Enhancer identification and activity evaluation in the red flour beetle,<i>Tribolium castaneum</i>

Lai, Yi-Ting; Deem, Kevin D.; Borràs-Castells, Ferran; Sambrani, Nagraj; Rudolf, Heike; Suryamohan, Kushal; El-Sherif, Ezzat; Halfon, Marc S.; McKay, Daniel J.; Tomoyasu, Yoshinori

doi:10.1101/199729

Cited by 18 publications

(30 citation statements)

References 62 publications

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“…This striking example of conservation illustrates that further comparative approaches have the potential to identify conserved regulatory networks involving microRNAs within insects based on the resources provided here. Enhanced coverage with RNA data revealed the transcription start sites of most genes, which helps in the design of genome editing approaches and of transgenic constructs based on endogenous enhancers and promoters [22,23,35,59].…”

Section: Discussionmentioning

confidence: 99%

Enhanced genome assembly and a new official gene set for Tribolium castaneum

et al. 2020

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Background: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. Results: Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. Conclusions: The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.

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Section: Discussionmentioning

confidence: 99%

Enhanced genome assembly and a new official gene set for Tribolium castaneum

et al. 2020

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“…A 'cross-wiring' of the two similar gene regulatory networks (GRNs) operating in the tergal and pleural wing serial homologs is one possible mechanism that has been proposed [2,4], while co-option of a GRN capable of inducing a certain characteristic (such as a flat outgrowth) into the lateral body wall is another [19]. The application of cis analyses to the investigation of wing origin (such as Requena et al) and the comparison of cis regulation of wing genes between various insects [20] will be quite powerful in elucidating the processes that facilitated the evolution of insect wings at the molecular level. The origin of insect wings is a fascinating mystery that has captivated scientists for many years.…”

Section: Current Biologymentioning

confidence: 99%

Evo–Devo: The Double Identity of Insect Wings

Tomoyasu

2018

Current Biology

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“…A particular enhancer was shown to drive comparable expression across 9 species of vertebrates including fishes, lizards, snakes and mice (Kvon et al, 2016). In insects, several enhancers have been tested and observed to drive similar expression patterns in Drosophila , mosquitoes (248 My divergence) and Tribolium (309 My divergence [Cande, Goltsev, & Levine, 2009; Lai et al, 2018]). Several native promoters of Drosophila have been tested and they have been found to function in Lepidoptera (286 My divergence [Imamura et al, 2003; Ramos, Kamal, Wimmer, Cartwright, & Monteiro, 2006; Tamura et al, 2000]) but not in Tribolium (Schinko et al, 2010).…”

Section: Resultsmentioning

confidence: 99%

Evaluating the probability of CRISPR‐based gene drive contaminating another species

Courtier‐Orgogozo

Danchin

Gouyon

et al. 2020

Evolutionary Applications

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The probability D that a given clustered regularly interspaced short palindromic repeats (CRISPR)‐based gene drive element contaminates another, nontarget species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D=hyb+transf×express×cut×flank×immune×nonextinct with hyb = probability of hybridization between the target species and a nontarget species; transf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a nontarget species (with no hybridization); express = probability that the Cas9 and guide RNA genes are expressed; cut = probability that the CRISPR‐guide RNA recognizes and cuts at a DNA site in the new host; flank = probability that the gene drive cassette inserts at the cut site; immune = probability that the immune system does not reject Cas9‐expressing cells; nonextinct = probability of invasion of the drive within the population. We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. We conclude from current data that the probability of a gene drive cassette to contaminate another species is not insignificant. We propose strategies to reduce this risk and call for more work on estimating all the parameters of the formula.

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Enhancer identification and activity evaluation in the red flour beetle,Tribolium castaneum

Cited by 18 publications

References 62 publications

Enhanced genome assembly and a new official gene set for Tribolium castaneum

Enhanced genome assembly and a new official gene set for Tribolium castaneum

Evo–Devo: The Double Identity of Insect Wings

Evaluating the probability of CRISPR‐based gene drive contaminating another species

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