Bioinformatics analysis of Pinus pinaster Aiton transcriptome in response to ammoniacal nutrition

Conifers have a great economic and environmental value. Nitrogen is an important limiting factor for the development of plants. Conifers are well adapted to ammonium nutrition since it is the main source of inorganic nitrogen in the ecosystems that they live. The present work is based on the study of ammonium uptake and management by maritime pine (Pinus pinaster Aiton) and its implication in the production of plant biomass. This conifer is present in western Mediterranean area and it is used for reforestation soil stabilization and industry. Due to its importance in this region maritime pine has been used as model conifer tree which has led to different omics studies and resources. For this purpose we have developed several experiments using pine seedlings subjected to different levels of ammonium at the short and long term using the latest biotechnological and bioinformatic advances. The studies of RNA-seq allow us to obtain a large amount of transcriptomic information of mRNA lncRNA and miRNA level in the roots under ammonium nutrition. These data need different bioinformatic workflows to extract expression results with reliability and biological context. Parallel to these studies we have performed direct RNA sequencing using the Minion device of Oxford Nanopore Technologies (ONT). Thanks to this kind of technology we have been able to identify epitranscriptomics changes in our samples under ammonium nutrition. With this aim we have had to develop a new bioinformatic workflow. The characteristics of this new kind of sequencing allow us to analyze the RNAseq studies from another perspective.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Transcriptomics of ammonium nutrition in the conifer Pinus pinaster Aiton

Nitrogen is an important element for all living beings because it is part of macromolecules as significant as nucleic acids or amino acids. For plants, it constitutes a limiting factor in their growth and development1 due to their low natural availability in soils thus limiting primary production in ecosystems2. Conifers are a group of gymnosperm plants that form large forest extensions of vegetation, being the main constituents of forests in boreal ecosystems3 where ammonium is the main source of inorganic nitrogen4. Due to the characteristics of the soils in which conifers usually grow, these plants have developed a high tolerance to the presence of ammonium, which may constitute their main source of inorganic nitrogen5. The maritime pine (Pinus pinaster Aiton) is a conifer that has a wide distribution in the western Mediterranean area and has been widely used in reforestation, soil stabilization tasks and industrially. In recent years, maritime pine has been the subject of multiple omic studies that have resulted in the acquisition of important tools and resources6,7. The present work is focused on the analysis of the ammonium uptake and management efficiency, and its relationship with the biomass accumulation in maritime pine. For this purpose, several experiments have been developed in which pine seedlings have undergone different levels of ammonium nutrition, both in the short and long term. As a result of short-term experiments, the characterization of transcriptomic response to the process of ammonium nutrition (uptake and assimilation) is being studied at mRNA, lncRNA and miRNA level in roots. In relation to long-term experiments, ten different provenances of maritime pine seedlings were treated with different ammonium levels and the biomass changes were measured. The results obtained suggest the existence a certain phenotypic plasticity grade for this conifer.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. This project was supported by a grant form the Spanish Ministerio de Ciencia, Innovación y Universidades (MicroNUpE, BIO2015-73512-JIN; MINECO/AEI/FEDER, UE). FO was supported by a grant from the Universidad de Málaga (Programa Operativo de Empleo Juvenil vía SNJG, UMAJI11, FEDER, FSE, Junta de Andalucía) and JMVM by a grant from the Spanish Ministerio de Educación y Formación Profesional (FPU17/03517

Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex

Ammonium is a prominent source of inorganic nitrogen for plant nutrition, but excessive amounts can be toxic for many species. However, most conifers are tolerant to ammonium, a relevant physiological feature of this ancient evolutionary lineage. For a better understanding of the molecular basis of this trait, ammonium‐induced changes in the transcriptome of maritime pine (Pinus pinaster Ait.) root apex have been determined by laser capture microdissection and RNA sequencing. Ammonium promoted changes in the transcriptional profiles of multiple transcription factors, such as SHORT‐ROOT, and phytohormone‐related transcripts, such as ACO, involved in the development of the root meristem. Nano‐PALDI‐MSI and transcriptomic analyses showed that the distributions of IAA and CKs were altered in the root apex in response to ammonium nutrition. Taken together, the data suggest that this early response is involved in the increased lateral root branching and principal root growth, which characterize the long‐term response to ammonium supply in pine. All these results suggest that ammonium induces changes in the root system architecture through the IAA‐CK‐ET phytohormone crosstalk and transcriptional regulation.This study was funded by Spanish Ministerio de Ciencia e Innovación, grant numbers BIO2015‐73512‐JIN MINECO/AEI/FEDER, UE; RTI2018‐094041‐B‐I00 and EQC2018‐004346‐P. Funding for open access charge: Universidad de Málaga/CBUA. FO was supported by grants from the Universidad de Málaga (Programa Operativo de Empleo Juvenil vía SNJG, UMAJI11, FEDER, FSE, Junta de Andalucía) and BIO‐114, Junta de Andalucí

Involvement of miRNAs in the short-term response of pine roots to ammonium nutrition

Post-transcriptonal gene regulation is an essential control point regarding gene expression programs. A class of small non-coding RNAs, microRNAs (miRNAs) play important roles during this process. They act on target mRNAs through post-transcriptional gene silencing, either by endonuclease mediated transcript cleavage or by translational repression of targeted mRNAs (Pattanayak et al., 2013). Thus, miRNAs are involved in the regulation mechanisms of important plant processes, including the regulation of the processes related to nitrogen nutrition (Gutiérrez, 2012). In the present work, maritime pine (Pinus pinaster Aiton) was used to study the role of miRNAs regarding NH4+ nutrition in conifers, a group of plants that exhibits tolerance to NH4+ nutrition compared to NO3- nutrition specially during seedling stage Ortigosa et al., 2022). This fact is of high interest since numerous NH4+ nutrition can negatively affect the growth and development of different crops. The global miRNA expression has been characterized in the roots of maritime pine seedlings after 2 h and 24 h from fertilization with two levels of NH4+ solutions (0.1 mM and 3 mM). The miRNA-seq analysis revealed 271 new miRNAs with an identified precursor although only 4 were differentially expressed. Gutiérrez RA. 2012. Science, 336:1673-1675. Ortigosa F, et al. 2022. Plant Cell and Environment, 45,915-935. Pattanayak D, et al. 2013. Plant Molecular Biology Reporter, 31, 493-506.Acknowledgements & Funding. This work was supported by the grants BIO2015-73512-JIN MINECO/AEI/FEDER, UE; P20_00036 PAIDI 2020/FEDER, UE, and B4-2021-01 (Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech). JMVM was supported by the grant FPU17/03517

Efecto del amonio sobre las raíces de Pinus pinaster: respuesta génica

Conferencia de 30 minutos.El amonio es un nutriente para las plantas capaz de inducir diferentes respuestas de crecimiento y desarrollo, modulando la expresión génica a diferentes niveles. No obstante, cuando se encuentra en exceso provoca toxicidad. En el caso de las coníferas, su relación con el amonio es muy importante debido a que es la forma más abundante de nitrógeno inorgánico en las capas superficiales del suelo de los bosques que forman. Por ello, las coníferas presentan tolerancia a concentraciones de amonio que son tóxicas para otras plantas. A pesar de ello y de constituir un linaje muy antiguo de plantas, el estudio del efecto del amonio sobre el crecimiento y desarrollo de las coníferas ha sido limitado. Para comprender mejor las bases moleculares de las respuestas inducidas por el amonio sobre las coníferas se han realizado diferentes aproximaciones en plántulas de pino resinero (Pinus pinaster Ait.), especie autóctona del mediterráneo occidental.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Psicothema

Resumen tomado de la publicaciónDesarrollo y validación de la Escala SERR para la detección del extremismo y radicalismo religioso Antecedentes: en consonancia con la creciente violencia religiosa, política y social en todo el mundo, este estudio evalúa las propiedades psicométricas de la escala para la detección del extremismo y el radicalismo religioso (SERR), una medida de autoinforme del extremismo y el radicalismo religioso. Método: los análisis factoriales y las evidencias de validez y fiabilidad se recopilaron utilizando una muestra de 1985 participantes de 58 ciudades distintas de España que se identificaron a sí mismos como practicantes activos de su religión. Resultados: los análisis estadísticos de las puntuaciones SERR arrojaron puntuaciones de consistencia interna aceptables (? > .74) y confirmaron los factores clave asociados con el radicalismo y el extremismo. La estructura de la escala se confirmó como bidimensional (?²(64) = 361.22, p < .001, CFI = 0.976, TLI = 0.970, RMSEA (90% CI) = 0.089 (0.080 - 0.098), SRMR = 0.064). Las puntuaciones de la dimensión de extremismo se correlacionaron significativa y positivamente con las puntuaciones del mismo factor en la Escala de Intención de Activismo y Radicalismo (r = 0,32, p < 0.001, n = 139). Conclusiones: los autores concluyen que el SERR muestra una fiabilidad y validez adecuadas para evaluar el grado de extremismo y radicalismo en creyentes cristianos/católicos y musulmanes.ES