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Cotton (genus Gossypium) is an important agricultural crop around the world because of its fiber. Gossypium turneri Fryxell is a wild cotton species endemic to the state of Sonora (northwestern Mexico), whose status has been recently raised to endangered in the IUCN Red List. This species has invaluable characteristics that could be useful in the cultivated cotton gene pool. Despite its importance, G. turneri has been studied very little. To the best of our knowledge, no previous study has characterized its seed morphology and cytogenetics. Therefore, in the present study the seed morphology and karyotype of G. turneri were analyzed. Seeds of G. turneri have nonuniform oval shape and brown-gray color. This species produces short fibers attached to its seed surface that are not long enough for commercial use. Our seed sizes were greater than those previously described for G. turneri and other diploid cottons. The length and width of seeds were 8.80 mm and 4.83 mm, respectively. Traits such as embryo and seed coat were measured and carefully observed, and gossypol glands were observed only in the embryo during the evaluation of internal features of seeds. Cytogenetic analysis revealed 26 chromosomes (2n = 2x = 26) in mitotic cells of G. turneri. The karyotype analysis showed mainly metacentric (m), submetacentric (sm) and subtelocentric (st) chromosomes. Our results reveal important biological traits of G. turneri that could be considered in future studies to improve cultivated cotton.

El suelo proporciona servicios ecosistémicos fundamentales como la regulación del ciclo del nitrógeno, el cual, es dirigido por la microbiota que éste alberga y su estabilidad depende ante perturbaciones bióticas o abióticas, como la contaminación por metales y metaloides. Altas concentraciones de níquel (Ni) y zinc (Zn) en suelos agrícolas están relacionadas con la aplicación de prácticas agrícolas convencionales, composta, biosólidos, así como riego con agua contaminada proveniente de la industria minera y termoeléctrica, principalmente. Con el objetivo de conocer los efectos de dicha perturbación abiótica, se realizó un estudio a nivel microcosmos con suelo agrícola proveniente de la Costa de Hermosillo, Sonora, México, perturbado con compuestos M-salfen de Ni(II) y Zn(II), para evaluar su efecto basado en el funcionamiento del ciclo del nitrógeno en el sistema a lo largo del tiempo. Análisis espectrofotométricos de la reserva de nitrógeno inorgánico, absorción atómica y pH revelaron la recuperación de la funcionalidad del ciclo del nitrógeno en 240 días posteriores a las perturbaciones con M-salfen aplicadas, sugiriendo la utilización de NiSB15 como promotor para el incremento de la concentración de nitrato a los 60 días, en conjunción con NiSA15 para aumentar la concentración de amonio en suelos agrícolas contaminados con metales pesados.

Chaetoceros muelleri is one of the most widely used microalgae species in aquaculture in northwestern Mexico as food for fish and crustaceans. Its importance is due to its fast growth, nutritional quality and lipid accumulation under nutrient-limiting conditions. However, the biochemical and molecular mechanisms of uptake of phosphorus (P) limiting conditions for this species is still unknown. This study aimed to analyze the growth and biochemical composition of C muelleri in response to different phosphorus concentrations. Four treatments under different phosphorus conditions were used: control (72 μM P), excess (144 μM P) and two treatments with phosphorus limitation, limited A (18 μM P) and limited B (7 μM P). The highest cell concentration was observed in control and excess of P (>3.4×106 cells mL−1). The highest dry mass concentration and chlorophyll-a content were found in control medium (72 μM P) whereas the highest total lipid (4.42%) was found in the lowest P-concentration medium (7 μM P). No significant differences were found in the total protein content, but we did find differences between the treatments with phosphorus limitation (7 and 18 μM P).

Chili pepper (Capsicumspp.) is both an important crop and a model for domestication studies. Here we performed a time course experiment to estimate standardized gene expression profiles across fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptome every 10 days, from flower to fruit at 60 Days After Anthesis (DAA), and found that the mean standardized expression profile for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time-shift in expression which explains some of the differences between domesticated and wild phenotypes.

Mining operations often generate tailing dams that contain toxic residues and are a source of contamination when left unconfined. The establishment of a plant community over the tailings has been proposed as a containment strategy known as phytostabilization. Previously, we described naturally occurring mine tailing colonizing plants such as Acacia farnesiana, Brickellia coulteri, Baccharis sarothroides, and Gnaphalium leucocephalum without finding local adaptation. We explored the rhizosphere microbes as contributors in plant establishment and described both the culturable and in situ diversity of rhizospheric bacteria using the 16S rRNA gene and metagenomic shotgun sequencing. We built a synthetic community (SC) of culturable rhizosphere bacteria from the mine tailings. The SC was then the foundation for a serial passes experiment grown in plant-derived nutrient sources, selecting for heavy metals tolerance, community cooperation, and competition. The outcome of the serial passes was named the 'final synthetic community' (FSC). Overall, diversity decreased from in situ uncultivable microbes from roots (399 bacteria genera) to the cultivated communities (291 genera), the SC (94 genera), and the lowest diversity was in the FSC (43 genera). Metagenomic diversity clustered into 94,245 protein families, where we found plant growth promotion-related genes such as the csgBAC and entCEBAH, coded in a metagenome-assembled genome named Kosakonia sp. Nacozari. Finally, we used the FSC to inoculate mine tailing colonizing plants in a greenhouse experiment. The plants with the FSC inocula observed higher relative plant growth rates in sterile substrates. The FSC presents promising features that might make it useful for phytostabilization tailored strategies.

Microalgae have great potential as biofactories for producing a wide variety of valuable products. Under stress conditions, it is well-known that microalgae accumulate various organic compounds. However, there is little information on the response of the diatom Chaetoceros muelleri to different nitrogen concentrations. In the present study, C. muelleri was grown in medium containing different concentrations of nitrogen (NaNO3; f: 1.76 mM, f/4: 0.44 mM, f/10: 0.18 mM, and 2f: 3.53 mM) and their proximal composition, fatty acid profile, and gene expression (AMT1, PTD9, GltD, DGAT2, and NRT2) compared. The results showed no significant differences in biomass content among nitrogen treatments. Treatment f/10 significantly increased accumulation of lipids and carbohydrates but lowered the concentration of proteins. This treatment also produced shorter-chain fatty acids and a low percentage of polyunsaturated fatty acids, demonstrating the potential of this medium for growing microalgae with a suitable fatty acid profile for biodiesel production. Furthermore, DGAT2 and NRT2 expression was highest at lower nitrogen concentrations, suggesting these genes could be important for modulating lipid biosynthesis in response to nitrogen limitation. Keywords: Chaetoceros muelleri, Nitrogen stress, Fatty acid methyl esters, Biochemical composition, Gene expression

Chiltepin, a wild chili mostly used in different traditional foods and traditional medicine in Northwest Mexico, represents a source of polyphenols. However, studies about the bioaccessibility of polyphenols as a parameter to measure the nutritional quality and bioefficacy of them in the fruit after consumption are scarce. Chiltepin showed phenolic acids and flavonoids contents between 387 and 65 μg/g, respectively. Nevertheless, these values decreased after the digestion process. Before digestion, gallic acid, 4-hydroxibenzoinc acid, chlorogenic acid, caffeic acid, p-coumaric acid, quercetin and luteolin were the main polyphenols found in chiltepin by HPLC-DAD and confirmed by FIA-ESI-IT-MS/MS. Gallic and chlorogenic acids were non-detected in the gastric phase, while only p-coumaric acid (5.35 ± 3.89 μg/g), quercetin (5.91 ± 0.92 μg/g) and luteolin (2.86 ± 0.62 μg/g) were found in the intestinal phase. The bioaccessibility of phenolic acids, flavonoids, and total polyphenols after the intestinal phase was around 24, 17 and 23%, respectively. Overall, results indicated that release of polyphenols from chiltepin fruit might be affected by the food matrix and gastrointestinal conditions due to the low bioaccessibility values observed.

Background RNA-Seq is the preferred method to explore transcriptomes and to estimate differential gene expression. When an organism has a well-characterized and annotated genome, reads obtained from RNA-Seq experiments can be directly mapped to that genome to estimate the number of transcripts present and relative expression levels of these transcripts. However, for unknown genomes, de novo assembly of RNA-Seq reads must be performed to generate a set of contigs that represents the transcriptome. These contig sets contain multiple transcripts, including immature mRNAs, spliced transcripts and allele variants, as well as products of close paralogs or gene families that can be difficult to distinguish. Thus, tools are needed to select a set of less redundant contigs to represent the transcriptome for downstream analyses. Here we describe the development of Compacta to produce contig sets from de novo assemblies. Results Compacta is a fast and flexible computational tool that allows selection of a representative set of contigs from de novo assemblies. Using a graph-based algorithm, Compacta groups contigs into clusters based on the proportion of shared reads. The user can determine the minimum coverage of the contigs to be clustered, as well as a threshold for the proportion of shared reads in the clustered contigs, thus providing a dynamic range of transcriptome compression that can be adapted according to experimental aims. We compared the performance of Compacta against state of the art clustering algorithms on assemblies from Arabidopsis, mouse and mango, and found that Compacta yielded more rapid results and had competitive precision and recall ratios. We describe and demonstrate a pipeline to tailor Compacta parameters to specific experimental aims. Conclusions Compacta is a fast and flexible algorithm for the determination of optimum contig sets that represent the transcriptome for downstream analyses.

Mine tailings phytostabilization has been proposed as a bioremediation strategy to constrain the contaminants dispersion using plants to limit the effects of erosion. Rhizospheric bacteria impact plant health and facilitate plant establishment through their metabolic functions, which could be relevant in bioremediation strategies. We studied both culturable and metagenomic diversity or rhizospheric bacteria of mine tailings colonizing plants of an abandoned mine operation in Nacozari de García, Sonora, Mexico. Diversity was described through amplification of the 16S rRNA gene and whole metagenome shotgun sequencing of both environmental and cultured rhizosphere associated microbes. The culturable bacteria were assembled in a synthetic community (SC; 235 bacteria genera). Subsequently, we performed an experimental evolution setup with the SC, selecting for heavy metal resistance, microbial competition, and the ability for growing in plant-derived nutrient sources. The selection experiment show that bacteria diversity decreases from the environmental culture-free microbiomes to the mine tailings rhizospheres and the experimental evolution outcome: the synthetic community (FSC; 43 bacteria genera). The rhizosphere communities shifted from the dominance of Actinobacteria in their environment to Proteobacteria in the cultivated consortia and the synthetic communities. Both environmental and cultured metagenomes contained plant-growth promotion, heavy-metal homeostasis, and antibiotic resistance predicted genes. The FSC included predicted proteins related to plant-growth promotion such as siderophore production and plant hormone regulation proteins. We reconstructed a metagenome assembled genomic sequence named Enterobacter sp., Nacozari. The recovered Enterobacter sp. Nacozari, have predicted coding genes for direct and indirect plant growth promotion along with adhesion and oxidative stress-related proteins. The metabolic potential of the FSC presents promising features that might make it useful for plant-growth promotion in tailored phytostabilization strategies for the abandoned mine-tailings of Nacozari.

As maize was domesticated in Mexico around 9,000 years ago, local farmers have selected and maintained seed stocks with particular traits and adapted to local conditions. In the present day, many of these landraces are still cultivated; however, increased urbanization and migration from rural areas implies a risk that this invaluable maize germplasm may be lost. In order to implement an efficient mechanism of conservation in situ, the diversity of these landrace populations must be estimated. Development of a method to select the minimum number of samples that would include the maximum number of alleles and identify germplasm harboring rare combinations of particular alleles will also safeguard the efficient ex‐situ conservation of this germplasm. To reach this goal, a strategy based on SSR analysis and a novel algorithm to define a minimum collection and rare genotypes using landrace populations from Puebla State, Mexico, was developed as a “proof of concept” for methodology that could be extended to all maize landrace populations in Mexico and eventually to other native crops. The SSR‐based strategy using bulked DNA samples allows rapid processing of large numbers of samples and can be set up in most laboratories equipped for basic molecular biology. Therefore, continuous monitoring of landrace populations locally could easily be carried out. This methodology can now be applied to support incentives for small farmers for the in situ conservation of these traditional cultivars.

El presente manual va dirigido a estudiantes de licenciatura en biología y contiene una serie de prácticas a realizar de manera sencilla, dinámica y de bajo costo que se puede adaptar a cualquier laboratorio con equipo y reactivos básicos de biología molecular. Además, tiene la finalidad de facilitar, complementar y consolidar el conocimiento teórico de biología molecular a los estudiantes, utilizando técnicas experimentales básicas desde extracción de ácidos nucleicos de vertebrados, invertebrados y plantas; así como técnicas de amplificación y análisis de ácido desoxirribonucleico. Cuenta además con una práctica para el diseño de oligonucleótidos. Cada práctica cuenta con una serie de preguntas para reforzar los conocimientos del estudiante y que le pueden ayudar a elaborar su reporte. Al final del manual, se encuentra un glosario con los términos empleados.

Las plantas del género Jatropha, pertenecientes a la familia de las Euphorbiaceae, pueden ser consideradas como alternativa para la obtención de semilla, con uso potencial en la fabricación de biocombustibles por su contenido alto de aceite. Se conocen alrededor de 186 especies distribuidas alrededor del mundo, de las cuales 48 se encuentran en México. En Sonora se conocen principalmente las especies de Jatropha cardiophylla, Jatropha cordata, Jatropha cinerea y Jatropha cuneata. La información que se tiene hasta el momento para especies adaptadas a zonas áridas en cuanto a la composición química de sus semillas es escasa y se desconoce el aspecto molecular relacionado con la síntesis de ácidos grasos. Por tal razón, se ha iniciado el estudio de la composición química y su relación con la expresión de genes, involucrados en la síntesis de ácidos grasos específicamente de los ácidos oleico y linoleico en las semillas de las especies de Jatropha nativas de Sonora.

Desiccation tolerance (DT) is a remarkable process that allows seeds in the dry state to remain viable for long periods of time that in some instances exceed 1,000 y. It has been postulated that seed DT evolved by rewiring the regulatory and signaling networks that controlled vegetative DT, which itself emerged as a crucial adaptive trait of early land plants. Understanding the networks that regulate seed desiccation tolerance in model plant systems would provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants. In this work, we used an integrated approach that included genomics, bioinformatics, metabolomics, and molecular genetics to identify and validate molecular networks that control the acquisition of DT in Arabidopsis seeds. Two DT-specific transcriptional subnetworks were identified related to storage of reserve compounds and cellular protection mechanisms that act downstream of the embryo development master regulators LEAFY COTYLEDON 1 and 2, FUSCA 3, and ABSCICIC ACID INSENSITIVE 3. Among the transcription factors identified as major nodes in the DT regulatory subnetworks, PLATZ1, PLATZ2, and AGL67 were confirmed by knockout mutants and overexpression in a desiccation-intolerant mutant background to play an important role in seed DT. Additionally, we found that constitutive expression of PLATZ1 in WT plants confers partial DT in vegetative tissues.

Phosphate (Pi) availability is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with such limiting conditions, plants have evolved a myriad of developmental and biochemical strategies to enhance the efficiency of Pi acquisition and assimilation to avoid nutrient starvation. In the past decade, these responses have been studied in detail at the level of gene expression; however, the possible epigenetic components modulating plant Pi starvation responses have not been thoroughly investigated. Here, we report that an extensive remodeling of global DNA methylation occurs in Arabidopsis plants exposed to low Pi availability, and in many instances, this effect is related to changes in gene expression. Modifications in methylation patterns within genic regions were often associated with transcriptional activation or repression, revealing the important role of dynamic methylation changes in modulating the expression of genes in response to Pi starvation. Moreover, Arabidopsis mutants affected in DNA methylation showed that changes in DNA methylation patterns are required for the accurate regulation of a number of Pi-starvation–responsive genes and that DNA methylation is necessary to establish proper morphological and physiological phosphate starvation responses.

Bacteria of the genus Citricoccus have been isolated from ecological niches characterized by diverse abiotic stress conditions. Here we report the first genome draft of a strain of the genus Citricoccus isolated from the extremely oligotrophic Churince system in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico.