Microbial metallophores are low-molecular-weight chelating agents produced by microorganisms to acquire essential metal ions. Their biosynthesis, transport, and regulation involve complex processes, specialized enzymatic machinery, and intricate regulatory networks. This review examines the multifaceted roles of metallophores in microbial ecology and their potential applications in sustainable agriculture, emphasizing their key role in trace metal acquisition, nutrient cycling, and plant–microbe interactions. Furthermore, it explores the potential applications of metallophores in agriculture, bioremediation, and biotechnology, connecting their potential to the development of novel strategies for sustainable agriculture.

Cacao (Theobroma cacao L.) production is significantly influenced by genotype-environment interactions, which affect key agronomic traits such as yield, fruit quality, and disease resistance. Despite advances in cacao breeding, one of the main challenges remains the identification of stable, high-performing clones that can adapt to different environmental conditions while maintaining desirable agronomic characteristics. In particular, the introduction of improved clones with high productivity and tolerance to diseases such as frosty pod rot is essential to ensure sustainable production. However, limited information exists on the environmental influence on these traits, making it crucial to assess the performance of new cacao clones in diverse agroecological conditions before their large-scale adoption. With the objective of evaluating the genotype-environment interaction of cacao clones generated by INIFAP and introduced for their tolerance to diseases (frosty pod rot), high yield, and quality, 23 cacao clones were established in three environments: (1) Campo Experimental Rosario Izapa-Tuxtla chico, Chiapas; (2) Ejido Umoa, Tapachula, Chiapas y (3) Vicente Guerreo, Teapa, Tabasco. The cacao clones were established in a Randomized Block Experimental Design with three replications and five trees per block. Statistical analysis was conducted in R 4.4.1 using the statgenGxE package and hierarchical clustering. The variance analysis showed highly significant differences among the genotypes for all the evaluated variables, indicating considerable genetic variability in terms of fruit length (FL), fruit weight (FW), total number of seeds (TNS), individual seed dry weight (ISDW), and pod index (PI). Environment 1, located in Rosario Izapa, Chiapas, stood out as the best for the variables FL, TNS, and ISDW. On the other hand, environment 3, situated in Vicente Guerrero, Teapa, Tabasco, proved to be the most suitable for FW and PI. In contrast, environment 2, located in Ejido Umoa, Tapachula, Chiapas, ranked as the worst for most of the variables, particularly for FL, FW, and TNS. The sensitivity analysis of the cacao genotypes depended on the type of variable; for the fruit variables, genotype 5 stood out for FL, genotype 18 for FW, genotype 4 for TNS, genotype 9 for ISDW, and genotype 15 for PI. In general, the best genotype for fruit variables was genotype 25 (F19P3). Finally, it was observed that among the 23 promising cacao genotypes, most exhibited interaction with the environment, suggesting that it is very important to consider the environmental conditions where the varieties will be established. The findings of this study provide valuable insights into the influence of environmental conditions on cacao productivity and quality, highlighting the need for site-specific clone selection. The identification of high-yielding and stable genotypes can facilitate more efficient breeding strategies and better decision-making for cacao producers and researchers. By understanding how different environments impact agronomic traits, this research contributes to the sustainable intensification of cacao cultivation, helping to optimize yields while mitigating the risks associated with environmental variability. These results are particularly relevant for breeding programs aimed at developing resilient cacao varieties suited to diverse agroecological regions.

Timber trees are targets of herbivorous attacks. The identification of genes associated with pest resistance can be accomplished through differential expression analysis using transcriptomes. We reported the de novo assembly of cedar (Cedrela odorata L.) transcriptome and the differential expression of genes involved in herbivore resistance. The assembly and annotation of the transcriptome were obtained using RNAseq from healthy cedar plants and those infested with Chrysobothris yucatanensis. A total of 325.6 million reads were obtained, and 127,031 (97.47%) sequences were successfully assembled. A total of 220 herbivory-related genes were detected, of which 170 genes were annotated using GO terms, and 161 genes with 245 functions were identified—165, 75, and 5 were molecular functions, biological processes, and cellular components, respectively. To protect against herbivorous infestation, trees produce toxins and volatile compounds which are modulated by signaling pathways and gene expression related to molecular functions and biological processes. The limited number of genes identified as cellular components suggests that there are minimal alterations in cellular structure in response to borer attack. The chitin recognition protein, jasmonate ZIM-domain (JAZ) motifs, and response regulator receiver domain were found to be overexpressed, whereas the terpene synthase, cytochrome P450, and protein kinase domain gene families were underexpressed. This is the first report of a cedar transcriptome focusing on genes that are overexpressed in healthy plants and underexpressed in infested plants. This method may be a viable option for identifying genes associated with herbivore resistance.

Forty-five accessions of the genus Phaseolus from the orthodox seed collection of the National Center for Genetic Resources (CNRG) of the National Institute of Forestry, Agricultural, and Livestock Research (INIFAP) of Mexico were sequenced using RADseq. The species utilized were: P. acutifolius (14), P. coccineus (12), P. lunatus (8), P. dumosus (6), P. leptostachyus (2), P. filiformis (2), and P. vulgaris (1). A variant call file (VCF) was generated using GATK with the P. vulgaris reference genome GCF_000499845.1, identifying 97,103 shared SNPs among the species. These data have the potential to be used for studies of genetic diversity intra and interspecies, phylogeny, evolution, genetic resource conservation, and agricultural improvement.

Introduction: The high-throughput genomic and transcriptomic approach has been developed and implemented to address the main challenges that the timber forestry sector faces, such as population growth, climate change, deforestation and the loss of forest ecosystem services. Objective: To carry out a bibliographic review focused on the genomes and transcriptomes of timber trees reported in the databases, with special attention to red cedar (Cedrela odorata L.), due to its importance as precious wood in Mexico. Methodology: A literature review was carried out, directed at studying timber trees with genomic and transcriptomic strategies in different databases such as Pubmed, Scopus, Google Scholar, ScienceDirect, Wiley Online Library, MDPI and Scielo to identify the timber species that have been reported genomes and transcriptomes. The structure of the review was the genomics of timber trees, the transcriptomics of wood, and the potential species for study due to their importance and finally, the databases for consultation. Subsequently, a bibliometric study was carried out with the bibliometrix library in R Studio. Main results: The first genome to be assembled at the chromosome level was the black cottonwood. Among the timber trees, the genomes of black cottonwood, desert poplar, eucalyptus and oak with a length of 392, 496, 691 and 789 Mb have been reported. Through study of the transcriptome, it has been possible to identify genes related to formation of the wood in a hybrid poplar (Populus alba L. × P. glandulosa) and P. tremula L. and with drought tolerance in Pinus massoniana and Pinus pinaster Aiton. In red cedar (Cedrela odorata L.), the transcriptome was obtained by sequencing a single leaf, identifying 52,181 gene models. In the NCBI, EMBL-EBI, TreeGenes, PLAZA databases and the hardwood genomics website it is possible to find information related to the genomics and transcriptomics of timber species. Implications: More research is required in omics in timber, particularly in red cedar, since the search on these topics yielded little information. Conclusion: Through the bibliographic review in databases, the timber trees that have a described genome and transcriptome were identified. This information can be used for the assembly and annotation of new genomes, identification of genes and molecular markers, among other applications.