Transposable element insertions are associated with batesian mimicry in the pantropical butterfly Hypolimnas misippus

Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three color morphs of D. chrysippus found in different regions of Africa. In this study, we examine the evolution of the M locus and identify it as an example of adaptive atavism. This phenomenon involves a morphological reversion to an ancestral character that results in an adaptive phenotype. We show that H. misippus has re-evolved an ancestral wing pattern present in other Hypolimnas species, repurposing it for Batesian mimicry of a D. chrysippus morph. Using haplotagging, a linked-read sequencing technology, and our new analytical tool, Wrath, we discover two large transposable element insertions located at the M locus and establish that these insertions are present in the dominant allele responsible for producing mimetic phenotype. By conducting a comparative analysis involving additional Hypolimnas species, we demonstrate that the dominant allele is derived. This suggests that, in the derived allele, the transposable elements disrupt a cis-regulatory element, leading to the reversion to an ancestral phenotype that is then utilized for Batesian mimicry of a distinct model, a different morph of D. chrysippus. Our findings present a compelling instance of convergent evolution and adaptive atavism, in which the same pattern element has independently evolved multiple times in Hypolimnas butterflies, repeatedly playing a role in Batesian mimicry of diverse model species

Haplotagging: haplotype phasing and single-tube combinatorial barcoding of nucleic acid molecules using bead-immobilized Tn5 transposase

The present invention relates to methods for producing solid supports. The present invention further provides a mixture of said solid supports for tagmentation of target DNA for DNA sequencing approaches, a corresponding kit comprising the same and methods employing said mixture of solid supports and/or kit. Specifically, methods for producing sequencing libraries and corresponding DNA sequencing methods for analyzing the generated sequencing libraries and tools used therein are provided. In particular, DNA sequencing approaches allowing preservation of contiguity information of long DN A fragments even when using short read sequencing approaches are disclosed. A key concept of the present invention is to employ segmented barcodes, with every barcode segmented allowing for barcode error detection and correction on a segment level. Preferred barcode sequences employed are characterized in that they comprise no linker sequences or only linker sequences of one or two nucleotides in length between the barcode segments

Allelic bias and genetic mapping of differentiation potential revealed by single-cell transcriptomics in recombinant hybrid mouse embryonic stem cells

Self-renewal and pluripotency are twin hallmarks of embryonic stem cells. Every cell in an early embryo must balance between differentiation and proliferation, often involving irreversible fate decisions. However, there are very few studies that directly investigate how these gene pathways evolve between species, because crosses between species usually fail. Here, we combine in vitro recombination (IVR) and single-cell transcriptomics in F1 hybrid embryonic stem (ES) cells to determine the genes and loci influencing the decision between renewal vs. differentiation. Through RNAi suppression of Blm helicase, we effectively produced recombinant ES cells between the laboratory C57BL/6N mouse and Mus spretus. We then induced differentiation and obtained single-cell transcriptomes on ~20,000 IVR cells. Using reference scRNAseq datasets from naïve and differentiated non-recombinant cells, we show that in vitro recombination boosted genotypic and expression diversity. We found that the genetic reshuffling under IVR produced cells that can sustain robust Nanog stemness marker expression despite differentiating treatments. Moreover, we observed that allele-specific expression increased with differentiation, possibly from recombinant cells. We also found that SPRET alleles were enriched in highly differentiated cells. Our work shows that by combining in vitro recombination and single-cell assays, it is now possible to directly map genes controlling otherwise inaccessible cellular phenotypes across species

Characterization of purinergic P2X4 receptor channels expressed in anterior pituitary cells

Anterior pituitary cells express cation-conducting P2X receptor channels (P2XRs), but their molecular identity, electrophysiological properties, cell-specific expression pattern, and physiological roles have been only partially characterized. In this study, we show by quantitative RT-PCR that mRNA transcripts for the P2X4 subunit are the most abundant in rat anterior pituitary tissue and confirm the P2X4R protein expression by Western blot analysis. Single-cell patch-clamp recordings show that extracellular ATP induced an inward depolarizing current in a majority of thyrotropin-releasing hormone-responsive pituitary cells, which resembled the current profile generated by recombinant P2X4R. The channels were activated and desensitized in a dose-dependent manner and deactivated rapidly. Activation of these channels led to stimulation of electrical activity and promotion of voltage-gated and voltage-insensitive Ca2+ influx. In the presence of ivermectin, a specific allosteric modulator of P2X4Rs, there was an approximately fourfold increase in the maximum amplitude of the ATP-induced inward current, accompanied by an increase in the sensitivity of receptors for ATP, slowed deactivation of receptors, and enhanced ATP-induced prolactin release. These results indicate that thyrotropin-releasing hormone-responsive cells, including lactotrophs, express homomeric and/or heteromeric P2X4Rs, which facilitate Ca2+ influx and hormone secretion

Rapid genotype imputation from sequence with reference panels

Inexpensive genotyping methods are essential to modern genomics. Here we present QUILT, which performs diploid genotype imputation using low-coverage whole-genome sequence data. QUILT employs Gibbs sampling to partition reads into maternal and paternal sets, facilitating rapid haploid imputation using large reference panels. We show this partitioning to be accurate over many megabases, enabling highly accurate imputation close to theoretical limits and outperforming existing methods. Moreover, QUILT can impute accurately using diverse technologies, including long reads from Oxford Nanopore Technologies, and a new form of low-cost barcoded Illumina sequencing called haplotagging, with the latter showing improved accuracy at low coverages. Relative to DNA genotyping microarrays, QUILT offers improved accuracy at reduced cost, particularly for diverse populations that are traditionally underserved in modern genomic analyses, with accuracy nearly doubling at rare SNPs. Finally, QUILT can accurately impute (four-digit) human leukocyte antigen types, the first such method from low-coverage sequence data