Identification and tissue-specific expression of rutin biosynthetic pathway genes in Capparis spinosa elicited with salicylic acid and methyl jasmonate

Capparis spinosa is an edible medicinal plant which is considered as an excellent source of rutin. Rutin is a glycoside of the flavonoid quercetin that has been reported to have a beneficial role in controlling various diseases such as hypertension, arteriosclerosis, diabetes, and obesity. In this study, the partial cDNA of four genes involved in the rutin biosynthetic pathway including 4-coumaroyl CoA ligase (4CL), flavonoid 3'-hydroxylase (F3'H), flavonol synthase (FLS) and flavonol-3-O-glucoside L-rhamnosyltransferase (RT) were identified in C.spinosa plants for the first time. The protein sequences of these genes shared high similarity with the same proteins in other plant species. Subsequently, the expression patterns of these genes as well as rutin accumulation in C.spinosa leaves treated with different concentrations of salicylic acid (SA) and methyl jasmonate (MeJA) and also in different tissues of Caper plants treated with 100 mgL(-1) SA and 150 mu M MeJA were evaluated. The expression of all four genes was clearly up-regulated and rutin contents increased in response to MeJA and SA treatments after 24 h. The highest rutin contents (5.30 mgg(-1) DW and 13.27 mgg(-1) DW), as well as the highest expression levels of all four genes, were obtained using 100 mgL(-1) SA and 150 mu M MeJA, respectively. Among the different tissues, the highest rutin content was observed in young leaves treated with 150 mu M MeJA, which corresponded to the expression of related genes, especially RT, as a key gene in the rutin biosynthetic pathway. These results suggest that rutin content in various tissues of C. spinosa can be enhanced to a significant extent by MeJA and SA treatments and the gene expression patterns of rutin-biosynthesis-related genes are regulated by these elicitors

Production of doubled haploid plants from anther cultures of borage (Borago officinalis L.) by the application of chemical and physical stress

[EN] Anther culture can be used as a powerful tool to produce doubled haploid (DH) lines in medicinal plants, thus accelerating breeding programs. In the particular case of borage (Borago officinalis L.), a method to produce DH plants has not been yet published. In this work we evaluated the effect of different culture media and of different chemical (colchicine and n-butanol) and physical stresses (centrifugation and electroporation) on androgenesis induction and plant regeneration in borage anther cultures. We found that the highest response can be obtained with culture medium containing B5 salts and NLN vitamins, the addition of 200 mg/l colchicine during 4 days, a pretreatment of anthers with 0.2% n-butanol for 5 hours, or the application to anthers of single physical stresses (either centrifugation at 300 g or a 100 v electrical shock, but not combined). This is the first report on the production of DH plants in borage. Together, the results presented hereby can be used as a basic framework for large-scale generation of DH plants in this important medicinal species.Hoveida, Z.; Abdollahi, MR.; Mirzaie-Asl, A.; Moosavi, SS.; Seguí-Simarro, JM. (2017). Production of doubled haploid plants from anther cultures of borage (Borago officinalis L.) by the application of chemical and physical stress. Plant Cell Tissue and Organ Culture (PCTOC). 130(2):369-378. doi:10.1007/s11240-017-1233-4S3693781302Alemanno L, Guiderdoni E (1994) Increased doubled haploid plant regeneration from rice (Oryza sativa L.) anthers cultured on colchicine-supplemented media. Plant Cell Rep 13:432–436Bayliss K, Wroth J, Cowling W (2004) Pro-embryos of Lupinus spp. produced from isolated microspore culture. Crop Pasture Sci 55:589–593Castillo AM, Cistué L, Vallés MP, Soriano M (2009) Chromosome doubling in monocots. In: Touraev A, Forster BP, Jain SM (eds) Advances in haploid production in higher plants. Springer, Dordrecht, pp 329–338Castillo AM, Nielsen NH, Jensen A, Vallés MP (2014) Effects of n-butanol on barley microspore embryogenesis. Plant Cell Tissue Organ Cult 117:411–418Chardoli Eshaghi Z, Abdollahi MR, Moosavi SS, Deljou A, Seguí-Simarro JM (2015) Induction of androgenesis and production of haploid embryos in anther cultures of borage (Borago officinalis L.). Plant Cell Tissue Organ Cult 122(2):1–9Chu CC (1978) The N6 medium and its applications to anther culture of cereal crops. In: Proceedings of symposium on plant tissue culture, 25–30 May 1978. Science Press, Beijing, pp 45–50Das UN (2006) Tumoricidal and anti-angiogenic actions of gamma-linolenic acid and its derivatives. Curr Pharm Biotechnol 7:457–466De Lisi A, Montesano V, Negro D, Sarli G, Blanco E, Sonnante G, Laghetti G (2014) Genetic diversity in Borago officinalis germplasm as revealed by seed oils and AFLP polymorphism. Genet Resour Crop Evol 61:853–859Delaitre C, Ochatt S, Deleury E (2001) Electroporation modulates the embryogénie responses of asparagus (Asparagus officinalis L.) microspores. Protoplasma 216:39–46Fábián A, Földesiné Füredi PK, Ambrus H, Jäger K, Szabó L, Barnabás B (2015) Effect of n-butanol and cold pretreatment on the cytoskeleton and the ultrastructure of maize microspores when cultured in vitro. Plant Cell Tissue Organ Cult 123:257–271Ferrie AMR (2007) Doubled haploid production in nutraceutical species: a review. Euphytica 158:347–357Ferrie AMR (2009) Current status of doubled haploids in medicinal plants. Advances in haploid production in higher plants. Springer, Dordrecht, pp 209–217Ferrie AMR (2013) Advances in microspore culture technology: a biotechnological tool for the improvement of medicinal plants. In: Chandra S, Lata H, Varma A (eds) Biotechnology for medicinal plants: micropropagation and improvement. Springer, Berlin, pp 191–206Ferrie AMR, Bethune TD, Mykytyshyn M (2011) Microspore embryogenesis in Apiaceae. Plant Cell Tissue Organ Cult 104:399–406Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50:151–158Germanà MA (2011) Anther culture for haploid and doubled haploid production. Plant Cell Tissue Organ Cult 104:283–300Grewal RK, Lulsdorf M, Croser J, Ochatt S, Vandenberg A, Warkentin TD (2009) Doubled-haploid production in chickpea (Cicer arietinum L.): role of stress treatments. Plant Cell Rep 28:1289–1299Kapoor R, Huang YS (2006) Gamma linolenic acid: an antiinflammatory omega-6 fatty acid. Curr Pharm Biotechnol 7:531–534Keller WA, Armstrong KC (1977) Embryogenesis and plant regeneration in Brassica napus anther cultures. Can J Bot 55:1383–1388Lichter R (1982) Induction of haploid plants from isolated pollen of Brassica napus. Z Pflanzenphysiol 105: 427–434Lulsdorf MM, Croser JS, Ochatt S (2011) Androgenesis and doubled-haploid production in food legumes. In Pratap A, Kumar J (eds) Biology and breeding of food legumes. CABI Publishers, Wallingford, pp 159–177Montaner C, Floris E, Alvarez JM (2000) Is self-compatibility the main breeding system in borage (Borago officinalis L.)? Theor Appl Genet 101:185–189Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–479Nitsch JP, Nitsch C (1969) Haploid plants from pollen grains. Science 163:85–87Obert B, Barnabás B (2004) Colchicine induced embryogenesis in maize. Plant Cell Tissue Organ Cult 77:283–285Ochatt S (2013) Plant cell electrophysiology: applications in growth enhancement, somatic hybridisation and gene transfer. Biotechnol Adv 31:1237–1246Ochatt S, Pech C, Grewal R, Conreux C, Lulsdorf M, Jacas L (2009) Abiotic stress enhances androgenesis from isolated microspores of some legume species (Fabaceae). J Plant Physiol 166:1314–1328Pathirana R, Frew T, Hedderley D, Timmerman-Vaughan G, Morgan E (2011) Haploid and doubled haploid plants from developing male and female gametes of Gentiana triflora. Plant Cell Rep 30:1055–1065Phillips GC, Collins GB (1979) In vitro tissue culture of selected legumes and plant regeneration from callus cultures of red clover. Crop Sci 19:59–64Ribalta FM, Croser JS, Ochatt SJ (2012) Flow cytometry enables identification of sporophytic eliciting stress treatments in gametic cells. J Plant Physiol 169:104–110Sales E, Montaner C, Muniozguren JM, Carravedo M, Alvarez JM (2008) Genetic diversity in a collection of borage (Borago officinalis) germplasm. Botany 86:603–609Seguí-Simarro JM (2010) Androgenesis revisited. Bot Rev 76:377–404Seguí-Simarro JM, Nuez F (2007) Embryogenesis induction, callogenesis, and plant regeneration by in vitro culture of tomato isolated microspores and whole anthers. J Exp Bot 58:1119–1132Seguí-Simarro JM, Nuez F (2008) Pathways to doubled haploidy: chromosome doubling during androgenesis. Cytogenet Genome Res 120:358–369Shariatpanahi ME, Bal U, Heberle-Bors E, Touraev A (2006) Stresses applied for the re-programming of plant microspores towards in vitro embryogenesis. Physiol Plant 127:519–534Soriano M, Cistué L, Vallés MP, Castillo AM (2007) Effects of colchicine on anther and microspore culture of bread wheat (Triticum aestivum L.). Plant Cell Tissue Organ Cult 91:225–234Soriano M, Cistue L, Castillo AM (2008) Enhanced induction of microspore embryogenesis after n-butanol treatment in wheat (Triticum aestivum L.) anther culture. Plant Cell Rep 27:805–811Szakács É, Barnabás B (1995) The effect of colchicine treatment on microspore division and microspore-derived embryo differentiation in wheat (Triticum aestivum L.) anther culture. Euphytica 83:209–213Tanaka M (1973) The effect of centrifugal treatment on the emergence of plantlet from cultured anther of tobacco. Japan J Breed 23: 171–174Touraev A, Ilham A, Vicente O, Heberle-Bors E (1996) Stress-induced microspore embryogenesis in tobacco: an optimized system for molecular studies. Plant Cell Rep 15:561–565Uno Y, Koda-Katayama H, Kobayashi H (2016) Application of anther culture for efficient haploid production in the genus Saintpaulia. Plant Cell Tissue Organ Cult 125:241–248Zhou WJ, Tang GX, Hagberg P (2002) Efficient production of doubled haploid plants by immediate colchicine treatment of isolated microspores in winter Brassica napus. Plant Growth Regul 37:185–19

Using PCR-DGGE and Soil Respiration to Characterize Bacterial Changes in Heavy Metal Contaminated Soils

Introduction:Soil contamination to heavy metals such as lead and zinc in and around mines causes a change in structure, complexity, diversity and activity of soil microbial communities like bacteria. Materials and methods: In the present research, PCR-DGGE approach was used to investigate the effects of Pb and Zn-contamination in Bama mine near Isfahan city on bacterial diversity, structure and complexity. Basal Respiration (BR) and Substrate Induced Respiration (SIR) was also used to assess microbial activities. Nine samples from three locations (3 for each) with different levels of heavy metal contamination were taken (from low to high), then their DNA were directly extracted. Also a 468 base pair of their 16S rRNA genes were amplified using specific primers, and their fingerprints were obtained by denaturing gradient gel electrophoresis (DGGE). BR and SIR were measured, and metabolic quotient was calculated. Finally, soil microbial activity in polluted conditions was achieved. Results: Our findings illustrate that heavy metal contamination has negative effects on bacterial diversity. By increasing the bioavailability of Pb and Zn, the complexity and diversity of bacterial communities decreased and the frequency of resistant bacteria increased. By increasing Pb and Cd contamination, SIR reduced and this shows the reduction in microbial biomass. In these conditions, SIR and metabolic quotient was more sensitive than BR, so they are better ecological indicators in polluted soils. Discussion and conclusion: Although bacterial diversity showed reduction in polluted soils, diversity is still relatively high. Bacterial ability to adapt in heavy metal contamination, bacterial resistance and their important functional roles in such conditions are valuable in soil ecosystem suggesting further researches on them

Comparative analysis of different artificial neural networks for predicting and optimizing in vitro seed germination and sterilization of petunia.

The process of optimizing in vitro seed sterilization and germination is a complicated task since this process is influenced by interactions of many factors (e.g., genotype, disinfectants, pH of the media, temperature, light, immersion time). This study investigated the role of various types and concentrations of disinfectants (i.e., NaOCl, Ca(ClO)2, HgCl2, H2O2, NWCN-Fe, MWCNT) as well as immersion time in successful in vitro seed sterilization and germination of petunia. Also, the utility of three artificial neural networks (ANNs) (e.g., multilayer perceptron (MLP), radial basis function (RBF), and generalized regression neural network (GRNN)) as modeling tools were evaluated to analyze the effect of disinfectants and immersion time on in vitro seed sterilization and germination. Moreover, non‑dominated sorting genetic algorithm‑II (NSGA‑II) was employed for optimizing the selected prediction model. The GRNN algorithm displayed superior predictive accuracy in comparison to MLP and RBF models. Also, the results showed that NSGA‑II can be considered as a reliable multi-objective optimization algorithm for finding the optimal level of disinfectants and immersion time to simultaneously minimize contamination rate and maximize germination percentage. Generally, GRNN-NSGA-II as an up-to-date and reliable computational tool can be applied in future plant in vitro culture studies

Changes in the expression of COI1, TIR1, and ERF1 genes and respective MiRNAs in Fusarium basal Rot-Stressed onion

Fusarium oxysporum f.sp. cepae (FOC), as basal rot fungus, is the most detrimental pathogen causing a serious threat to onion productivity in the world. In this study, we first determined FOC tolerance in seven Iranian onion cultivars, two known international onions (Texas Early Grano and Sweet Yellow Spanish), and an Allium species related to the onion (Allium asarence) based on the infection severity. Then, a transcriptional screen was performed by comparing the transcript levels of some pathogen-responsive genes (ERF1, COI1, and TIR1) and their predicted miRNAs in the sensitive (Ghermeze Azarshahr Cv.) and the resistant (A. asarence) onions to determine key genes and their miRNAs involved in the defense responses of onions to FOC. From our results, a difference was found in the COI1 and ERF1 expression 48 h after inoculation with FOC as compared to the respective 24 and 72 h. It can be explained by either special mechanisms involved in raising energy consumption efficiency or the interactive effects of other genes in the jasmonic acid (JA) and ethylene (ET) signaling pathways. Moreover, expression analysis of the pathogen-responsive genes and their targeting miRNAs identified the miR-5629, which targets the COI1 gene as a likely key factor in conferring resistance in the FOC-resistant onion, i.e., A. asarence. However, exploring the function of the miRNA/target pair is highly recommended to deeply understand the effect of the miRNA/target pair-associated pathway in the control of A. asarense-FOC interaction

A refined method for ovule culture in sugar beet (Beta vulgaris L.)

[EN] Induction of gynogenesis through ovule culture is a valuable tool to produce haploid and doubled haploid plants in sugar beet (Beta vulgaris L.). However, there is still large room for refining the method. In this study we investigated the gynogenic response of cultured ovules of three sugar beet genotypes, the effect of the application to inflorescences of different pretreatments with mannitol at 4oC and with 5-azacytidine and 2,4-D, and the effect of the use of different basal culture media and sucrose concentrations. The response was evaluated in terms of percentages of induction of gynogenesis, embryogenesis and callogenesis, as well as of regenerated plants. We showed that a pretreatment with 0.5 M mannitol at 4 degrees C for 4 days, and with 50 mu M 5-AzaC for 1 h, notably improved the percentage of embryogenesis and plant regeneration. Besides, the use of MS basal medium and 60 g/L sucrose was also found beneficial. This study provides new ways to improve the efficiency of haploid induction and plant regeneration through ovule culture in sugar beet, and is potentially applicable to ovule culture in other crops. Key message This study provides new ways to improve the efficiency of haploid induction and plant regeneration through ovule culture in sugar beet.Sohrabi, S.; Abdollahi, MR.; Mirzaie-Asl, A.; Koulaei, HE.; Aghaeezadeh, M.; Seguí-Simarro, JM. (2021). A refined method for ovule culture in sugar beet (Beta vulgaris L.). Plant Cell Tissue and Organ Culture (PCTOC). 146(2):259-267. https://doi.org/10.1007/s11240-021-02065-82592671462Abdollahi MR, Rashidi S (2018) Production and conversion of haploid embryos in chickpea (Cicer arietinum L.) anther cultures using high 2, 4-D and silver nitrate containing media. Plant Cell Tiss Organ Cult 133:39–49Aflaki F, Pazuki A, Gurel S, Stevanato P, Biancardi E, Gurel E (2017) Doubled haploid sugar beet: an integrated view of factors influencing the processes of gynogenesis and chromosome doubling. International Sugar Journal 119:884–895Ardebili SH, Shariatpanahi ME, Amiri R, Emamifar M, Oroojloo M, Nematzadeh G, Sadat Noori SA, Heberle-Bors E (2011) Effect of 2, 4-D as a Novel Inducer of Embryogenesis in Microspores of Brassica napus L. Czech J Genet Plant Breed 47:114–122Barański R (1996) In vitro gynogenesis in red beet (Beta vulgaris L.): effects of ovule culture conditions. Acta Soc Bot Pol 65:57–60Bohanec B (2009) Doubled Haploids via Gynogenesis. In: Touraev AF, Forster BP, Jain SM (eds) Advances in Haploid Production in Higher Plants. Springer, pp 35–46Chen JF, Cui L, Malik AA, Mbira KG (2011) In vitro haploid and dihaploid production via unfertilized ovule culture. Plant Cell Tiss Organ Cult 104:311–319Corral-Martínez P, Seguí-Simarro JM (2012) Efficient production of callus-derived doubled haploids through isolated microspore culture in eggplant (Solanum melongena L.). Euphytica 187(1):47–61Corral-Martínez P, Seguí-Simarro JM (2014) Refining the method for eggplant microspore culture: effect of abscisic acid, epibrassinolide, polyethylene glycol, naphthaleneacetic acid, 6-benzylaminopurine and arabinogalactan proteins. Euphytica 195(3):369–382De Greef W, Jacobs M (1979) In vitro culture of the sugarbeet: description of a cell line with high regeneration capacity. Plant Sci Lett 17:55–61Fraga HP, Vieira LN, Caprestano CA, Steinmacher DA, Micke GA, Spudeit DA, Pescador R, Guerra MP (2012) 5-Azacytidine combined with 2,4-D improves somatic embryogenesis of Acca sellowiana (O. Berg) Burret by means of changes in global DNA methylation levels. Plant Cell Rep 31:2165–2176Grzybkowska D, Morończyk J, Wójcikowska B, Gaj MD (2018) Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis. Plant Growth Regul 85:243–256Gürel S, Gürel E, Kaya Z (2000) Doubled haploid plant production from unpollinated ovules of sugar beet (Beta vulgaris L.). Plant Cell Rep 19:1155–1159Gürel S, Gürel E, Kaya Z, Erdal M, Güler E (2003) Effects of antimitotic agents on haploid plant production from unpollinated ovules of sugar beet (Beta vulgaris L.). Biotechnol Biotechnol Equip 17:97–101Hassani M, Heidari B, Dadkhodaie A, Stevanato P (2018) Genotype by environment interaction components underlying variations in root, sugar and white sugar yield in sugar beet (Beta vulgaris L.). Euphytica 214:79Klimek-Chodacka M, Baranski R (2013) Comparison of haploid and doubled haploid sugar beet clones in their ability to micropropagate and regenerate. Electron J Biotechnol 16:1–10Leljak-Levanić D, Bauer N, Mihaljević S, Jelaska S (2004) Changes in DNA methylation during somatic embryogenesis in Cucurbita pepo L. Plant Cell Rep 23:120–127Li H, Soriano M, Cordewener J, Muiño JM, Riksen T, Fukuoka H, Angenent GC, Boutilier K (2014) The histone deacetylase inhibitor Trichostatin A promotes totipotency in the male gametophyte. Plant Cell 26(1):195–209Lipavska H, Vreugdenhil D (1996) Uptake of mannitol from the media by in vitro grown plants. Plant Cell Tiss Organ Cult 45:103–107Lux H, Herrmann L, Wetzel C (1990) Production of haploid sugar beet (Beta vulgaris L.) by culturing unpollinated ovules. Plant Breed 104:177–183Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497Nagl N, Mezei S, Kovačev L, Vasić D, Čačić N (2004) Induction and micropropagation potential of sugar beet haploids. Genetika 36:187–194Nowaczyk L, Nowaczyk P, Olszewska D, Niklas-Nowak A (2015) Effect of 2,4-dichlorophenoxyacetic acid pretreatment of Capsicum spp. donor plants on the anther culture efficiency of lines selected by capsaicinoid content. Biotechnologia 96:179–183Osorio-Montalvo P, Sáenz-Carbonell L, De-la-Peña C (2018) 5-Azacytidine: a promoter of epigenetic changes in the quest to improve plant somatic embryogenesis. Int J Mol Sci 19:3182Parra-Vega V, Renau-Morata B, Sifres A, Seguí-Simarro JM (2013) Stress treatments and in vitro culture conditions influence microspore embryogenesis and growth of callus from anther walls of sweet pepper (Capsicum annuum L.). Plant Cell Tissue Organ Cult 112(3):353–360Pazuki A, Aflaki F, Gürel E, Ergül A, Gürel S (2017) A robust method for haploid sugar beet in vitro proliferation and hyperhydricity reduction. Folia Hortic 29:241–250Pazuki A, Aflaki F, Gürel E, Ergül A, Gürel S (2018a) Gynogenesis induction in sugar beet (Beta vulgaris) improved by 6-benzylaminopurine (BAP) and synergized with cold pretreatment. Sugar Tech 20:69–77Pazuki A, Aflaki F, Gürel S, Ergül A, Gürel E (2018b) Production of doubled haploids in sugar beet (Beta vulgaris): an efficient method by a multivariate experiment. Plant Cell Tiss Organ Cult 132:85–97Pazuki A, Aflaki F, Gurel S, Ergul A, Gurel E (2018c) The effects of proline on in vitro proliferation and propagation of doubled haploid sugar beet (Beta vulgaris). Turk J Bot 42:280–288Salas P, Prohens J, Seguí-Simarro JM (2011) Evaluation of androgenic competence through anther culture in common eggplant and related species. Euphytica 182(2):261–274Seguí-Simarro JM (2016) Androgenesis in solanaceae. In: Germanà MA, Lambardi M (eds) In vitro embryogenesis, vol 1359. Methods in Molecular Biology. Springer Science + Business Media, New York, pp 209–244Shariatpanahi ME, Bal U, Heberle-Bors E, Touraev A (2006) Stresses applied for the re-programming of plant microspores towards in vitro embryogenesis. Physiol Plant 127:519–534Testillano PS (2019) Microspore embryogenesis: targeting the determinant factors of stress-induced cell reprogramming for crop improvement. J Exp Bot 70(11):2965–2978Tomaszewska-Sowa M (2010) Cytometric analyses of sugar beet (Beta vulgaris L.) plants regenerated from unfertilized ovules cultured in vitro. Electron J Pol Agric Univ 13:1–10Yamamoto N, Kobayashi H, Togashi T, Mori Y, Kikuchi K, Kuriyama K, Tokuji Y (2005) Formation of embryogenic cell clumps from carrot epidermal cells is suppressed by 5-azacytidine, a DNA methylation inhibitor. J Plant Physiol 162:47–54Yaseen M, Ahmad T, Sablok G, Standardi A, Hafiz IA (2013) Role of carbon sources for in vitro plant growth and development. Mol Biol Rep 40:2837–284

The mRNA sequence polymorphisms of flowering key genes in bolting sensitive or tolerant sugar beet genotypes

One of the most important characteristics of sugar beet planting in temperate climates is the tolerance against early bolting. Understanding the genetic control of sugar beet flowering can help to develop the bolting-tolerant cultivars. In this study, the transcript sequences of 2 VIN3 copies, frigida, VRN1, EMF2, BvFT1 , and BTC1 genes in 4 bolting tolerant and sensitive sugar beet genotypes were evaluated. Leaf samples were taken from plants in 2 growing stages, before and during cold exposure. The amplified fragments of both tolerant and sensitive genotypes were similar in length and the comparison of their transcript sequence showed polymorphism. In overall, 18 mutations comprising 1 mutation in frigida sequence, 14 single nucleotide polymorphisms (SNPs) in 2 copies of BvVIN3 sequence, 2 SNPs in BvFT1 sequence, and 1 insertion/deletion mutation for BTC1 were characterized. The last one caused a frameshift in the encoded protein. Despite the key role of the above mentioned genes, results showed that SNPs identified in this study were not associated with bolting tolerance or sensitivity. There may be differences in the expression levels of these proteins, which necessitates further exploration

Toxic trace element resistance genes and systems identified using the shotgun metagenomics approach in an Iranian mine soil

This study aimed to identify the microbial communities, resistance genes, and resistance systems in an Iranian mine soil polluted with toxic trace elements (TTE). The polluted soil samples were collected from a mining area and compared against non-polluted (control) collected soils from the vicinity of the mine. The soil total DNA was extracted and sequenced, and bioinformatic analysis of the assembled metagenomes was conducted to identify soil microbial biodiversity, TTE resistance genes, and resistance systems. The results of the employed shotgun approach indicated that the relative abundance of Proteobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus was significantly higher in the TTE-polluted soils compared with those in the control soils, while the relative abundance of Actinobacteria and Acidobacteria was significantly lower in the polluted soils. The high concentration of TTE increased the ratio of archaea to bacteria and decreased the alpha diversity in the polluted soils compared with the control soils. Canonical correspondence analysis (CCA) demonstrated that heavy metal pollution was the major driving factor in shaping microbial communities compared with any other soil characteristics. In the identified heavy metal resistome (HV-resistome) of TTE-polluted soils, major functional pathways were carbohydrates metabolism, stress response, amino acid and derivative metabolism, clustering-based subsystems, iron acquisition and metabolism, cell wall synthesis and capsulation, and membrane transportation. Ten TTE resistance systems were identified in the HV-resistome of TTE-polluted soils, dominated by “P-type ATPases,” “cation diffusion facilitators,” and “heavy metal efflux-resistance nodulation cell division (HME-RND).” Most of the resistance genes (69%) involved in resistance systems are affiliated to cell wall, outer membrane, periplasm, and cytoplasmic membrane. The finding of this study provides insight into the microbial community in Iranian TTE-polluted soils and their resistance genes and systems