Biology subjects

Van Sluys, M.-A.

Publications and source records attributed to Van Sluys, M.-A..

6 recordsLinked to original sources

bioRxiv2025

Unmmaped RNA-Seq reads from inoculated sugarcane reveals long non-coding RNAs related to retrotransposons and suggest microbiome modulation

BackgroundTranscriptome studies have contributed to the understanding of protein coding and non-coding gene expression of several organisms. They also provide knowledge into host responses to pathogen infections. Not common yet is to detect transcripts from multiple interacting organisms present in a given sample. In addition, transcriptome studies with complex polyploid hybrid genomes and not completely sequenced, such as the one of sugarcane, remains a challenge. In such studies, a considerable set of reads may not align on any reference genome but still hold significant relevance to the study, allowing to gather information beyond the complex organism itself. ResultsA complete transcriptome analysis of sugarcane inoculated with a pathogen, with and without the addition of a beneficial bacteria, generated a subset of reads that did not map to their respective genome references. Here, we report a pipeline based on the assembly of a collection of unmapped reads that potentially interfere with the gene expression of the associated microbiome, as well as the identification of long non-coding RNAs related to transposable elements present in a host-pathogen interaction. In addition, the detection of transcripts of naturally occurring microorganisms in sugarcane allowed the identification of its microbiome at the species level. Further studies support changes in microorganism transcription levels according to the biotic stress the plant was conditioned. ConclusionA quick and practical pipeline is proposed to study unmapped reads to infer relevant information that would remain otherwise unnoticed. New sequences from hybrid sugarcane transcriptome, such as long non-coding genes related to known retrotransposons are described. Also, changes in microbiome gene expression provides insights to the microbiome alterations and bring knowledge to the sugarcane "pathobiome".

bioinformatics↗

bioRxiv2024

Bridging Genomic Gaps: The Pan-Grass Syntenic Gene Set in Grass Crop Evolution

Understanding orthologous and homeologous relationships among genes can inform our understanding of how evolution and artificial selection have shaped the genomes of related species to adapt to different niches and produce different phenotypes. High-confidence information on orthologous relationships can also increase the impact of the functional characterization in one species by ensuring this information is available to researchers studying orthologs in other species. The grasses are ecologically and economically critical plants, and many genes are conserved in syntenic blocks between species. Here we leverage that conserved gene order to create and describe the Pan-Grass Syntenic Gene Set (PGSGS), a curated database of orthologous and homeologous relationships among the genes of 17 grass species, including both major and orphan crops as well as wild grasses. As a demonstration of the utility of the PGSGS, the dynamics of chromosome structure and gene content changes after polypoidy in several grass lineages are analyzed. This dataset serves as a seminal foundation for improving our understanding of genome evolution subsequent to polyploidy, as well as encouraging and enabling integration of functional genetic and functional genomic information across the grasses, the original promise of the "grasses as a single genetic system" model. SIGNIFICANCE STATEMENTThe Pan-Grass Syntenic Gene Set (PGSGS) leverages our understanding of the genomic background of major grass species, including rice, maize, sorghum, wheat, barley, millet, and sugarcane. It represents a milestone for deciphering the genetic foundations of essential traits such as yield, disease resistance, and environmental adaptability - key factors contributing to agriculture and food security. Scrutinizing pan-syntenic genes unveils the intricate interplay of diverse gene acquisition and loss mechanisms, potentially speeding molecular breeding knowledge transference. The PGSGS emerges as a valuable resource for gene annotation, with implications for improving grass crops.

genomics↗

bioRxiv2024

The Genetic Puzzle of Multicopy Genes: Challenges and Troubleshooting

BackgroundStudies with multicopy genes impose challenges related to gene redundancy and sequence similarity among copies. Recent advances in molecular biology and genomics tools associated with dedicated databases facilitate their study. Thus, the present work emphasizes the need for rigorous methodologies and standardized approaches to interpret RT-qPCR results accurately. ResultsThe present work in Physcomitrium patens provides a comprehensive five-step protocol, using thiamine thiazole synthase (THI1) and sucrose 6-phosphate phosphohydrolase (S6PP) genes as proof of concept, to showcase a systematic workflow for studying multicopy genes. Beyond examining genes of interest, we highlight the critical role of choosing appropriate internal controls in the analytical process for accurately interpreting gene expression patterns. We emphasized the importance of identifying the most relevant orthologous gene, recognizing the inherent challenges in determining the most functional copy for subsequent studies. Our objective is to enhance comprehension of gene redundancy by dissecting multicopy genes genomic landscape and its characteristics. Furthermore, we address the decision-making process surrounding the quantification of expression levels of multicopy genes. ConclusionsThe study of multicopy genes discloses early events of functional adaptation. We emphasize the significance of multicopy genes in plant biology and provide a practical protocol for their study. Plant systems are strongly influenced by light/dark cycles, and the challenges inherent to this process are acknowledged. In conclusion, our comprehensive approach aims to advance the understanding of multicopy gene dynamics, offering practical methodologies and contributing valuable insights to the scientific community.

molecular biology↗

bioRxiv2023

THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually necessitates access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast datasets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and crucial cofactor in primary metabolic pathways. We conducted a comprehensive search for THI1 information within public repositories with careful curation to achieve this. Our searches reveal an evolutionary trend of 702 THI1 homologs of Archaea and Eukarya, with a detailed focus on plants. The green lineage of these organisms preserved the THI4 protein domain throughout its diversification by incorporating the N-terminus and targeting chloroplasts. Furthermore, evolutionary pressures and lifestyle appear to be associated with retention of TPP-riboswitch sites and consequent dual post-transcriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even successive rounds of genome duplications. Additionally, we identified the diversification of cis-regulatory sites in plants with the conservation of biological processes associated with the initial stages of seed development and preservation of the transcriptional pattern during the diurnal cycle. Our data mining of 484 transcriptome datasets supports this finding and brings a new look at public repositories and evolutionary trends to THI1.

plant biology↗

bioRxiv2020

Evidence-based gene expression modulation correlates with transposable element knock-down

BackgroundTransposable elements (TEs) are major components of plant genomes. Despite being regarded as "junk DNA" at first, TEs play important roles for the organisms they are found in. The most obvious and easily recognizable effects caused by TEs result from their mobility, which can disrupt coding sequences or promoter regions. However, with the recent advances in transcriptomics, it is becoming increasingly evident that TEs can act as an additional layer of gene expression regulation through a number of processes, which can involve production of non-coding RNAs. Here, we describe how Tnt1, a stress-responsive LTR-retrotransposon, interferes with gene expression and modulate a number of developmental aspects in tobacco. ResultsThrough an RNAi approach, we generated tobacco (HP) lines knocked-down for Tnt1 expression. Quantitative RT-PCR experiments confirm that Tnt1 is downregulated in HP lines after ethylene exposure. A RNA-seq experiment was performed and through two independent bioinformatic approaches (with different stringencies) we found 932 and 97 differentially expressed genes in HP lines. A number of phenotypes were observed in such lines, namely lesion mimicry in leaves, underdevelopment of the root system, overproduction of root hairs and early loss of seed viability. Folding prediction of part of the Tnt1 mRNA reveals putative stem-loop secondary structures containing transcriptional regulation sequences, suggesting it could be a source of small RNAs. We also propose a model to explain the Tnt1 expression in both homeostatic and stress conditions, and how it could interact with stress-responsive genes. ConclusionsOur results are consistent that interferences with Tnt1 transcript levels correlate with transcriptomic and phenotypic changes, suggesting a functional role for this element during plant development and stress response.

molecular biology↗

bioRxiv2018

Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane

BackgroundSugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (approximately 10 Gb) and a high content of repetitive regions. Gene expression mechanisms are poorly understood in these cultivars. An approach using genomic, transcriptomic and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane.\n\nResultsThe hypothetical HP600 and centromere protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behavior of this complex polyploid. The genomically side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog with all haplotypes of HP600 and CENP- C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing duplications of HP600 and CENP-C (paralogs). This duplication occurred before the Saccharum genus formation and after the separation of sorghum and sugarcane, resulting in a nonexpressed HP600 pseudogene and a recombined fusion version of CENP-C and orthologous gene Sobic.003G299500 with at least two chimerical gene haplotypes expressed. The genetic map construction supported the difficulty of mapping markers located in duplicated regions of complex polyploid genomes.\n\nConclusionAll these findings describe a low synteny region in sugarcane, formed by events occurring in all members of the Saccharum genus. Additionally, evidence of duplicated and truncate gene expression and the behavior of genetic markers in a duplicated region was found. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding the complex polyploid genome.

plant biology↗