Estudio de la domesticación de plantas usando cultivos ornamentales del siglo XVIII

Conferencia impartida para estudiantes de grado y postgradoLa domesticación de plantas ha sido un proceso esencial en el desarrollo de la agricultura. Este proceso implica la selección de fenotipos de acuerdo a necesidades humanas como alimento. Aunque el proceso de domesticación puede ser estudiado desde un punto de vista arqueológico, son los estudios genéticos los que nos ayudan a entender como el ser humano ha seleccionado genes relacionados con fenotipos concretos. Buenos ejemplos de estos estudios son la caracterización de los genes Tga1 y Ramosa1 (maíz), qSH1 y Sh4 (arroz) y fw2.2 (tomate). Begonias, gloxinias y petunias son cultivos ornamentales que domesticaron en el siglo XVIII cumpliendo con las necesidades estéticas de los jardines europeos. Su proceso de domesticación es un ejemplo de selección de fenotipos concretos como forma y color de las flores. En nuestro estudio presentamos los primeros pasos para el estudio de la domesticación de estas especies como la creación de un genoma de referencia y la evaluación de su diversidad genética y fenotípica.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Genomas y rompecabezas: una visión sobre el ensamblaje de genomas

The development of new sequencing technologies has revolutionized genome analysis. Large sequencing projects have been replaced by more modest approaches, both in personnel and costs. It is currently possible to sequence, assemble, and analyze a medium-sized plant genome with a limited amount of resources, although we are still far from being able to assemble any genome. Large genomes, with a high content of repetitions, polyploids, or genomes with a high heterozygosity can be a difficult problem to solve.El desarrollo nuevas tecnologías de secuenciación ha revolucionado el análisis de genomas. Los grandes proyectos de secuenciación se han ido sustituyendo por aproximaciones más modestas, tanto en personal como en costes. Actualmente es posible secuenciar, ensamblar y analizar un genoma vegetal de tamaño medio con una cantidad limitada de recursos, si bien todavía estamos lejos de poder ensamblar cualquier genoma. Genomas de gran tamaño, con un gran contenido en repeticiones, poliploides, o genomas con una elevada heterocigosidad pueden ser un problema de difícil solución

Organelle_PBA, a Pipeline for Assembling Chloroplast and Mitochondrial Genomes from PacBio DNA Sequencing Data

Background: The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. Results: We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and then performs read correction and de novo assembly using Sprai. Organelle-PBA completes the assembly process with the additional step of scaffolding by SSPACE-LongRead. The program then detects the chloroplast inverted repeats and reassembles and re-orients the assembly based on the organelle origin of the reference. We have evaluated the performance of the software using PacBio reads from different species, read coverage, and reference genomes. Finally, we present the assembly of two novel chloroplast genomes from the species Picea glauca (Pinaceae) and Sinningia speciosa (Gesneriaceae). Conclusion: Organelle-PBA is an easy-to-use Perl-based software pipeline that was written specifically to assemble mitochondrial and chloroplast genomes from whole genome PacBio reads. The program is available at https://github.com/aubombarely/Organelle_PBA

Organelle_PBA, a Pipeline for Assembling Chloroplast and Mitochondrial Genomes from PacBio DNA Sequencing Data

Background: The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. Results: We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and then performs read correction and de novo assembly using Sprai. Organelle-PBA completes the assembly process with the additional step of scaffolding by SSPACE-LongRead. The program then detects the chloroplast inverted repeats and reassembles and re-orients the assembly based on the organelle origin of the reference. We have evaluated the performance of the software using PacBio reads from different species, read coverage, and reference genomes. Finally, we present the assembly of two novel chloroplast genomes from the species Picea glauca (Pinaceae) and Sinningia speciosa (Gesneriaceae). Conclusion: Organelle-PBA is an easy-to-use Perl-based software pipeline that was written specifically to assemble mitochondrial and chloroplast genomes from whole genome PacBio reads. The program is available at https://github.com/aubombarely/Organelle_PBA

The SOL Genomics Network Model: Making Community Annotation Work

The concept of community annotation is a growing discipline for achieving participation of the research community in depositing up‐to‐date knowledge in biological databases.
The Solanaceae Genomics Network ("SGN":http://sgn.cornell.edu/) is a clade‐oriented database (COD) focusing on plants of the nightshade family, including tomato, potato, pepper, eggplant, and tobacco, and is one of the bioinformatics nodes of the international tomato genome sequencing project. One of our major efforts is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN has introduced a database for locus names and descriptors, and a database for phenotypes of natural and induced variation. These two databases have web interfaces that allow cross references, associations with tomato gene models, and in‐house curated information of sequences, literature, ontologies, gene networks, and the Solanaceae biochemical pathways database ("SolCyc":http://solcyc.sgn.cornell.edu). All of our curator tools are open for online community annotation, through specially assigned “submitter” accounts. 

Currently the community database consists of 5,548 phenotyped accessions, and 5,739 curated loci, out of which more than 300 loci where contributed or annotated by 66 active submitters, creating a database that is truly community driven.
This framework is easily adaptable for other projects working on other taxa (for example see "http://chlamybase.org":http://chlamybase.org), greatly expanding the application of this user‐friendly online annotation system. Community participation is fostered by an active outreach program that includes contacting potential submitters via emails, at meetings and conferences, and by promoting featured user submitted annotations on the SGN homepage. The source code and database schema for all SGN functionalities are freely available. Please contact SGN at "sgn‐feedback[at]sgn.cornell.edu":mailto:[email protected] for more information

Comparative transcriptional analysis of Persea americana MYB, WRKY and AP2/ERF transcription factors following Phytophthora cinnamomi infection

DATA AVAILABILITY STATEMENT : The data sets used in this study can be found in online repositories. Raw RNA-seq data used in this study has been deposited in the Sequence Read Archive of NCBI GenBank at https://www.ncbi.nlm.nih.gov/sra under accession number PRJNA675400.Plant cells undergo extensive transcriptional reprogramming following pathogen infection, with these reprogramming patterns becoming more complex when pathogens, such as hemibiotrophs, exhibit different lifestyles. These transcriptional changes are often orchestrated by MYB, WRKY and AP2/ERF transcription factors (TFs), which modulate both growth and defence-related gene expression. Transcriptional analysis of defence-related genes in avocado (Persea americana) infected with Phytophthora cinnamomi indicated differential immune response activation when comparing a partially resistant and susceptible rootstock. This study identified 226 MYB, 82 WRKY, and 174 AP2/ERF TF-encoding genes in avocado, using a genome-wide approach. Phylogenetic analysis revealed substantial sequence conservation within TF groups underscoring their functional significance. RNA-sequencing analysis in a partially resistant and susceptible avocado rootstock infected with P. cinnamomi was indicative of an immune response switch occurring in either rootstock after 24 and 6 h post-inoculation, respectively. Different clusters of co-expressed TF genes were observed at these times, suggesting the activation of necrotroph-related immune responses at varying intervals between the two rootstocks. This study aids our understanding of avocado immune response activation following P. cinnamomi infection, and the role of the TFs therein, elucidating the transcriptional reprogramming disparities between partially resistant and susceptible rootstocks.Hans Merensky Foundationhttp://www.wileyonlinelibrary.com/journal/mpphj2024BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologySDG-15:Life on lan

K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

[EN] Background: K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results: As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. Conclusion: K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.This work was supported by the University Polytechnic of Valencia, Grant Number 20180051 "Desarrollo de herramientas para la identificacion de genes y loci de interes en la mejora genetica del tomate y otras horticolas".Ziarsolo, P.; Hasing, T.; Hilario, R.; García-Carpintero, V.; Blanca Postigo, JM.; Bombarely, A.; Cañizares Sales, J. (2021). K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology. Plant Methods. 17(1):1-11. https://doi.org/10.1186/s13007-021-00733-6S11117

TobEA: an atlas of tobacco gene expression from seed to senescence.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Transcriptomics has resulted in the development of large data sets and tools for the progression of functional genomics and systems biology in many model organisms. Currently there is no commercially available microarray to allow such expression studies in Nicotiana tabacum (tobacco). RESULTS: A custom designed Affymetrix tobacco expression microarray was generated from a set of over 40k unigenes and used to measure gene expression in 19 different tobacco samples to produce the Tobacco Expression Atlas (TobEA). TobEA provides a snap shot of the transcriptional activity for thousands of tobacco genes in different tissues throughout the lifecycle of the plant and enables the identification of the biological processes occurring in these different tissues. 772 of 2513 transcription factors previously identified in tobacco were mapped to the array, with 87% of them being expressed in at least one tissue in the atlas. Putative transcriptional networks were identified based on the co-expression of these transcription factors. Several interactions in a floral identity transcription factor network were consistent with previous results from other plant species. To broaden access and maximise the benefit of TobEA a set of tools were developed to provide researchers with expression information on their genes of interest via the Solanaceae Genomics Network (SGN) web site. The array has also been made available for public use via the Nottingham Arabidopsis Stock Centre microarray service. CONCLUSIONS: The generation of a tobacco expression microarray is an important development for research in this model plant. The data provided by TobEA represents a valuable resource for plant functional genomics and systems biology research and can be used to identify gene targets for both fundamental and applied scientific applications in tobacco

Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles

Phytophthora cinnamomi is a hemibiotrophic oomycete causing Phytophthora root rot in over 5,000 plant species, threatening natural ecosystems, forestry, and agriculture. Genomic studies of P. cinnamomi are limited compared to other Phytophthora spp. despite the importance of this destructive and highly invasive pathogen. The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing. Genome sizes were estimated by flow cytometry and assembled de novo to 140-141 Mb genomes with 21,111-21,402 gene models. Genome analyses revealed that both isolates exhibited complex heterozygous genomes fitting the two-speed genome model. The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate. Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana, and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors. Overall, our results suggested that clonal P. cinnamomi isolates employ similar strategies as other Phytophthora spp. to increase phenotypic diversity (e.g., polyploidization, gene duplications, and a bipartite genome architecture) to cope with environmental changes. Our study also provides insights into common and host-specific P. cinnamomi infection strategies and may serve as a method for narrowing and selecting key candidate effectors for functional studies to determine their contributions to plant resistance or susceptibility

The Grapevine Genomics Encyclopedia: an innovative portal to integrate knowledge, resources and services for the grape scientific community and industry

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