Brayer, M. | Search bioRxiv

bioRxiv2026

The ivory:mir-193 non-coding RNA gene controls melanic camouflage in a polymorphic moth

A majority of moths use melanic pigmentation to blend into the visual environment, and some species display genetically controlled color polymorphisms that provide tractable systems for dissecting the genetic basis of camouflage. Here we leveraged the natural polymorphism of Anticarsia gemmatalis moths to map a major-effect gene that controls melanic variation, and study its developmental roles using expression and loss-of-function assays. A genome-wide association mapping identifies the ivory:mir-193 non-coding RNA locus as a major locus of melanic variation, with highly-divergent haplotypes differentiating the Light and Dark morphs. Second, the expression of ivory:mir-193 prefigures the melanic coloration of each morph, and suggests that cis-regulatory variation at this locus determines the difference in adult pattern. Finally, CRISPR disruption of the ivory promoter and mir-193 hairpin region each abolish melanic scale pigmentation, demonstrating that this lnc-pri-miRNA module is required for dark-scale differentiation. These findings corroborate the emerging role of ivory:mir-193 as a key factor in the development of melanic patterning, and highlight its unique propensity to repeatedly drive phenotypic variation of adaptive potential in butterflies and moths. HighlightsO_LIAnticarsia gemmatalis display striking variation in camouflage patterns C_LIO_LIDark vs. Light color polymorphism map to the ivory:mir-193 hotspot locus C_LIO_LIHighly-diverged haplotypes drive morph-specific expression of ivory:mir-193 C_LIO_LIThe miR-193 miRNA is required for melanic scale development C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/707733v2_ufig1.gif" ALT="Figure 1"> View larger version (80K): org.highwire.dtl.DTLVardef@8e491eorg.highwire.dtl.DTLVardef@1628425org.highwire.dtl.DTLVardef@d1b691org.highwire.dtl.DTLVardef@29247b_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2020

Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

BackgroundSARS-CoV-2 genotyping has been instrumental to monitor virus evolution and transmission during the pandemic. The reliability of the information extracted from the genotyping efforts depends on a number of aspects, including the quality of the input material, applied technology and potential laboratory-specific biases. These variables must be monitored to ensure genotype reliability. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in studies of viral spread and evolution. ResultsWe used clinical samples and synthetic viral genomes to evaluate the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination using an amplicon-based approach. We found that at least 1000 viral genomes are necessary to confidently detect variants in the genome at frequencies of 10% or higher. The broad applicability of our recommendations was validated in >200 clinical samples from six independent laboratories. The genotypes of clinical isolates with viral load above the recommended threshold cluster by sampling location and period. Our analysis also supports the rise in frequency of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was favoured by travelling during the summer 2020. ConclusionsWe present much-needed recommendations for reliable determination of SARS-CoV-2 genome sequence and demonstrate their broad applicability in a large cohort of clinical samples.

genomics↗