Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis

Arte contemporáneo, inclusión y transformación social.

Actividad CePIAbierto (RHCD FA Nº 103/2018). El eje central del proyecto es una exposición de los procesos realizados en los talleres de artes del Centro Vida Nueva (San Juan) y el Centro Educativo Terapéutico Lihue Vidas (Córdoba), junto a una selección de sus producciones visuales. Tanto éstas producciones como su montaje se propone desde un planteo contemporáneo y ampliado de las artes visuales, donde diversas disciplinas (como pintura, fotografía, video, registro de experiencias, textos e instalaciones) y diversos campos no artísticos (como pedagógico, social, psicológico, etc) se entrecruzan y construyen de manera colaborativa la experiencia propuesta, rescatando y revalorizando sobre todo el proceso de trabajo y no sólo el resultado final. Se realizó también una charla-debate con lxs artistas que pone en cuestión ideas ejes que atraviesan el trabajo artístico de las personas con discapacidad, la valoración positiva de la diferencia, la importancia y necesidad de poner en práctica concreta la inclusión en los diferentes ámbitos educativos-artísticos-culturales. Por último, se pintó colectivamente un mural como modo de compartir una experiencia de creación colectiva, junto a lxs artistas expositorxs.Actividad CePIAbierto (RHCD FA Nº 103/2018). Una experiencia artística expositiva que propone pensar la discapacidad no como un problema, sino como una pregunta que nos despierta. Pinturas, dibujos, charlas y un mural colectivo, dan cuenta de un proceso de trabajo artístico y de encuentro entre diversas personas que comparten un mismo hacer y placer: pintar, dibujar (¡y bailar!).Fil: Tamagni, Julia. Universidad Nacional de Córdoba. Centro Educativo Terapéutico Lihue Vidas; Argentina.Fil: Bula, Nadia. Centro Vida Nueva, Institución Aleluya-ARID.Fil: Maggio, Natalia. Universidad Católica de Cuyo. Centro Vida Nueva, Institución Aleluya-ARID.Fil: Scheidegger, Emiliano. Universidad Nacional de Córdoba. Facultad de Artes; Argentina.Fil: Walter, Florencia. Universidad Nacional de Córdoba. Facultad de Artes; Argentina.Fil: Belkys Scolamieri, Delia Lozano. Universidad Católica de Córdoba. Facultad de Educación. Apukay; Argentina

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis

SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark

<p>In this repository, we present the PacBio and ONT simulated datasets used for benchmarking transcriptome reconstruction tools, as evaluated in the manuscript titled "<i>SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark</i>". The dataset includes simulated long reads, short reads, CAGE peaks, and a reduced reference annotation. Additionally, we have included reconstructed transcriptomes from each method, along with SQANTI3 output files. The SQANTI-SIM software can be accessed on GitHub at the following URL: <a href="https://github.com/ConesaLab/SQANTI-SIM">https://github.com/ConesaLab/SQANTI-SIM</a>.</p><p>- Please ensure to cite the original publication (listed below) when using these datasets.</p&gt

SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark

SQANTI-SIM is available at https://github.com/ConesaLab/SQANTI-SIM under GNU GPLv3 license. The human reference genome sequence (primary assembly, GRCh38) and gene annotation v43 from GENCODE can be obtained from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43. The long-read sequencing data obtained from the human WTC11 cell line is available at ENCODE (https://www.encodeproject.org/search): the cDNA ONT FASTQ file can be found under accession ENCFF263YFG, the dRNA ONT sample under file accession ENCFF155CFF, and the cDNA PacBio data under experiment accession ENCSR507JOF. Short-read sequencing data can be retrieved from accession number ENCSR673UKZ. The CAGE-Seq data is available at NCBI Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE185917. The simulated datasets generated and analyzed during the current study can be reproduced using the code provided in the SQANTI-SIM v0.2 software repository and supplementary materials. Additionally, the processed data and the SQANTI-SIM source code used in this study are also accessible on Zenodo (https://doi.org/10.5281/zenodo.10160381) [37].Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy of different methods in identifying annotated and novel transcripts remains a challenge. Here, we present SQANTI-SIM, a versatile tool that wraps around popular long-read simulators to allow precise management of transcript novelty based on the structural categories defined by SQANTI3. By selectively excluding specific transcripts from the reference dataset, SQANTI-SIM effectively emulates scenarios involving unannotated transcripts. Furthermore, the tool provides customizable features and supports the simulation of additional types of data, representing the first multi-omics simulation tool for the lrRNA-seq field.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature.This work has been funded by NIH grant R21HG011280 and by the Spanish Ministry of Science grant PID2020-119537RB-100.Peer reviewe

Supplementary material: Chitosan modulates volatile organic compound emission from the biocontrol fungus Pochonia chlamydosporia

Table S1: Bayes Factor between treatment and control of VOCs from P. chlamydosporia in rice cultures on different DAI, Table S2: Bayes Factor between treatment and control of VOCs from P. chlamydosporia in Czapek–Dox broth cultures after different times of exposure to chitosan, Figure S1: Line plots with the median values and standard deviations of the peak heights of VOCs produced by P. chlamydosporia in rice cultures, Figure S2: GC-MS chromatogram of headspace volatile compounds produced by P. chlamydosporia 15 days after inoculation with control buffer solution (BS) and with chitosan solution (CH), Figure S3: Line plots with the median values and standard deviations of the peak heights of VOCs produced by P. chlamydosporia in modified Czapek–Dox broth cultures, Figure S4: GC-MS chromatogram of headspace volatile compounds produced by P. chlamydosporia cultured in modified Czapek–Dox broth for 5 days after 24 h with control buffer solution (BS) and 24 h of exposure to chitosan (CH).Peer reviewe

Chitosan Modulates Volatile Organic Compound Emission from the Biocontrol Fungus Pochonia chlamydosporia

Fungal volatile organic compounds (VOCs) are responsible for fungal odor and play a key role in biological processes and ecological interactions. VOCs represent a promising area of research to find natural metabolites for human exploitation. Pochonia chlamydosporia is a chitosan-resistant nematophagous fungus used in agriculture to control plant pathogens and widely studied in combination with chitosan. The effect of chitosan on the production of VOCs from P. chlamydosporia was analyzed using gas chromatography–mass spectrometry (GC-MS). Several growth stages in rice culture medium and different times of exposure to chitosan in modified Czapek–Dox broth cultures were analyzed. GC-MS analysis resulted in the tentative identification of 25 VOCs in the rice experiment and 19 VOCs in the Czapek–Dox broth cultures. The presence of chitosan in at least one of the experimental conditions resulted in the de novo production of 3-methylbutanoic acid and methyl 2,4-dimethylhexanoate, and oct-1-en-3-ol and tetradec-1-ene in the rice and Czapek–Dox experiments, respectively. Other VOCs changed their abundance because of the effect of chitosan and fungal age. Our findings suggest that chitosan can be used as a modulator of the production of VOCs in P. chlamydosporia and that there is also an effect of fungal age and exposure time.This research was funded by PID2020-119734RB-I00, Project from the Spanish Ministry of Science and Innovation, and by European Project H2020 MUSA, grant number 727624