scholarly journals Identification of genes encoding ALMT and MATE transporters as candidate aluminum tolerance genes from a typical acid soil plant, Psychotria rubra (Rubiaceae)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7739 ◽  
Author(s):  
Akira Iguchi ◽  
Kazutsuka Sanmiya ◽  
Kenta Watanabe
Keyword(s):  
Molecular Basis ◽  
Acid Soil ◽  
Aluminum Tolerance ◽  
Acid Soils ◽  
Rna Seq ◽  
Tropical Plants ◽  
Ecological Aspects ◽  
Genes Encoding ◽  
Molecular Phylogenetic ◽  
Malate Transporter

To understand how tropical plants have adapted to acid soils, we analyzed the transcriptome of seedlings of Psychotria rubra, a typical species found on acid soils. Using RNA-seq, we identified 22,798 genes, including several encoding proteins of the Al3+-activated malate transporter (ALMT) and multidrug and toxic compound extrusion (MATE) families. Molecular phylogenetic analysis of ALMTs and MATEs revealed the grouping of those from P. rubra, which may be useful to select targets for elucidating the molecular basis of P. rubra adaptation to acid soils in the future. The transcriptome datasets obtained in this study would help us to further understand the physiological and ecological aspects of soil adaptation of Psychotria species.

scholarly journals Field comparison between selection methods at the maize seedling stage in relation to aluminum tolerance

2002 ◽  
Vol 59 (2) ◽  
pp. 397-401 ◽  
Author(s):  
Carlos Daniel Giaveno ◽  
José Branco de Miranda Filho
Keyword(s):  
Grain Yield ◽  
Nutrient Solution ◽  
Acid Soil ◽  
Aluminum Tolerance ◽  
Acid Soils ◽  
Field Trials ◽  
High Productivity ◽  
Maize Population ◽  
Maize Populations ◽  
Aluminum Saturation

Selection and breeding for aluminum tolerance is a useful approach to increase maize (Zea mays L.) grain yield in acid soils. The objective of this work was the comparison between two screening approaches for the development of Al tolerant maize populations. One cycle of divergent selection for aluminum tolerance, using both nutrient solution and pots with acid soil, were completed in the maize population SIKALQ. The four sub-populations selected through both selection procedures were compared with the original population and checks in field trials repeated over locations. Eight environments stratified into four groups varying from non acid to high aluminum saturation were used. Three variables were analyzed for comparisons of methodologies: grain yield, plant height and days to male flowering. The populations performed similarly in the high productivity locations and the differences between tolerant and sensitive ones were more evident for increasing levels of toxic aluminum. In spite of little differences, selection in pots with acid soil was more efficient than nutrient solution in changing the genetic structure of the population toward more tolerant and sensitive levels.

scholarly journals The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
James G Baldwin-Brown ◽  
Scott M Villa ◽  
Anna I Vickrey ◽  
Kevin P Johnson ◽  
Sarah E Bush ◽  
...  
Keyword(s):  
Low Cost ◽  
Single Copy ◽  
Odorant Receptors ◽  
Rna Seq ◽  
Pediculus Humanus ◽  
Final Assembly ◽  
Oxford Nanopore ◽  
Genes Encoding ◽  
Host Parasite ◽  
G Protein Coupled

Abstract The pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.

scholarly journals Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

AN ASSESSMENT OF THE SOIL ACIDITY PROBLEM IN ALBERTA AND NORTHEASTERN BRITISH COLUMBIA

1977 ◽  
Vol 57 (2) ◽  
pp. 157-164 ◽  
Author(s):  
D. C. PENNEY ◽  
M. NYBORG ◽  
P. B. HOYT ◽  
W. A. RICE ◽  
B. SIEMENS ◽  
...  
Keyword(s):  
British Columbia ◽  
Soil Ph ◽  
Soil Acidity ◽  
Field Experiments ◽  
Trifolium Pratense ◽  
Acid Soil ◽  
Acid Soils ◽  
Red Clover ◽  
Hordeum Vulgare L ◽  
Crop Species

The amount of cultivated acid soil in Alberta and northeastern British Columbia was estimated from pH values of farm samples analyzed by the Alberta Soil Testing Laboratory, and the effect of soil acidity on crops was assessed from field experiments on 28 typical acid soils. The field experiments consisted of two cultivars of barley (Hordeum vulgare L.) and one cultivar each of rapeseed (Brassica campestris L.), red clover (Trifolium pratense L.) and alfalfa (Medicago sativa L.) grown with and without lime for 2 yr. There are about 30,000 ha of soils with a pH of 5.0 or less where soil acidity seriously restricts yields of all four crop species. There are approximately 300,000 ha with a soil pH of 5.1–5.5 where liming will on the average increase yields of alfalfa by 100%, yields of barley by 10–15%, and yields of rapeseed and red clover by 5–10%. There are a further 1,600,000 ha where soil pH ranges from 5.6 to 6.0 and liming will increase yields of alfalfa by approximately 50% and yields of barley, rapeseed and red clover by at least 4–5%.

scholarly journals Coapplication of Chicken Litter Biochar and Urea Only to Improve Nutrients Use Efficiency and Yield ofOryza sativaL. Cultivation on a Tropical Acid Soil

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Ali Maru ◽  
Osumanu Ahmed Haruna ◽  
Walter Charles Primus
Keyword(s):  
Acid Soil ◽  
Nutrient Use Efficiency ◽  
Chemical Properties ◽  
Acid Soils ◽  
Field Trials ◽  
Soil Chemical Properties ◽  
Nutrient Use ◽  
Chicken Litter ◽  
Rice Yields ◽  
Use Efficiency

The excessive use of nitrogen (N) fertilizers in sustaining high rice yields due to N dynamics in tropical acid soils not only is economically unsustainable but also causes environmental pollution. The objective of this study was to coapply biochar and urea to improve soil chemical properties and productivity of rice. Biochar (5 t ha−1) and different rates of urea (100%, 75%, 50%, 25%, and 0% of recommended N application) were evaluated in both pot and field trials. Selected soil chemical properties, rice plants growth variables, nutrient use efficiency, and yield were determined using standard procedures. Coapplication of biochar with 100% and 75% urea recommendation rates significantly increased nutrients availability (especially P and K) and their use efficiency in both pot and field trials. These treatments also significantly increased rice growth variables and grain yield. Coapplication of biochar and urea application at 75% of the recommended rate can be used to improve soil chemical properties and productivity and reduce urea use by 25%.

scholarly journals A Transcriptomic Approach to the Metabolism of Tetrapyrrolic Photosensitizers in a Marine Annelid

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3924
Author(s):  
Maria Leonor Santos ◽  
Mariaelena D’Ambrosio ◽  
Ana P. Rodrigo ◽  
A. Jorge Parola ◽  
Pedro M. Costa
Keyword(s):  
Metabolic Pathways ◽  
Molecular Networks ◽  
Bile Pigments ◽  
Rna Seq ◽  
The Past ◽  
Wide Range ◽  
Genes Encoding ◽  
Organ Specific ◽  
Bright Green ◽  
Green Coloration

The past decade has seen growing interest in marine natural pigments for biotechnological applications. One of the most abundant classes of biological pigments is the tetrapyrroles, which are prized targets due their photodynamic properties; porphyrins are the best known examples of this group. Many animal porphyrinoids and other tetrapyrroles are produced through heme metabolic pathways, the best known of which are the bile pigments biliverdin and bilirubin. Eulalia is a marine Polychaeta characterized by its bright green coloration resulting from a remarkably wide range of greenish and yellowish tetrapyrroles, some of which have promising photodynamic properties. The present study combined metabolomics based on HPLC-DAD with RNA-seq transcriptomics to investigate the molecular pathways of porphyrinoid metabolism by comparing the worm’s proboscis and epidermis, which display distinct pigmentation patterns. The results showed that pigments are endogenous and seemingly heme-derived. The worm possesses homologs in both organs for genes encoding enzymes involved in heme metabolism such as ALAD, FECH, UROS, and PPOX. However, the findings also indicate that variants of the canonical enzymes of the heme biosynthesis pathway can be species- and organ-specific. These differences between molecular networks contribute to explain not only the differential pigmentation patterns between organs, but also the worm’s variety of novel endogenous tetrapyrrolic compounds.

Preferential nitrate immobilization in alkaline soils

Soil Research ◽  
1992 ◽  
Vol 30 (5) ◽  
pp. 737 ◽  
Author(s):  
IJ Rochester ◽  
GA Constable ◽  
DA Macleod
Keyword(s):  
Acid Soil ◽  
Nitrification Inhibitor ◽  
Biological Significance ◽  
Nitrate Assimilation ◽  
Acid Soils ◽  
Ammonium Assimilation ◽  
Potassium Nitrate ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Nitrate Immobilization

The literature pertaining to N immobilization indicates that ammonium is immobilized in preference to nitrate. Our previous research in an alkaline clay soil has indicated substantial immobilization of nitrate. To verify the preference for immobilization of nitrate or ammonium by the microbial biomass in this and other soil types, the immobilization of ammonium and nitrate from applications of ammonium sulfate and potassium nitrate following the addition of cotton crop stubble was monitored in six soils. The preference for ammonium or nitrate immobilization was highly correlated with each soil's pH, C/N ratio and its nitrification capacity. Nitrate was immobilized in preference to ammonium in neutral and alkaline soils; ammonium was preferentially immobilized in acid soils. No assimilation of nitrate (or nitrification) occurred in the most acid soil. Similarly, little assimilation of ammonium occurred in the most alkaline soil. Two physiological pathways, the nitrate assimilation pathway and the ammonium assimilation pathway, appear to operate concurrently; the dominance of one pathway over the other is indicated by soil pH. The addition of a nitrification inhibitor to an alkaline soil enhanced the immobilization of ammonium. Recovery of 15N confirmed that N was not denitrified, but was biologically immobilized. The immobilization of 1 5 ~ and the apparent immobilization of N were similar in magnitude. The identification of preferential nitrate immobilization has profound biological significance for the cycling of N in alkaline soils.

scholarly journals Uji Pendahuluan Genotipe-genotipe Kedelai Hasil Seleksi In Vitro terhadap Cekaman Aluminium dan pH Rendah

2016 ◽  
Vol 1 (2) ◽  
pp. 73
Author(s):  
Arief Vivi Noviati ◽  
Sri Hutami ◽  
Ika Mariska ◽  
Endang Sjamsudin
Keyword(s):  
Yield Components ◽  
Aluminum Toxicity ◽  
Acid Soil ◽  
Acid Soils ◽  
Mutation Breeding ◽  
Low Ph ◽  
Al Tolerance ◽  
Major Constraint ◽  
Gamma Irradiated

<p class="p1">Aluminum toxicity is a major constraint to soybean production in acid soils. Since variabilities on Al tolerance in plants are very limited, mutation breeding, and <em>in vitro </em>selection were used to increase the variability. Three soyben genotypes were produced from cultivars Wilis and Sindoro that have been gamma irradiated and selected <em>in vitro </em>for their tolerance to Al on Al and low pH media. These genotypes and their original cultivars were then planted in a greenhouse in an acid soil on May 2001. The results showed that the plant performances were varied, some were shorter and more compact than the original. Based on the yield components, a number of plants from the genotypes showed higher than those of the control cultivars. These plants were considered more tolerant to Al than the original cultivars.</p>

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