SSR identification and phylogenetic analysis in four plant species based on complete chloroplast genome sequences.

The effective utilization of traditional Chinese medicine (TCM) has been challenged by the difficulty to accurately distinguish between similar plant varieties. The stability and conservation of the chloroplast genome can aid in resolving genotypes. Previous studies using nuclear sequences and molecular markers have not effectively differentiated the species from related taxa, such as Machilus leptophylla, Hanceola exserta, Rubus bambusarum, and Rubus henryi. This study aimed to characterize the chloroplast genomes of these four plant species, and analyze their simple sequence repeats (SSRs) and phylogenetic positions. The results demonstrated the four chloroplast genomes consisted of 152.624 kb, 153.296 kb, 156.309 kb, and 158.953 kb in length, involving 124, 130, 129, and 131 genes, respectively. They also contained four specific regions with mononucleotide being the class with the most members. Moreover, these repeating types of SSR were various in individual class. Phylogenetic analysis showed that M. leptophylla was clustered with M. yunnanensis, and H. exserta was confirmed as belonging to the family Ocimeae. Additionally, R. bambusarum and R. henryi were grouped together but differed in their SSR features, indicating that they were not the same species. This research provides evidence for resolving species and contributes new genetic information for further studies.

Pesticide-induced oxidative stress and antioxidant responses in tomato (Solanum lycopersicum) seedlings.

Excessive use of pesticides can adversely affect the growth of non-target host plants in different ways. Pesticide-induced stress can affect non-target plants through elevated levels of reactive oxygen species (ROS) responsible for detrimental effects on cell metabolism, biochemical and other physiological activities. In response to oxidative stress, plant activates antioxidant defense system consisting of both enzymatic and non-enzymatic components. In the present investigation, three commonly used pesticides, emamectin benzoate, alpha-cypermethrin and imidacloprid, were assessed for causing oxidative stress in tomato. The oxidative damage induced by these pesticides at five different concentrations i.e. 1/4X, 1/2X, recommended application dose (X), 2X and 4X in the root and shoot tissues of tomato plant/seedlings were evaluated. Following pesticide exposure for 35 days, cell viability, cell injury, total soluble sugar (TSS) and total soluble proteins (TSP) were measured. Antioxidant activities were estimated by measuring activity levels of superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR) peroxidase (POD), ascorbate peroxidase (APX) and proline. Hydrogen peroxide (H2O2) levels were analysed as ROS, lipid peroxidation was measured in term of thiobarbituric acid reactive substances (TBARS) as membrane damage caused by ROS was also assessed. Analysis of the data revealed that pesticides application at higher concentrations significantly elevated ROS levels and caused membrane damage by the formation of TBARS, increased cell injury and reduced cell viability both in root and shoot tissues compared with non-treated plants. Moreover, a gradual decrease in the levels of TSS and TSP was observed in plants subjected to increasing doses of pesticides. To cope with pesticide-induced oxidative stress, a significant increase in levels of antioxidants was observed in the plants exposed to higher doses of pesticides. Shoot tissues responded more drastically by producing higher levels of antioxidants as compared to root tissues indicating the direct exposure of shoots to foliar application of pesticides. Taken together, these results strongly suggested that the application of pesticides above the recommended dose can provoke the state of oxidative stress and can cause oxidative damages in non-target host plants.

Ecotoxicological evaluation of two anti-dandruff hair shampoos using Lemna minor.

Hair shampoos, a mixture of various organic and organic compounds, are commonly used personnel care products. Since shampoos are used in almost every household and beauty shop, their ingredients are common components of domestic and municipal wastewater. However, studies on the effect of shampoos to aquatic plants can hardly be found in literature. Therefore, the present study was conducted to investigate the phytotoxic effects of two commonly used anti-dandruff shampoos (named here AD 1 and AD 2) using Lemna minor as a biotest organism. For toxicity assessment, frond number, fresh and dry biomass, and light-harvesting pigments (chlorophyll a, b and total carotenoids) of Lemna were used as end points. Five different concentrations (0.001, 0.01, 0.1, 1, and 5%) of each shampoo were tested in comparison to the control. At lower concentrations of shampoos, some minor and non-significant stimulatory effects were observed in some parameters, but at concentrations above 0.01% both the shampoos significantly inhibited almost all parameters in Lemna. The EC50 values obtained for frond number were 0.034 and 0.11% for AD 1 and AD 2, respectively. The fresh biomass gave EC50 values of 0.07 and 0.066% for AD 1 and AD 2, respectively. Based on the preset study, it can be speculated that shampoo contamination at higher concentrations in water bodies can be a threat to aquatic organisms. This study can be used as a baseline to further investigate shampoo toxicity using other species and to explore the mechanism of shampoo toxicity in aquatic plants.

A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol.

The pigment gland is a morphological characteristic of Gossypium and its related genera. Gossypium bickii (G1) is characterized by delayed pigment gland morphogenesis in the cotyledons. In this study, a reference-grade genome of G1 was generated, and comparative genomics analysis showed that G1 was closest to Gossypium australe (G2), followed by A- and D-genome species. Two large fragment translocations in chromosomes 5 and 13 were detected between the G genome and other Gossypium genomes and were unique to the G1 and G2 genomes. Compared with the G2 genome, two large fragment inversions in chromosomes 12 and 13 were detected in G1. According to the phylogeny, divergence time, and similarity analysis of nuclear and chloroplast genomes, G1 was formed by hybridization between Gossypium sturtianum (C1) and a common ancestor of G2 and Gossypium nelsonii (G3). The coordinated expression patterns of pigment gland formation (GoPGF) and gossypol biosynthesis genes in G1 were verified to be consistent with its phenotype, and nine genes that were related to the process of pigment gland formation were identified. A novel gene, GbiCYP76B6, regulated by GoPGF, was found to affect gossypol biosynthesis. These findings offer insights into the origin and evolution of G1 and its mechanism of pigment gland formation and gossypol biosynthesis.

Mercury-Induced Phytotoxicity and Responses in Upland Cotton (Gossypium hirsutum L.) Seedlings.

Cotton is a potential and excellent candidate to balance both agricultural production and remediation of mercury-contained soil, as its main production fiber hardly involves into food chains. However, in cotton, there is known rarely about the tolerance and response to mercury (Hg) environments. In this study, the biochemical and physiological damages, in response to Hg concentrations (0, 1, 10, 50 and 100 µM), were investigated in upland cotton seedlings. The results on germination of cottonseeds indicated the germination rates were suppressed by high Hg levels, as the decrease of percentage was more than 10% at 1000 µM Hg. Shoots and roots' growth were significantly inhibited over 10 µM Hg. The inhibitor rates (IR) in fresh weight were close in values between shoots and roots, whereas those in dry weight the root growth were more obviously influenced by Hg. In comparison of organs, the growth inhibition ranked as root > leaf > stem. The declining of translocation factor (TF) opposed the Hg level as even low to 0.05 at 50 µM Hg. The assimilation in terms of photosynthesis, of cotton plants, was affected negatively by Hg, as evidenced from the performances on pigments (chlorophyll a and b) and gas exchange (Intercellular CO2 concentration (Ci), CO2 assimilation rate (Pn) and stomatal conductance (Gs)). Sick phenotypes on leaf surface included small white zone, shrinking and necrosis. Membrane lipid peroxidation and leakage were Hg dose-dependent as indicated by malondialdehyde (MDA) content and relative conductivity (RC) values in leaves and roots. More than 10 µM Hg damaged antioxidant enzyme system in both leaves and roots (p < 0.05). Concludingly, 10 µM Hg post negative consequences to upland cotton plants in growth, physiology and biochemistry, whereas high phytotoxicity and damage appeared at more than 50 µM Hg concentration.

Characterization of 19 Genes Encoding Membrane-Bound Fatty Acid Desaturases and their Expression Profiles in Gossypium raimondii Under Low Temperature.

To produce unsaturated fatty acids, membrane-bound fatty acid desaturases (FADs) can be exploited to introduce double bonds into the acyl chains of fatty acids. In this study, 19 membrane-bound FAD genes were identified in Gossypium raimondii through database searches and were classified into four different subfamilies based on phylogenetic analysis. All 19 membrane-bound FAD proteins shared three highly conserved histidine boxes, except for GrFAD2.1, which lost the third histidine box in the C-terminal region. In the G. raimondii genome, tandem duplication might have led to the increasing size of the FAD2 cluster in the Omega Desaturase subfamily, whereas segmental duplication appeared to be the dominant mechanism for the expansion of the Sphingolipid and Front-end Desaturase subfamilies. Gene expression analysis showed that seven membrane-bound FAD genes were significantly up-regulated and that five genes were greatly suppressed in G. raimondii leaves exposed to low temperature conditions.

Genome-wide survey and expression analysis of calcium-dependent protein kinase in Gossypium raimondii.

Calcium-dependent protein kinases (CDPKs) are one of the largest protein kinases in plants and participate in different physiological processes through regulating downstream components of calcium signaling pathways. In this study, 41 CDPK genes, from GrCPK1 to GrCPK41, were identified in the genome of the diploid cotton, Gossypium raimondii. The phylogenetic analysis indicated that all these genes were divided into four subgroups and members within the same subgroup shared conserved exon-intron structures. The expansion of GrCPKs family in G. raimondii was due to the segmental duplication events, and the analysis of Ka/Ks ratios implied that the duplicated GrCPKs had mainly undergone strong purifying selection pressure with limited functional divergence. The cold-responsive elements in promoter regions were detected in the majority of GrCPKs. The expression analysis of 11 selected genes showed that GrCPKs exhibited tissue-specific expression patterns and the expression of GrCPKs were induced or repressed by cold treatment. These observations would lay an important foundation for functional and evolutionary analysis of CDPK gene family in Gossypium species.