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Chromosome behaviour in meiosis of pollen. The pollen was dyed with DAPI and the samples were mounted on the slides for fluorescence microscopy. a Meiosis I, Metaphase. b Meiosis II, Metaphase of two poles. c Meiosis Metaphase of one pole
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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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... number of many species have been determined by observing the meiosis of pollen mother cells [28]. For Suaeda salsa, several reports have given different chromosome counts [29]. To confirm the chromosome number of our Suaeda salsa cultivar. The chromosome spreads of microsporophytes were prepared and observed under the microscope. As shown in Fig. 6, we found 18 chromosomes in metaphase of meiosis I (Fig. 6a). Meanwhile, two sets of 9 chromosomes were observed in dyad cells in metaphase of meiosis II (Fig. 6b). Those observations indicated that the diploid Suaeda salsa has nine pairs of chromosomes (2n = ...
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... the meiosis of pollen mother cells [28]. For Suaeda salsa, several reports have given different chromosome counts [29]. To confirm the chromosome number of our Suaeda salsa cultivar. The chromosome spreads of microsporophytes were prepared and observed under the microscope. As shown in Fig. 6, we found 18 chromosomes in metaphase of meiosis I (Fig. 6a). Meanwhile, two sets of 9 chromosomes were observed in dyad cells in metaphase of meiosis II (Fig. 6b). Those observations indicated that the diploid Suaeda salsa has nine pairs of chromosomes (2n = ...
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... counts [29]. To confirm the chromosome number of our Suaeda salsa cultivar. The chromosome spreads of microsporophytes were prepared and observed under the microscope. As shown in Fig. 6, we found 18 chromosomes in metaphase of meiosis I (Fig. 6a). Meanwhile, two sets of 9 chromosomes were observed in dyad cells in metaphase of meiosis II (Fig. 6b). Those observations indicated that the diploid Suaeda salsa has nine pairs of chromosomes (2n = ...
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... different ecotypes that were investigated. Most of the records have 36 or 54 chromosomes were from Siberia area [48][49][50][51][52]. To confirm this significant characteristic of Suaeda salsa of our ecotype, we observed its chromosome behaviour during male gametogenesis. Our results showed that the chromosome number of Suaeda salsa is 2n = 18 (Fig. 6). It has been reported that most of the species form Chenopodiaceae have relatively stable chromosome organization with the basic number of 9. The exceptions are Camphorosma and Spinacia, whose basic chromosome numbers are 6. Our observation is consistent with this conclusion [53]. Taken together, we can speculate that X = 9 might be ...
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... 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. ...
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... 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). ...
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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.
