Tianshan Mountains and expansive deserts, provides a special study area for investigating how plant response and adaptation to such environments. Tamarix hispida, a species well adapted to saline-alkaline and drought conditions, dominates in the saline-alkali lands of the Tarim Basin. This study aims to examine the genetic diversity and environmental adaptation of T. hispida in the Tarim Basin. Genomic SNPs for a total of 160 individuals from 17 populations were generated using dd-RAD sequencing approach. Population genetic structure and genetic diversity were analyzed by methods including ADMIXTURE, PCA, and phylogenetic tree. Environmental association analysis (EAA) was performed using LFMM and RDA analyses. The results revealed two major genetic lineages with geographical substitution patterns from west to east, indicating significant gene flow and hybridization. Environmental factors such as Precipitation Seasonality (bio15) and Topsoil Sand Fraction (T_SAND) significantly shaped allele frequencies, supporting the species' genetic adaptability. Several genes associated with environmental adaptation were identified and annotated, highlighting physiological and metabolic processes crucial for survival in arid conditions. The study highlights the role of geographical isolation and environmental factors in shaping genetic structure and adaptive evolution. The identified adaptive genes related to stress tolerance emphasize the species' resilience and highlight the importance of specific physiological and metabolic pathways.

Comparative study on chloroplast genome of Tamarix species

Tamaricaceae comprises about 120 species and has a long evolutionary history, Tamarix Linn accounts for approximately 75% of the total species in this family. It is the most widely distributed and diverse genus in the family. They have important ecological significance for transforming deserts and improving climate conditions. However, Tamarix is the most poorly classified genera among flowering plants owing to its large variability and high susceptibility to interspecific hybridization. In this study, the complete chloroplast genomes of three Tamarix species and one draft chloroplast genome were obtained in this study. Combined with eight chloroplast genomes deposited in GenBank, complete chloroplast sequences of 12 Tamarix species were used for further analysis. There are 176 non-SSR-related indels and 681 non-indel-related SSRs in the 12 Tamarix chloroplast genomes. The mononucleotide SSRs are the most prevalent among all types of SSRs. The mVISTA results indicate high sequence similarities across the chloroplast genome, suggesting that the chloroplast genomes are highly conserved, except for sample Tamarix androssowii (ENC850343). The IR regions and the coding regions are more conserved than the single-copy and noncoding regions. The trnF-ndhJ, ndhC-trnM-CAU, ycf1, and trnL-UAG-ndhF regions are the most variable and have higher variability than those of the universal DNA markers. Finally, the first phylogenetic tree of Tamaricaceae was constructed which confirmed the monophyly of Tamarix in Tamaricaceae. The first phylogenetic tree of Tamarix was based on the complete chloroplast genome to date, the changes in branch length and support rate can potentially help us clarify the phylogenetic relationships of Tamarix. All the obtained genetic resources will facilitate future studies in population genetics, species identification, and conservation biology of Tamarix.

Differences in Metabolic Characteristics of Rhizosphere Fungal Community of Typical Arboreal, Shrubby and Herbaceous Species in Oasis of Arid Region

Populus euphratica, Tamarix ramosissima, and Sophora alopecuroides are, respectively, typical arboreal, shrubby, and herbaceous species in oases of arid regions. It is important to study the difference in metabolic characteristics of the rhizosphere fungal community of these plant species and their relationships with soil factors for the preservation of delicate arid oasis ecosystems with future environmental changes. In this study, we, respectively, collected 18 rhizosphere soil samples of P. euphratica, T. ramosissima, and S. alopecuroides to explore the difference in rhizosphere fungal metabolic characteristics of different plant life forms and their underlying driving factors. The results showed that (1) soil physicochemical properties (including soil water content, pH, etc.) were significantly different among different plant species (p < 0.05). (2) Rhizosphere fungal metabolic characteristics were significantly different between S. alopecuroides and T. ramosissima (ANOSIM, p < 0.05), which was mainly caused by the different utilization of carboxylic carbon. (3) The RDA showed that the main driving factors of the variations in rhizosphere fungal metabolic characteristics were different among different plant species. The main explanatory variables of the variations in the metabolic characteristics of the rhizosphere fungal community were carbon to nitrogen ratio (23%) and available potassium (17.4%) for P. euphratica, while soil organic carbon (23.1%), pH (8.6%), and total nitrogen (8.2%) for T. ramosissima, and soil clay content (36.6%) and soil organic carbon (12.6%) for S. alopecuroides. In conclusion, the variations in rhizosphere fungal metabolic characteristics in arid oases are dominantly affected by soil factors rather than plant life forms.

The Yellow River is the key corridor for Tamarix austromongolica to disperse from Asia inlands to east seashores

Plants of the Tamarix L. genus (Tamaricaceae) mainly occur in arid inlands of Asia, but a few species occur in the coastal areas of China, and the Yellow River may account for this. This study was conducted to elucidate whether and how the Yellow River affects the pattern and development of the Tamarix genus, involving two critical species of Tamarix austromongolica Nakai and Tamarix chinensis Lour. With geographical distribution data, relationships of T. austromongolica with the Yellow River and the pertaining watershed were examined using the method of random permutation. The base-diameter structures of T. austromongolica populations were investigated and compared between different riparian lands that suffer discriminative water inundation. The nearest distances from T. austromongolica locations to the Yellow River and the pertaining watershed were significantly lower than the theoretical expectations in the condition of random distribution (p < .05). In many riparian lands along the Yellow River, wild T. austromongolica populations occurred with vigorous juveniles, despite frequent human disturbances. In coastal areas near the present estuary of the river, wild T. austromongolica plants were still found. In T. austromongolica populations near the Yellow River and sea, the rates of juvenile plants were significantly higher than in other populations situated farther from the river or sea. These findings suggest that the Yellow River can facilitate the eastward dispersal of Tamarix plants that reasonably caused the evolution from T. austromongolica to T. chinensis in ancient coasts in the China east.

A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China

Tamarix austromongolica is endemic to the Yellow River Basin and has adapted to diverse ecological settings in the region, including the arid areas of northwestern China and the saline soil regions of the Yellow River Delta. However, the genetic basis of its local adaptation remains unclear. We report a chromosome-level assembly of the T. austromongolica genome based on PacBio high-fidelity sequencing and Hi-C technology. The 12 pseudochromosomes cover 98.44% of the 1.32 Gb assembly, with a contig N50 of 52.57 Mb and a BUSCO score of 98.2%. The genome comprises 913.6 Mb (68.83%) of repetitive sequences and 22,374 protein-coding genes. Genome evolution analyses suggest that genes under positive selection and significantly expanded gene families have facilitated T. austromongolica's adaptability to diverse environmental factors and high resistance to diseases. Using genotyping-by-sequencing, we conducted population structure and selection analyses of 114 samples from 15 sites. Two genetic groups were identified, and 114 and 289 candidate genes were assigned to the populations of the northwestern and eastern parts of the Yellow River, respectively. Furthermore, we discovered numerous candidate genes associated with high-altitude adaptability and salt tolerance. This research provides valuable genomic resources for the evolutionary study and genetic breeding of tamarisk.

Chromosome-level genome assembly and annotation of xerophyte secretohalophyte Reaumuria soongarica

Reaumuria soongarica is a xerophytic shrub belonging to the Tamaricaceae family. The species is widely distributed in the deserts of Central Asia and is characterized by its remarkable adaptability to saline and barren desert environments. Using PacBio long-read sequencing and Hi-C technologies, we assembled a chromosome-level genome of R. soongarica. The genome assembly has a size of 1.28 Gb with a scaffold N50 of 116.15 Mb, and approximately 1.25 Gb sequences were anchored in 11 pseudo-chromosomes. A completeness assessment of the assembled genome revealed a BUSCO score of 97.5% and an LTR Assembly Index of 12.37. R. soongarica genome had approximately 60.07% repeat sequences. In total, 21,791 protein-coding genes were predicted, of which 95.64% were functionally annotated. This high-quality genome will serve as a foundation for studying the genomic evolution and adaptive mechanisms to arid-saline environments in R. soongarica, facilitating the exploration and utilization of its unique genetic resources.

The role of WRKY transcription factors in exogenous potassium (K+) response to NaCl stress in Tamarix ramosissima

Introduction: Soil salinization poses a significant challenge to plant growth and vitality. Plants like Tamarix ramosissima Ledeb (T. ramosissima), which are halophytes, are often integrated into planting schemes tailored for saline environments. Yet, the role of WRKY transcription factors in T. ramosissima, especially under sodium chloride (NaCl) stress mitigated by exogenous K+ application, is not well-understood. This research endeavors to bridge this knowledge gap. Methods: Using Pfam protein domain prediction and physicochemical property analysis, we delved into the WRKY genes in T. ramosissima roots that are implicated in counteracting NaCl stress when aided by exogenous K+ applications. By observing shifts in the expression levels of WRKY genes annotated to the KEGG pathway under NaCl stress at 0, 48, and 168 h, we aimed to identify potential key WRKY genes. Results: We found that the expression of 56 WRKY genes in T. ramosissima roots responded to exogenous K+ application during NaCl stress at the indicated time points. Particularly, the expression levels of these genes were primarily upregulated within 168 h. From these, 10 WRKY genes were found to be relevant in the KEGG pathways. Moreover, six genes, namely Unigene0024962, Unigene0024963, Unigene0010090, Unigene0007135, Unigene0070215, and Unigene0077293, were annotated to the Plant-pathogen interaction pathway or the MAPK signaling pathway in plants. These genes exhibited dynamic expression regulation at 48 h with the application of exogenous K+ under NaCl stress. Discussion: Our research highlights that WRKY transcription factors can modulate the activation or inhibition of related genes during NaCl stress with the application of exogenous K+. This regulation enhances the plant's adaptability to saline environments and mitigates the damage induced by NaCl. These findings provide valuable gene resources for future salt-tolerant Tamarix breeding and expand our understanding of the molecular mechanisms of WRKY transcription factors in alleviating NaCl toxicity.