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Seed structure and seed germination pattern of Suaeda salsa. a-f Endocarp appearance and early germination pattern of Suaeda salsa. Bar = 0.5 mm. g-l Seed germination pattern at different stages of planospiral embryo. Bar = 0.5 mm. m The Seed treated with KI/I 2 for the starch test. Bar = 0.5 mm. n Endocarp having honeycomb-like structure. Bar = 0.5 mm. o-s Epigeal germination pattern of Suaeda salsa. Figures showed the seedlings at 48, 60, 72 h, and 5 and 40 days after germination. Bar = 1 cm
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Background:
Soil salinization and alkalization are among the major agricultural threats that affect crop productivity worldwide, which are increasing day by day with an alarming rate. In recent years, several halophytes have been investigated for their utilization in soil remediation and to decipher the mechanism of salt-tolerance in these high sa...
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... seeds. The mature seeds of Suaeda salsa also consisted of thin fleshy mesocarp and exocarp. Endocarp is hard and thin with blackish colour. During germination, endocarp was split into two parts. This splitting can be easily observed after 24 h of germination and split becoming wider after 48 h of germination, allowing radical to grow easily ( Fig. 1a-f). Careful observation of the endocarp surface showed the honeycomblike pattern (Fig. 1n). Having thin hard endocarp makes seed germination obstructed delaying the propagation process, which is required to meet the agricultural demand. When the pericarp was removed, seeds appeared flat, disc-shaped with a size of 1.8-2.1 mm in diameter. ...
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... Endocarp is hard and thin with blackish colour. During germination, endocarp was split into two parts. This splitting can be easily observed after 24 h of germination and split becoming wider after 48 h of germination, allowing radical to grow easily ( Fig. 1a-f). Careful observation of the endocarp surface showed the honeycomblike pattern (Fig. 1n). Having thin hard endocarp makes seed germination obstructed delaying the propagation process, which is required to meet the agricultural demand. When the pericarp was removed, seeds appeared flat, disc-shaped with a size of 1.8-2.1 mm in diameter. The seed has a thin brownish seed coat (Fig. 1g). Once the seed coat was removed, we ...
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... endocarp surface showed the honeycomblike pattern (Fig. 1n). Having thin hard endocarp makes seed germination obstructed delaying the propagation process, which is required to meet the agricultural demand. When the pericarp was removed, seeds appeared flat, disc-shaped with a size of 1.8-2.1 mm in diameter. The seed has a thin brownish seed coat (Fig. 1g). Once the seed coat was removed, we observed a brown thin whitish colour layer consisted of starch, which turned to a blackish-blue colour when treated with KI/I 2 (Fig. 1m) . With the start of germination, the seed coat and thin starchy layer started to disappear. At this stage, we observed mature germinating planospiral embryo that ...
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... to meet the agricultural demand. When the pericarp was removed, seeds appeared flat, disc-shaped with a size of 1.8-2.1 mm in diameter. The seed has a thin brownish seed coat (Fig. 1g). Once the seed coat was removed, we observed a brown thin whitish colour layer consisted of starch, which turned to a blackish-blue colour when treated with KI/I 2 (Fig. 1m) . With the start of germination, the seed coat and thin starchy layer started to disappear. At this stage, we observed mature germinating planospiral embryo that is the distinguishing feature in this plant family [22] (Fig. 1g-l). The outermost end of the planospiral embryo act as radical, giving rise to root. The innermost end of the ...
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... a brown thin whitish colour layer consisted of starch, which turned to a blackish-blue colour when treated with KI/I 2 (Fig. 1m) . With the start of germination, the seed coat and thin starchy layer started to disappear. At this stage, we observed mature germinating planospiral embryo that is the distinguishing feature in this plant family [22] (Fig. 1g-l). The outermost end of the planospiral embryo act as radical, giving rise to root. The innermost end of the embryo act as plumule that later develops into the shoot. During Suaeda salsa seeds germination, we observed radical growth into roots first and then followed by two cotyledons appearance at the other end of the embryo. Later we ...
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... as plumule that later develops into the shoot. During Suaeda salsa seeds germination, we observed radical growth into roots first and then followed by two cotyledons appearance at the other end of the embryo. Later we observed the emergence of true leaves. This germination study revealed that the Suaeda salsa possesses epigeal germination pattern (Fig. ...
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... of the developmental type of female gametophyte can promote understanding and carrying out the process of sexual reproduction and hybridization in plants. Taking the developmental process of female gametophyte in Arabidopsis as a control (Additional file 3: Figure S1), we observed the female gametophyte development process of Suaeda salsa using WCLSM (Whole-mount-stain clearing laser scanning confocal microscopy) theology. The results showed that the female gametophyte development of Suaeda salsa could also be divided into seven stages: Stages I to VII. ...
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... plant enclosed in a protective outer covering [35]. Yielding seeds have been an important development in the sexual reproduction and the success of gymnosperm and angiosperm plants during the evolution, compared to the primitive plants such as ferns, mosses, and liverworts [36]. The seed of Suaeda salsa is of typical type with a tough seed coat (Fig. 1a, n). This characteristic is an adaption of Suaeda salsa to drought and salinity conditions in the seashore, which could prolong the dormancy and is beneficial for the diffusion prorogation of the species. Seed germination in plants mainly is three types: Hypogeal Germination, Epigeal Germination and, Vivipary (Viviparous Germination). When ...
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... beneficial for the diffusion prorogation of the species. Seed germination in plants mainly is three types: Hypogeal Germination, Epigeal Germination and, Vivipary (Viviparous Germination). When the Suaeda salsa seeds are germinating, the hypocotyl significantly elongates before the emergence of true leaves and brings the cotyledon above the soil (Fig. 1q-s), showing its epigeal germination type. The model plant Arabidopsis, and most other dicots species such as castor, cotton, papaya, onion also belong to epigeal germination type ...
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Citations
... GO enrichment analysis showed that these genes were mainly enriched in biological processes, followed by molecular functions, and to a lesser extent in cellular components (Fig. 3c). KEGG enrichment analysis showed that these genes were significantly enriched in the pathways of genetic information, metabolism, and biological systems [36] . Following the combination of the up-regulated gene screen, it was hypothesized that flavonoid biosynthesis and carotenoid synthesis, two of the enriched genes, may be involved in the variations in the color of finger lemon peel. ...
The Australian native plant finger lemon (Citrus australasica) is well-known for its distinct flavor and high economic and medicinal value. 'YaoJi' is a typical purple variety of finger lemon, but its genome has not been analyzed yet. In this study, we used three-generation nanopore sequencing technology to sequence and assemble the genome of the finger lemon and combined it with the transcriptome analysis of different varieties with different colors of rinds at the same developmental period to investigate the mechanism of the differences in the color of the rinds of finger lemons. According to the results, the finger lemon genome was built and has nine chromosomes and a size of 314.63 Mb (Contig N50, 6.60 Mb; Scaffold N50, 32.81 Mb). By using homologous protein comparison and gene annotation, a total of 21,154 protein-coding genes and 164.7 Mb (52.35%) of repetitive sequences have been identified. The phylogenetic evolutionary tree shows that 10 Mya years ago finger lemon diverged from sweet orange (Citrus sinensis (L.) Osbeck) and Cremantine red orange (Citrus × clementina). Presumably it's a whole genome duplication (WGD) event according to the synonymous substitution rates (KS). Transcriptome analysis showed that the differences in the rind color of finger lemon were associated with higher expression of PAL, 4CL, and ANS genes in flavonoid biosynthesis and VDE and PSY genes in carotenoid synthesis. Transcription factors regulating flavonoid biosynthesis, such as bHLH, MYB, WD40, and NAC were also identified, which provides insights into the origin and evolution of finger lemon species and functional gene mining.
... Salt-tolerant plants exhibit thickened or succulent leaves, a waxy outer layer, extensively suberized apoplastic barriers in roots, and seeds with a rigid seed coat maintaining dormancy in unfavorable conditions [60][61][62][63]. Seeds obtained from the mother plant grown on saline conditions (e.g., 200 mM NaCl) showed significantly higher seed viability, and their morphological parameters such as plant height, stem diameter, total branch length, and reproductive parameters such as flowering branch length, flowering branch ratio, and seed production are better than those seeds whose mother plants were grown under normal conditions [19]. ...
Over the years, the changes in the agriculture industry have been inevitable, considering the need to feed the growing population. As the world population continues to grow, food security has become challenged. Resources such as arable land and freshwater have become scarce due to quick urbanization in developing countries and anthropologic activities; expanding agricultural production areas is not an option. Environmental and climatic factors such as drought, heat, and salt stresses pose serious threats to food production worldwide. Therefore, the need to utilize the remaining arable land and water effectively and efficiently and to maximize the yield to support the increasing food demand has become crucial. It is essential to develop climate-resilient crops that will outperform traditional crops under any abiotic stress conditions such as heat, drought, and salt, as well as these stresses in any combinations. This review provides a glimpse of how plant breeding in agriculture has evolved to overcome the harsh environmental conditions and what the future would be like.
... The homogenated samples were then filtered through a 42-mm nylon mesh, and 10 ul of DNA fluorochrome solution (50 mg/ml PI, 50 mg/ml RNase) was added to the flowthrough for staining the nuclei. After 5 minutes of incubation at room temperature, the nuclei solutions were subject to FLC analysis on a BD FACScalibur Flow cytometry platform (Cheng et al., 2019). ...
... The chromosome spreads of microspores were prepared as described previously (Ross et al., 1996) and stained with 1.5 mg/ml 4,6-diamidino-2phenylindole (DAPI) before microscopy. Images of chromosome spreads were taken with a Zeiss (Model) microscope following the method reported by Cheng et al. (2019). ...
Ipomoeapes-caprae (L.) (IPC) is a common species in tropical and subtropical coastal areas and one of the world’s most widely distributed plants. It has attracted researchers for its outstanding biological, ecological and medicinal values. It has been reported that the genetic diversity of IPCs located on different continents is very low because of their frequent gene flow. During the long journey of evolution, every aspect of the plant morphologies has evolved to the best adaptivity to the environment, seeking their survival and progeny expansion. However, the fundamental genetic characteristics of IPC and how their seed adapted to the success of population expansion remain unknown. In this study, the fundamental genetic characteristics, including the genome size and the chromosome number of IPC, were investigated. The results showed that IPC’s genome size is approximately 0.98-1.08 GB, and the chromosome number is 2n=30, providing the basic information for further genome analysis. In order to decipher the long-distance dispersal secret of this species, the fruit and seed developments, seed morphology, and seed germination were extensively investigated and described. The results showed an exquisite adaptive mechanism of IPC seeds to fulfil the population expansion via ocean currents. The large cavity inside the seeds and the dense tomenta on the surface provide the buoyancy force for the seeds to float on the seawater. The hard seed coats significantly obstructed the water absorption, thus preventing the seed from germination during the dispersal. Meanwhile, the fully developed embryos of IPC also have physiological dormancy. The physical and physiological characteristics of IPC seeds provide insight into the mechanism of their long-distance dispersal across the oceans. Moreover, based on morphological observation and semi-section microscopy, the development pattern of IPC glander trichomes was described, and their physiological functions were also discussed.
... Salinized soil has high salt content and poor soil physical and chemical properties, which seriously hindered the growth and development of plants [1]. Salinized soil contains a lot of Na + type salt which can destroy the stability of protein and membrane, and produces osmotic stress and ion poisoning to initiate reactive oxygen ROS (reactive oxygen species) signals in the cell, make dysfunction of the cell, affect the growth of plants, and causes plant death in severe cases [2]. ...
... NaCl-48h comparison group. The largest number of up-regulated genes is GST (7), followed by POD (4), CAT (4), APX (3), GR (2) and SOD (1). The largest number of down-regulated genes is GST (8), followed by POD (4), SOD (3), APX (2) and GPX (1). ...
Halophyte Tamarix ramosissima. Lcdcb (T. ramosissima) are known as the representative of Tamarix plants that are widely planted in salinized soil. However, molecular mechanisms towards salt tolerance and adaptation are largely rare. In this study, we carried out RNA-sequence and transcriptome analysis of T. ramosissima in response to NaCl stress, screened differentially expressed genes (DEGs) and further verified by qRT-PCR. Results showed that 105702 unigenes were spliced from the raw data of transcriptome sequencing, where 54238 unigenes were retrieved from KEGG, KOG, NR, and SwissProt. After 48 hours of NaCl treatment, the expression levels of 6374 genes were increased, and 5380 genes were decreased in leaves. After 168 hours, the expression levels of 3837 genes were up-regulated and 7808 genes were down-regulated. In particular, 8 transcription factors annotated to the KEGG Pathway were obtained, involving the WRKY and bZIP transcription family. In addition, KEGG pathway annotation showed that expression of 39 genes involved in ROS scavenging mechanisms were significantly changed, in which 21 genes were up-regulated and 18 genes were down-regulated after 48 hours as well as 15 genes were up-regulated and 24 genes were down-regulated after 168h. Simultaneously, the enzyme activities of SOD and POD were significantly enhanced under NaCl treatment, but the enzyme activity of CAT was not significantly enhanced. Moreover, WRKY, MYB and bZIP may participate in the process of salt resistance in T. ramosissima. This study provides gene resources and a theoretical basis for further molecular mechanisms of salt tolerance in T. ramosissima.
... Suaeda salsa (L.) Pall. (Amaranthaceae) is an annual herb and a typical halophyte (Cheng et al. 2019). It is observed to grow in coastal salt marshes and saline inland sites in nearly 20 provinces in China (Jia et al. 2021). ...
Vermicompost is a commonly used organic fertilizer that can effectively improve the fertility and structure of saline soil. However, the effect of vermicompost on the growth of halophytes in coastal saline soil, especially under flooding conditions, is obscure. We conducted two greenhouse experiments in which seeds and seedlings, respectively, of the Suaeda salsa were subjected to no flooding, episodic flooding, or continuous flooding, crossed with or without vermicompost addition, in a factorial design. Continuous flooding decreased seed germination and seedling biomass of S. salsa. Under no flooding or episodic flooding, vermicompost addition significantly increased seed germination and seedling growth in S. salsa, but vermicompost addition had no significant effects under continuous flooding. Vermicompost addition increased the stability of soil aggregates and decreased soil electrical conductivity, thereby improving the soil quality. Our results suggest that vermicompost addition could be an effective strategy for enhancing the population growth of S. salsa in saline soil and benefit the restoration of the S. salsa community in the Yellow River Delta, China.
Halophytes possess unique genetic traits that enable them to withstand harsh environmental conditions such as high salinity, extreme temperatures, drought, and metal pollution. Although draft genomes are accessible for a limited halophyte, existing multi-omics datasets provide thorough insights into the regulatory pathways and gene networks essential for constructing comprehensive models of multi-stress tolerance. Bioengineering strategies involving the transfer and expression of halophyte genes in glycophytes have shown significant promise for enhancing crop resilience, agricultural profitability, and ecosystem health. Genes isolated from species of the genera Atriplex, Haloxylon, Lobularia, Nitraria, Salicornia, Suaeda, and Thellungiella have been successfully in many salt-sensitive crops such as cotton, groundnut, rice, soybean, and tobacco, resulting in stress-tolerant transgenic crops. The development of such robust transgenic will not only contribute to food security but also enable the cultivation of crops on marginal lands without chemical and fertilizer inputs. Furthermore, engineered halophytes hold significant potential for producing bioproducts with applications in renewable energy, environmental remediation, food, and pharmaceuticals. These include bio-alcohols, biodiesel, biohydrogen, metabolites, nanocomposites, and specialty chemicals. To maximize the underlying of halophytes for future transgenic breakthroughs, it is essential to integrate multi-omics datasets, precise gene editing tools, and systems biology approaches with ongoing interdisciplinary research.
Suaeda salsa L. is a typical halophyte with high value as a vegetable. Here, we report a 447.98 Mb, chromosomal‐level genome of S. salsa , assembled into nine pseudomolecules (contig N50 = 1.36 Mb) and annotated with 27,927 annotated protein‐coding genes. Most of the assembled S. salsa genome, 58.03%, consists of transposable elements. Some gene families including HKT1 , NHX , SOS and CASP related to salt resistance were significantly amplified. We also observed expansion of genes encoding protein that bind the trace elements Zn, Fe, Cu and Mn, and genes related to flavonoid and α‐linolenic acid metabolism. Many expanded genes were significantly up‐regulated under salinity, which might have contributed to the acquisition of salt tolerance in S. salsa . Transcriptomic data showed that high salinity markedly up‐regulated salt‐resistance related genes, compared to low salinity. Abundant metabolic pathways of secondary metabolites including flavonoid, unsaturated fatty acids and selenocompound were enriched, which indicates that the species is a nutrient‐rich vegetable. Particularly worth mentioning is that there was no significant difference in the numbers of cis ‐elements in the promoters of salt‐related and randomly selected genes in S. salsa when compared with Arabidopsis thaliana , which may affirm that plant salt tolerance is a quantitative rather than a qualitative trait in terms of promoter evolution. Our findings provide deep insight into the adaptation of halophytes to salinity from a genetic evolution perspective.
Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is important to identify all members of a given gene family in a genome. We developed a method for identifying most, if not all, members of a gene family from raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method’s usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifying plasma membrane H⁺-ATPase family members (P3A ATPases) in various plant genomes of varying quality, we tested the hypothesis that the number of P3A ATPases correlates with the ability of the plant to tolerate saline conditions. In 19 genomes of glycophytes and halophytes, the total number of P3A ATPase genes was found to vary from 7 to 22, but no significant difference was found between the two groups. The method successfully identified P-type ATPase family members in raw genomes that are poorly assembled.
Supplementary Information
The online version contains supplementary material available at 10.1186/s12864-023-09859-4.
Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is of interest to identify all members of a given gene family in a genome. In this work, we developed a method for identifying most, if not all, members of a gene family from a raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method's usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley ( Hordeum vulgare ). Subsequently, after successfully identifying plasma membrane H ⁺ -ATPase family members (P3A ATPases) in various plant genomes of varying quality, we tested the hypothesis that the number of P3A ATPases correlates with the ability of the plant to tolerate saline conditions. In 19 genomes of glycophytes and halophytes, the total number of P3A ATPase genes was found to vary from 7 to 22. Taken together, the method developed proved useful for identification of P-type ATPase family members in raw genomes that are poorly assembled.
Soil salinity is a growing concern for global crop production and the sustainable development of humanity. Therefore, it is crucial to comprehend salt tolerance mechanisms and identify salt-tolerant genes to enhance crop resistance to salt. Suaeda glauca (S. glauca), a halophyte species well-adapted to the seawater environment and capable of direct irrigation with seawater, possesses a unique ability to absorb and retain high salt concentrations within its cells, particularly in its leaves. This suggests the presence of a distinct mechanism for salt tolerance. In this study, we characterized and performed de novo sequencing of S. glauca. The genome size is 1.02 Gb (consisting of two sets of haplotypes) and contains 54,761 annotated genes, including alleles and repeats. Comparative genomic analysis revealed a stronger synteny between the genomes of S. glauca and B. vulgaris. Of the S. glauca genome, 70.56% comprises repeat sequences, with Retroelements being the most abundant. Leveraging the allele-aware assembly of the S. glauca gene, we investigated genome-wide allele-specific expression in the analyzed samples. The results indicated that the diversity in promoter sequences might contribute to consistent allele-specific expression. Moreover, a systematic analysis of the ABCE gene family shed light on the formation of S. glauca's flower morphology, suggesting that dysfunction of A genes is responsible for the absence of petals in S. glauca. Gene family expansion analysis demonstrated significant enrichment of GO terms associated with DNA repair, chromosome stability, DNA demethylation, cation binding, and red/far-red light signaling pathways in the co-expanded gene families of S. glauca and S. Aralocaspica, in comparison to glycophytic species within the Chenopodium family. Time-course transcriptome analysis under salt treatments revealed detailed responses of S. glauca to salt tolerance, and the enrichment of the transition-up regulated genes in the leave resulted in GOs associated with DNA repair and chromosome stability, lipid biosynthetic process, and isoprenoid metabolic process. Additionally, genome-wide analysis of transcription factors indicated a significant expansion of FAR1 genes. However, further investigation is needed to determine the exact role of the FAR1 gene family in salt tolerance in S. glauca.
