Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

BACKGROUND: In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C₄ grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light: dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. RESULTS: Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C₄ photosynthesis were down-regulated during drought, while C₄ metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. CONCLUSIONS: Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C₄ grasses.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by BioMed Central Ltd. The published article can be found at: http://www.biomedcentral.com/bmcgenomics/.Keywords: Gene expression, Panicum virgatum, Recovery, Drought, Switchgrass, RNA-se

Prevalencia de desesperanza en estudiantes del último semestre del programa de psicología de la corporación universitaria minuto de dios, seccional bello 2020

Determinarla prevalencia de desesperanza en los estudiantesque cursan el último semestre del programa de psicología de la Corporación Universitaria Minuto de Dios rectoría Antioquia-Chocó, seccional Bello en el periodo 2020-1.La desesperanza es un estado anímico desfavorable,producto de esquemas cognitivos que interfieren en la interpretación de las propias capacidades para resolver los problemas, se relaciona con sentimientos de minusvalía y desmotivación, afectando el bienestar mental y la percepción del futuro. Debido a la relación de la desesperanza con la salud mental, se planea el objetivo de determinar la prevalencia de desesperanza en los estudiantes de último semestre de psicología de la Corporación Universitaria Minuto de Dios, rectoría Antioquia -Chocó, seccional Bello, 2020-1. El estudio es de enfoque cuantitativo, de tipo no experimental, de diseño transversal/transeccional, de alcance descriptivo, bajo el paradigma positivista. Lapoblación estudiada fueron65 estudiantes de último semestre de psicología, utilizando como instrumento la Escala de Desesperanza de Becky una encuesta sociodemográfica. Para el procesamiento de la información los datos fueron tabulados en una matriz, haciendo uso de Microsoft Excel 365 y el Software Estadístico SPSS, obteniendo así medidas estadísticas descriptivas como tablas de distribución porcentual y de frecuencia.Los resultados obtenidos indican que el 63,9% de la muestra se encuentra en un nivelbajo de desesperanza, el 24,6% presenta una alteración leve y el 11,5% se ubica en una alteración moderada. De acuerdo con estos resultados se concluye que, el mayor porcentaje de los estudiantes del último semestre del programa de psicología de la Corporación Universitaria Minuto de Dios se encuentran en un nivel bajo de desesperanza. Estos resultados muestran evidencia de que los estudiantes en su mayoría gozan de buena salud mental

Diversidad genética intra e inter-específica de ñame (Dioscorea spp.) de la región Caribe de Colombia mediante marcadores AFLP Genetic diversity intra and inter-specific yam (Dioscorea spp.) from the colombian caribbean region by AFLP markers

Conocer la variabilidad genética del ñame, Dioscorea spp., permite apoyar estrategias de mejoramiento y conservación de este recurso fitogenético. El objetivo de este estudio fue la caracterización molecular de 20 accesiones de Dioscorea spp. mediante la técnica molecular de AFLP para determinar cómo se distribuye la variabilidad genética de manera intra e inter-específica. Los datos fueron analizados mediante los métodos de agrupación de correspondencia múltiple y análisis de similaridad de Dice, estableciendo los niveles de confiabilidad de los grupos genéticos mediante remuestreos. En términos de diversidad interespecífica, los valores promedios de similitud variaron entre 41.81% entre D. alata L. y D. rotundata Poir., y 33.51% entre D. trifida L.f. y D. esculenta (Lour.) Burkill, lo que sugiere alta diversidad genética entre las accesiones estudiadas, que formaron cuatro grupos genéticos: D. alata, D. rotundata, D. esculenta y D. trifida, confirmando correspondencia entre la caracterización morfológica, clasificación botánica y la caracterización molecular. En términos de diversidad intraespecífica para la especie D. alata, el análisis también reveló una composición heterogénea en la región Caribe colombiana. Estos estudios ayudarán a definir una estrategia adecuada para fines de conservación y apoyar los esfuerzos futuros en los programas de mejoramiento genético.Knowing the genetic variability of yams, Dioscorea spp., is a good tool to support development and conservation strategies of this plant as genetic resource. The aim of this study was to carried out the molecular characterization of 20 accessions of Dioscorea spp. using the AFLP molecular technique to determine how genetic variation is distributed intra-and inter-specifically. Using multiple correspondence analysis and level of reliability of the genetic groups by resampling, the results showed high genetic variability among the accessions studied giving as a result four genetic groups: D. alata L., D. rotundata Poir., D. esculenta (Lour.) Burkill and D. trifida L.f., which confirmed a correspondence between the morphological and molecular characterization. The average values of similarity ranged from 41.81% in D. alata and D. rotundata, and 33.51% in D. trifida and D. esculenta. These data are consistent with previous morphological characterizations and systematics of the species in relation to their botanical sections. The analysis also revealed the heterogeneous composition of D. alata in the colombian Caribbean region; these studies will help to define an appropriate strategy for conservation to support future efforts in breeding programs

COLOMBIAN FROZEN BIODIVERSITY: 16 YEARS OF THE TISSUE COLLECTION OF THE HUMBOLDT INSTITUTE

Collections of frozen tissue samples stand as keystone sources of molecular information to construct biodiversity knowledge, and are particularly challenged if they focus  on megadiverse countries. In 1998 the Humboldt Institute (Instituto de Investigación de Recursos Biológicos Alexander von Humboldt) began a tissue collection of Colombian biodiversity (IAvH-CT) and the aim of this work is to present a diagnostic and an historical perspective for that collection, constructed by compiling information and experiences on its management as well as by organizing and curating the information of each catalogued sample. After 16 years, the IAvH-CT harbors 16,469 samples, which represent around 2530 species from 1289 genera, and 323 families of the Colombian biodiversity. Samples are biased toward plants (44 %) and birds (40 %), but also include other animal taxa. Geographically, IAvH-CT includes samples from all Colombian departments, but there is broad variation in their coverage. When compared with other international collections, IAvH-CT fulfills several standards of sample storage and data management, but its major weakness is that several tissues seem to lack a vouchered specimen. Tissues housed at IAvH-CT have been included in at least 48 studies published in several scientific journals. IAvH-CT is implementing strategies to improve curatorial standards, fill-in taxonomic gaps, and to explore the potential of its samples to understand the outstanding Colombian biota in a cooperative research framework among institutions. RESUMEN Las colecciones de tejidos son fuentes fundamentales de información molecular para el conocimiento de la biodiversidad, y son particularmente desafiantes si están enfocadas en países megadiversos. En 1998 el Instituto Humboldt (Instituto de Investigación de Recursos Biológicos Alexander von Humboldt) inició una colección de tejidos de biodiversidad colombiana (IAvH-CT) y el objetivo de este trabajo es presentar un diagnóstico y una perspectiva histórica de esta colección, mediante la compilación de información y de experiencias sobre su manejo y organizando y curando la información de cada muestra catalogada. Después de 16 años IAvH-CT resguarda 16 469 muestras, que representan alrededor de 2530 especies de 1289 géneros y 323 familias de la biodiversidad colombiana. Las muestras están sesgadas hacia plantas (44 %) y aves (40 %), pero también incluyen otros taxones animales. Geográficamente, IAvH-CT incluye muestras de todos los departamentos colombianos, pero hay una gran variación en su cobertura. Al ser comparada con otras colecciones internacionales se encuentra que IAvH-CT cumple varios estándares de almacenamiento de muestras y de  manejo de datos, pero su gran debilidad es que varios tejidos aparentemente carecen de un ejemplar de referencia. Varios tejidos almacenados en IAvH-CT han sido incluidos en al menos 48 estudios publicados en varias revistas científicas. IAvH-CT está implementando estrategias para mejorar la curaduría, llenar vacíos taxonómicos y explorar el potencial de sus muestras para entender la impresionante biota colombiana en un marco de investigación en cooperación con otras instituciones

Data from: Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

Background: In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light:dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. Results: Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. Conclusions: Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses

MeyerEliIntegrativeBiologyIntegratingTranscriptional_AdditionalFiles.zip

BACKGROUND: In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C₄ grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light: dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. RESULTS: Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C₄ photosynthesis were down-regulated during drought, while C₄ metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. CONCLUSIONS: Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C₄ grasses.Keywords: Switchgrass, Drought, RNA-seq, Gene expression, Panicum virgatum, RecoveryKeywords: Switchgrass, Drought, RNA-seq, Gene expression, Panicum virgatum, Recover

MeyerEliIntegrativeBiologyIntegratingTranscriptional.pdf

BACKGROUND: In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C₄ grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light: dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. RESULTS: Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C₄ photosynthesis were down-regulated during drought, while C₄ metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. CONCLUSIONS: Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C₄ grasses.Keywords: RNA-seq, Drought, Panicum virgatum, Gene expression, Switchgrass, RecoveryKeywords: RNA-seq, Drought, Panicum virgatum, Gene expression, Switchgrass, RecoveryKeywords: RNA-seq, Drought, Panicum virgatum, Gene expression, Switchgrass, RecoveryKeywords: RNA-seq, Drought, Panicum virgatum, Gene expression, Switchgrass, Recover

Annotated FASTA file of custom Panicum virgatum (Alamo AP13) transcriptome assembly

A custom transcriptome assembly produced from publicly available EST data from accession Alamo AP13 (454 data from NCBI’s Sequence Read Archive: accessions SRR187765-SRR187775; Sanger sequences from cDNA libraries CFNU, CFNT, and EXTA; Zhang et al., 2013). Reads were quality filtered, screened for adaptor and vector contamination, and assembled in Roche De Novo Assembler v2.6 with the ‘-cdna’ option. This FASTA file has been compressed using the GZIP utility

Geographic patterns of genomic diversity and structure in the C4 grass Panicum hallii across its natural distribution

Abstract Geographic patterns of within-species genomic diversity are shaped by evolutionary processes, life history and historical and contemporary factors. New genomic approaches can be used to infer the influence of such factors on the current distribution of infraspecific lineages. In this study, we evaluated the genomic and morphological diversity as well as the genetic structure of the C4 grass Panicum hallii across its complex natural distribution in North America. We sampled extensively across the natural range of P. hallii in Mexico and the USA to generate double-digestion restriction-associated DNA (ddRAD) sequence data for 423 individuals from 118 localities. We used these individuals to study the divergence between the two varieties of P. hallii, P. hallii var. filipes and P. hallii var. hallii as well as the genetic diversity and structure within these groups. We also examined the possibility of admixture in the geographically sympatric zone shared by both varieties, and assessed distribution shifts related with past climatic fluctuations. There is strong genetic and morphological divergence between the varieties and consistent genetic structure defining seven genetic clusters that follow major ecoregions across the range. South Texas constitutes a hotspot of genetic diversity with the co-occurrence of all genetic clusters and admixture between the two varieties. It is likely a recolonization and convergence point of populations that previously diverged in isolation during fragmentation events following glaciation periods.</jats:p

AlamoAP13_transcriptome_annotations

Homology-based annotations for the custom P. virgatum Alamo AP13 transcriptome. A tab-delimited text file. Column IDs: Seq=sequence identifier; Isogroup=cluster of transcripts thought to originate from the same gene; Len=length in base pairs; Match=accession number of best match; Gene=name of the best match; GO=Gene Ontology terms associated with the best match