Improved Protocol for Isolation of High-Quality Total RNA from Different Organs of
            <i>Phaseolus Vulgaris</i>
            L.

Acosta‐Maspons, Alexis; González-Lemes, Ingrid; Covarrubias, Alejandra A.

doi:10.2144/btn-2018-0129

Cited by 7 publications

(5 citation statements)

References 19 publications

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“…(2019, ref. 68 ), which is a CTAB based method for high-quality total RNA applications from different plant tissues. The remaining DNA was removed with the TURBO DNA-free Kit (Invitrogen), designed for optimal preservation of RNA during the DNase treatment.…”

Section: Rna Extraction and Library Preparation For Long-read Pacbio Iso-sequencingmentioning

confidence: 99%

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Kersten

Chang

Voichek

et al. 2021

Preprint

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Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.

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Section: Rna Extraction and Library Preparation For Long-read Pacbio Iso-sequencingmentioning

confidence: 99%

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Kersten

Chang

Voichek

et al. 2021

Preprint

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“…The RNeasy kit (2.02 ± 0.13; succinate), RNeasy power plant kit (2.12 ± 0.05; succinate, 2.02 ± 0.18; phenol) and modified RNAzol RT (2.32 ± 0.07; succinate, 2.10 ± 0.27; phenol, 1.95 ± 0.11; 2,4-TDA) showed values that correspond to high RNA purity ( Table 1 ). On the other hand, phenol/chloroform and TriFast methods revealed lower A 260 /A 280 (≤ 1.85) and A 260 /A 230 (≤ 1.65) ratios for succinate and phenol samples, which indicates organic contamination that compromises the RNA quality [ 23 , 26 , 38 , 41 , 42 ]. For these two methods, the ratios could not be measured for 2,4-TDA because the RNA concentration was below the detection limit [ 43 ].…”

Section: Resultsmentioning

confidence: 99%

An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene

et al. 2021

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Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.

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“…To increase transcriptome diversity, we extracted more RNA using a different method. Total RNA was extracted for RNA-Seq (RCC1521 and rt-383) and Iso-Seq (from rt-383) following Acosta-Maspons et al (2019) with slight modifications. Cells were first pelleted by centrifugation (300 g , 5 min).…”

Section: Methodsmentioning

confidence: 99%

Massive genome reduction occurred prior to the origin of coral algal symbionts

Shah

Dougan

Chen

et al. 2023

Preprint

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Dinoflagellates in the Family Symbiodiniaceae (Order Suessiales) represent diverse, predominantly symbiotic lineages that associate with taxa such as corals and jellyfish. Their ancestor is believed to have been free-living, and the establishment of symbiosis (i.e., symbiogenesis) is hypothesised to have occurred multiple times during Symbiodiniaceae evolution. Among Symbiodiniaceae taxa, the genusEffreniumis an early diverging, free-living lineage that is phylogenetically positioned between two robustly supported groups of genera within which symbiotic taxa have emerged. The lack of symbiogenesis inEffreniumsuggests that the ancestral features of Symbiodiniaceae may have been retained in this lineage. Here we present de novo assembled genomes and associated transcriptome data from three isolates ofEffrenium voratum. We compared theEffreniumgenomes (1.2-1.9 Gbp in size) and gene features with those of 16 Symbiodiniaceae taxa and other outgroup dinoflagellates. Surprisingly, we find that genome reduction predates the origin of Symbiodiniaceae and is not primarily explained by their symbiotic lifestyle. We postulate that adaptation to an extreme habitat (e.g., as inPolarella glacialis) or life in oligotrophic conditions resulted in the Suessiales ancestor having a haploid genome size < 2Gbp, which is retained (or smaller) among all extant algae in this lineage. Our data reveal that the free-living lifestyle distinguishesEffreniumfrom symbiotic Symbiodiniaceae vis-à-vis longer introns, more-extensive mRNA editing, fewer (~30%) lineage-specific gene families, and lower (~10%) level of pseudogenisation. These results demonstrate how genome reduction and the adaptation to symbiotic versus free-living lifestyles intersect, and have driven the diversification and genome evolution of Symbiodiniaceae.

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Improved Protocol for Isolation of High-Quality Total RNA from Different Organs of Phaseolus Vulgaris L.

Cited by 7 publications

References 19 publications

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene

Massive genome reduction occurred prior to the origin of coral algal symbionts

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