A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance

Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae

Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.

Development of a marker-free engineered durum wheat overexpressing Lobularia maritima GASA1 with improved drought tolerance

Due to their fixed lifestyle, plants must adapt to abiotic or biotic stresses by orchestrating various responses, including protective and growth control measures. Growth arrest is provoked upon abiotic stress and can impair plant production. Members of the plant-specific GASA (gibberellic acid-stimulated Arabidopsis) gene family play crucial roles in phytohormone responses, abiotic and biotic stresses, and plant growth. Here, we recognized and examined the LmGASA1 gene from the halophyte plant Lobularia maritima and developed marker-free engineered durum wheat plants overexpressing the gene. The LmGASA1 transcript profile revealed that it's induced by stressful events as well as by phytohormones including GA3, MeJA, and ABA, suggesting that the LmGASA1 gene may contribute to these stress and hormone signal transduction pathways. Transient expression of GFP-LmGASA1 fusion in onion epidermal cells indicated that LmGASA1 is localized to the cell membrane. Further analysis showed that overexpression of LmGASA1 in durum wheat plants enhanced tolerance to drought stress compared with that in non-transgenic (NT) plants, imposing no yield penalty and enabling seed production even following drought stress at the vegetative stage. Altogether, our data indicate that LmGASA1 regulates both the scavenging capacity of the antioxidant enzymatic system and the activation of at least six stress-related genes that function as positive regulators of drought stress tolerance. LmGASA1 appears to be a novel gene useful for further functional analysis and potential engineering for drought stress tolerance in crops.

Responses of different invasive and non-invasive ornamental plants to water stress during seed germination and vegetative growth

Biological invasions represent a major threat to natural ecosystems. A primary source of invasive plants is ornamental horticulture, which selects traits related to invasiveness. This study evaluated the responses to water stress during germination and vegetative growth of six species used as ornamental or medicinal plants. Three of them are recognised as invasive weeds in many world areas. Seeds were exposed to increasing concentrations of polyethylene glycol (PEG) mimicking drought stress, and young plants in the vegetative growth stage were subjected to two levels of water stress. Results indicated that in the absence of stress in control conditions, the most competitive species were those reported as weeds, namely Bidens pilosa L., Oenothera biennis L., and Centaurea cyanus L., the last regarding germination velocity. Under stress, only two species, Limonium sinuatum (L.) Mill. and C. cyanus, maintained germination at -1 MPa osmotic potential, but in the recovery experiment, an osmopriming effect of PEG was observed. The most tolerant species during growth were two natives in the Mediterranean region, L. sinuatum and Lobularia maritima (L.) Desv., both accumulating the highest proline concentrations. The sixth species studied, Echinacea purpurea (L.) Moench., proved to be more susceptible to stress in the two developmental stages. This study reveals that the most significant traits associated with invasiveness were related to germination, especially in the absence of stress.

A high-quality chromosome-level Eutrema salsugineum genome, an extremophile plant model

BACKGROUND

Eutrema salsugineum (2n = 14), a halophyte in the family Brassicaceae, is an attractive model to study abiotic stress tolerance in plants. Two versions of E. salsugineum genomes that previously reported were based on relatively short reads; thus, the repetitive regions were difficult to characterize.

RESULTS

We report the sequencing and assembly of the E. salsugineum (Shandong accession) genome using long-read sequencing and chromosome conformation capture data. We generated Oxford Nanopore long reads at high depth (> 60X) of genome coverage with additional short reads for error correction. The new assembly has a total size of 295.5 Mb with 52.8% repetitive sequences, and the karyotype of E. salsugineum is consistent with the ancestral translocation Proto-Calepineae Karyotype structure in both order and orientation. Compared with previous assemblies, this assembly has higher contiguity, especially in the centromere region. Based on this new assembly, we predicted 25,399 protein-coding genes and identified the positively selected genes associated with salt and drought stress responses.

CONCLUSION

The new genome assembly will provide a valuable resource for future genomic studies and facilitate comparative genomic analysis with other plants.

Evaluation of Halophyte Biopotential as an Unused Natural Resource: The Case of Lobularia maritima

Halophytes are plant species widely distributed in saline habitats, such as beaches, postindustrial wastelands, irrigated lands, salt flats, and others. Excessive salt level, known to limit plant growth, is not harmful to halophytes, which have developed a variety of defense mechanisms allowing them to colonize harsh environments. Plants under stress are known to respond with several morpho-anatomical adaptations, but also to enhance the production of secondary metabolites to better cope with difficult conditions. Owing to these adaptations, halophytes are an interesting group of undemanding plants with a high potential for application in the food and pharmaceutical industries. Therefore, this review aims to present the characteristics of halophytes, describe changes in their gene expression, and discuss their synthesized metabolites of pharmacognostic and pharmacological significance. Lobularia maritima is characterized as a widely spread halophyte that has been shown to exhibit various pharmacological properties in vitro and in vivo. It is concluded that halophytes may become important sources of natural products for the treatment of various ailments and for supplementing the human diet with necessary non-nutrients and minerals. However, extensive studies are needed to deepen the knowledge of their biological potential in vivo, so that they can be introduced to the pharmaceutical and food industries.

Investigation of Brassica and its relative genomes in the post-genomics era

The Brassicaceae family includes many economically important crop species, as well as cosmopolitan agricultural weed species. In addition, Arabidopsis thaliana, a member of this family, is used as a molecular model plant species. The genus Brassica is mesopolyploid, and the genus comprises comparatively recently originated tetrapolyploid species. With these characteristics, Brassicas have achieved the commonly accepted status of model organisms for genomic studies. This paper reviews the rapid research progress in the Brassicaceae family from diverse omics studies, including genomics, transcriptomics, epigenomics, and three-dimensional (3D) genomics, with a focus on cultivated crops. The morphological plasticity of Brassicaceae crops is largely due to their highly variable genomes. The origin of several important Brassicaceae crops has been established. Genes or loci domesticated or contributing to important traits are summarized. Epigenetic alterations and 3D structures have been found to play roles in subgenome dominance, either in tetraploid Brassica species or their diploid ancestors. Based on this progress, we propose future directions and prospects for the genomic investigation of Brassicaceae crops.

Idahoa and Subularia: Hidden polyploid origins of two enigmatic genera of crucifers

PREMISE

The monotypic Idahoa (I. scapigera) and the bispecific Subularia (S. aquatica and S. monticola) belong to Brassicaceae with unclear phylogenetic relationships and no tribal assignment. To fill this knowledge gap, we investigated these species and their closest relatives by combining cytogenomic and phylogenomic methods.

METHODS

We used whole plastome sequences in maximum likelihood and Bayesian inference analyses. We tested the phylogenetic informativeness of shared genomic repeats. We combined nuclear gene tree reconciliation and comparative chromosome painting (CCP) to examine the occurrence of past whole-genome duplications (WGDs).

RESULTS

The plastid data set corroborated the sister relationship between Idahoa and Subularia within the crucifer Lineage V but failed to resolve consistent topologies using both inference methods. The shared repetitive sequences provided conflicting pwhylogenetic signals. CCP analysis unexpectedly revealed that Idahoa (2n = 16) has a diploidized mesotetraploid genome, whereas two Subularia species (2n = 28 and 30) have diploidized mesoctoploid genomes. Several ancient allopolyploidy events have also been detected in closely related taxa (Chamira circaeoides, Cremolobeae, Eudemeae, and Notothlaspideae).

CONCLUSIONS

Our results suggest that the contentious phylogenetic placement of Idahoa and Subularia is best explained by two WGDs involving one or more shared parental genomes. The newly identified mesopolyploid genomes highlight the challenges of studying plant clades with complex polyploidy histories and provide a better framework for understanding genome evolution in the crucifer family.

Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions

Whole-genome duplication (WGD) has occurred repeatedly during plant evolution and diversification, providing genetic layers for evolving new functions and phenotypes. Advances in long-read sequencing technologies have enabled sequencing and assembly of over 1000 plant genomes spanning nearly 800 species, in which a large set of ancient WGDs has been uncovered. Here, we review the recently reported WGDs that occurred in major plant lineages and key evolutionary positions, and highlight their contributions to morphological innovation and adaptive evolution. Current gaps and challenges in integrating enormous volumes of sequenced plant genomes, accurately inferring WGDs, and developing web-based analysis tools are emphasized. Looking to the future, ambitious genome sequencing projects and global efforts may substantially recapitulate the plant tree of life based on broader sampling of phylogenetic diversity, reveal much of the timetable of ancient WGDs, and address the biological significance of WGDs in plant adaptation and radiation.