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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.

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).

Jatropha species have been shown to be an important source of secondary metabolites with different biological effects. Jatropha cinerea (Ortega) M&uuml, ll. Arg and Jatropha cordata (Ortega) M&uuml, ll. Arg are distributed in the Northwestern region of Mexico, are adapted to extreme weather conditions and are widely used (stems, leaves, and sap) in traditional medicine. The aim of the present study was to carry out the phytochemical characterization and the evaluation of the antioxidant activity in methanolic extracts of stems and leaves from J. cinerea and J. cordata. The compounds present in the extracts of both species were characterized by ESI-IT-MS/MS and quantified by HPLC-DAD. The results showed that the stem extracts of both species are rich in phenolic acids, while the leaf extracts are rich in flavonoids. Some of the main compounds found were gallic acid, gentisic acid, 3,4-Dihydroxybenzoic acid, vitexin, isovitexin, and catechol. Both species showed high concentrations of phenols and total flavonoids and antioxidant activity. J. cordata showed the highest antioxidant capacity and the highest concentration of phenolic compounds. Overall, both Jatropha species are a natural source of antioxidant compounds with potential biotechnological uses.

Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles 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.

Simple Summary Phosphorus (P) is a key nutrient involved in the transfer of energy and the synthesis of several cellular components. It has been reported that P limitation in diatoms induces the synthesis of biomolecules and the accumulation of storage compounds, such as pigments, carbohydrates and lipids, with diverse biological activities, which can be used in diverse biotechnological applications. However, the molecular and biochemical mechanisms related to how diatoms cope with P deficiency are not clear, and research into this has been limited to a few species. The integration of results obtained from omics sciences could provide a broad understanding of the response of diatoms to P limitation, and the information obtained could help to solve challenges such as biomass production, by-products yield and genetic improvement of strains. Abstract Diatoms are the most abundant group of phytoplankton, and their success lies in their significant adaptation ability to stress conditions, such as nutrient limitation. Phosphorus (P) is a key nutrient involved in the transfer of energy and the synthesis of several cellular components. Molecular and biochemical mechanisms related to how diatoms cope with P deficiency are not clear, and research into this has been limited to a few species. Among the molecular responses that have been reported in diatoms cultured under P deficient conditions is the upregulation of genes encoding enzymes related to the transport, assimilation, remobilization and recycling of this nutrient. Regarding biochemical responses, due to the reduction of the requirements for carbon structures for the synthesis of proteins and phospholipids, more CO2 is fixed than is consumed by the Calvin cycle. To deal with this excess, diatoms redirect the carbon flow toward the synthesis of storage compounds such as triacylglycerides and carbohydrates, which are excreted as extracellular polymeric substances. This review aimed to gather all current knowledge regarding the biochemical and molecular mechanisms of diatoms related to managing P deficiency in order to provide a wider insight into and understanding of their responses, as well as the metabolic pathways affected by the limitation of this nutrient.

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.

EnglishPlants belonging to genus Jatropha has arisen interest because of its high oil content that could be used to produce biodiesel. It is also widely reported that the main fatty acids in Jatropha oilseed are oleic and linoleic acids. However, there are scarce studies related to native species of Jatropha from Northwestern Mexico which are adapted to arid conditions, and the expression of genes involved in fatty acid synthesis for these species is still unknown. Therefore, the aim of this study was to analyze the expression of five genes, ACP1, KASII, D9SD, FAD2-1 and FAD2-2, which are involved in the oleic and linoleic acids synthesis in mature wild-seeds of Jatropha cinerea, a native species from Sonoran Desert, using semi-quantitative RT-PCR. The J. cinerea seeds were randomly collected in Bahia de Kino, Sonora (Mexico) which is a region characterized by its harsh environments such as saline soils and extreme temperature changes and J. curcas mature seeds from a non-toxic variety from Veracruz, Mexico were used as a reference. The RT-PCR analysis of three biological replicates were considered to ensure data consistent. Our analysis showed a higher expression of KASII and FAD2-1 genes in J. cinerea seeds compared to J. curcas, meanwhile the expression of ACP1, D9SD and FAD2-2 were higher in J. curcas. Furthermore, Actin and FAD2-1 genes sequences here obtained are the first reported for J. cinerea, thus providing information to develop further studies. Key words: fatty acids biosynthesis; PCR; KASII; FAD2-1 portuguesPlantas pertencentes ao genero Jatropha tem despertado interesse devido ao seu alto teor de oleo que poderia ser usado para produzir biodiesel. Tambem e amplamente relatado que os principais acidos graxos das oleaginosas da Jatropha sao os acidos oleico e linoleico. No entanto, existem poucos estudos relacionados a especies nativas de pinhao-manso do noroeste do Mexico que estao adaptados a condicoes aridas, e a expressao de genes envolvidos na sintese de acidos graxos para essas especies ainda e desconhecida. Portanto, o objetivo deste estudo foi analisar a expressao de cinco genes, ACP1, KASII, D9SD, FAD2-1 e FAD2-2, que estao envolvidos na sintese de acidos oleico e linoleico em sementes selvagens maduras de Jatropha cinerea, especies nativas do Deserto de Sonora, usando RT-PCR semi-quantitativa. Sementes de J. cinerea foram coletadas aleatoriamente em Bahia de Kino, Sonora (Mexico), regiao caracterizada por ambientes agressivos como solos salinos e mudancas extremas de temperatura, e sementes de J. curcas maduras de uma variedade nao-toxica de Veracruz, Mexico, usado como referencia. Analise RT-PCR de tres repeticoes biologicas foram consideradas para garantir dados consistentes. Nossa analise mostrou uma maior expressao dos genes KASII e FAD2-1 em sementes de J. cinerea comparado a J. curcas, enquanto a expressao de ACP1, D9SD e FAD2-2 foi maior em J. curcas. Alem disso, as sequencias dos genes Actin e FAD2-1 obtidas sao as primeiras relatadas para J. cinerea, fornecendo, assim, informacoes para o desenvolvimento de novos estudos. Palavras-chave: Biossintese de acidos graxos; PCR; KASII; FAD2-1

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.