Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus

This is the final version. Available on open access from Oxford University Press via the DOI in this recordData availability: The assembly and annotation are available at the European Nucleotide Archive project accession: PRJEB47812. Additional data files are provided at https://doi.org/10.5281/zenodo.5731560: purged haplotigs, assembly before manual edits, details of manual edits made to the assembly, and repeat library and functional annotation files. Scripts for genome assembly are available at https://github.com/kumarsaurabh20/DChry2.1 (last accessed 5 October 2021) and scripts for the genome annotation and analysis of introns and exons at https://github.com/RishiDeKayne/Danaus_Dchry2.2_annotation (last accessed 5 October 2021).Milkweed butterflies in the genus Danaus are studied in a diverse range of research fields including the neurobiology of migration, biochemistry of plant detoxification, host-parasite interactions, evolution of sex chromosomes, and speciation. We have assembled a nearly chromosomal genome for Danaus chrysippus (known as the African Monarch, African Queen, and Plain Tiger) using long-read sequencing data. This species is of particular interest for the study of genome structural change and its consequences for evolution. Comparison with the genome of the North American Monarch Danaus plexippus reveals generally strong synteny but highlights 3 inversion differences. The 3 chromosomes involved were previously found to carry peaks of intraspecific differentiation in D. chrysippus in Africa, suggesting that these inversions may be polymorphic and associated with local adaptation. The D. chrysippus genome is over 40% larger than that of D. plexippus, and nearly all of the additional ∼100 Megabases of DNA comprises repeats. Future comparative genomic studies within this genus will shed light on the evolution of genome architecture.Royal SocietySwiss National Science FoundationEuropean Union Horizon 202

Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus

This is the final version. Available on open access from Oxford University Press via the DOI in this recordData availability: The assembly and annotation are available at the European Nucleotide Archive project accession: PRJEB47812. Additional data files are provided at https://doi.org/10.5281/zenodo.5731560: purged haplotigs, assembly before manual edits, details of manual edits made to the assembly, and repeat library and functional annotation files. Scripts for genome assembly are available at https://github.com/kumarsaurabh20/DChry2.1 (last accessed 5 October 2021) and scripts for the genome annotation and analysis of introns and exons at https://github.com/RishiDeKayne/Danaus_Dchry2.2_annotation (last accessed 5 October 2021).Milkweed butterflies in the genus Danaus are studied in a diverse range of research fields including the neurobiology of migration, biochemistry of plant detoxification, host-parasite interactions, evolution of sex chromosomes, and speciation. We have assembled a nearly chromosomal genome for Danaus chrysippus (known as the African Monarch, African Queen, and Plain Tiger) using long-read sequencing data. This species is of particular interest for the study of genome structural change and its consequences for evolution. Comparison with the genome of the North American Monarch Danaus plexippus reveals generally strong synteny but highlights 3 inversion differences. The 3 chromosomes involved were previously found to carry peaks of intraspecific differentiation in D. chrysippus in Africa, suggesting that these inversions may be polymorphic and associated with local adaptation. The D. chrysippus genome is over 40% larger than that of D. plexippus, and nearly all of the additional ∼100 Megabases of DNA comprises repeats. Future comparative genomic studies within this genus will shed light on the evolution of genome architecture.Royal SocietySwiss National Science FoundationEuropean Union Horizon 202

Stepwise evolution of a butterfly supergene via duplication and inversion.

This is the final version. Available from the Royal Society via the DOI in this record. Data accessibility Sequencing reads and assemblies are available at the European Nucleotide Archive project (see the electronic supplementary material, table S1 for accession numbers [48]). Assemblies are available in the European Nucleotide Archive project accession PRJEB52180. Additional data files are available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.xwdbrv1g0 [49], including genome assemblies and annotations, repeat library and windowed repeat content, whole-genome alignments, VCF and genotype files, window-based diversity and divergence measures and read depth, sequence alignments for genes and phylogenetic trees. Scripts for assembly polishing, the analysis of repeat content, genome annotation and phylogenetic tree construction are available at https://github.com/RishiDeKayne/Danaus_supergene_structure. Scripts for genome alignment and synteny block inference, ancestry painting and divergence analyses, and read depth and copy number analyses are available at https://github.com/simonhmartin/Danaus_supergene_structure.Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning coloration in the African monarch butterfly, Danaus chrysippus. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that a region of more than 1 million bp underwent several segmental duplications at least 7.5 Ma. The resulting duplicated fragments appear to have triggered four inversions in surrounding parts of the chromosome, resulting in stepwise growth of the region of suppressed recombination. Phylogenies for the inversions are incongruent with the species tree and suggest that structural polymorphisms have persisted for at least 4.1 Myr. In addition to the role of duplications in triggering inversions, our results suggest a previously undescribed mechanism of recombination suppression through independent losses of divergent duplicated tracts. Overall, our findings add support for a stepwise model of supergene evolution involving a variety of structural changes. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.Royal SocietyRoyal SocietySwiss National Science Foundation (SNSF)National Geographic Societ

The role of morphological markedness in the processing of number and gender agreement in Spanish: an event-related potential investigation

Current morphological theory assumes that feature values, such as masculine and feminine or singular and plural, are asymmetrically represented. That is, one member of the opposition (e.g. feminine for gender, plural for number) is assumed to be marked, and the other one, unmarked. The present study examines how these asymmetries impact agreement resolution in Spanish. Agreement was manipulated between a noun acting as head of a relative clause and an adjective located inside the relative clause (e.g. catedral que parecía inmensa “cathedral that looked huge”). Half of the nouns were feminine (marked) and the other half, masculine (unmarked). Half of the nouns were used in the plural (marked) and the other half, in the singular (unmarked). Twenty-seven Spanish native speakers read 240 sentences while their brain activity was recorded with EEG and performed a grammaticality judgment. Results showed that both number and gender violations elicited a central-posterior P600, a component associated with syntactic repair, and a late anterior negativity, argued to reflect working memory costs. Only the P600 was affected by markedness. It started earlier for violations where the mismatching feature was marked. Moreover, it was larger for errors where the mismatching feature was marked, although this amplitude modulation only emerged for number, possibly due to differences in how number and gender cues were realized (i.e. both masculine and feminine showed overt inflection, but singular was uninflected relative to plural). These results suggest that the parser is sensitive to markedness asymmetries in the course of online processing

The application of rules in morphology, syntax and number processing: a case of selective deficit of procedural or executive mechanisms?: Deficit of procedural or executive mechanisms

International audienceDeclarative memory is a long-term store for facts, concepts and words. Procedural memory subserves the learning and control of sensorimotor and cognitive skills, including the mental grammar. In this study, we report a single-case study of a mild aphasic patient who showed procedural deficits in the presence of preserved declarative memory abilities. We administered several experiments to explore rule application in morphology, syntax and number processing. Results partly support the differentiation between declarative and procedural memory. Moreover, the patient's performance varied according to the domain in which rules were to be applied, which underlines the need for more fine-grained distinctions in cognition between procedural rules

Negative Concord in Russian. An Overview

In this article I will describe the general properties of Negative Concord in Russian, which is a strict Negative Concord language, where all negative indefinites must co-occur with sentential negation. However, there are several cases where the negation marker can be absent (like in fragment answers) or can appear in a non-standard position (like at the left of an embedded infinitival). I will take into consideration all these specific cases described by the literature on the negation system of Russian and analyse them according to current approaches to Negative Concord

Infinitive Wh-relatives in romance : consequences for the truncation-versus-intervention debate

Romance clitic left dislocation is widespread across all kinds of nonroot contexts, but it is forbidden in infinitive wh-relatives. This article investigates the extent and nature of this restriction and the consequences it raises for the truncation and intervention analyses of the left periphery of embedded sentences. We will show that current proposals cannot account for the whole gamut of data. In consequence, we will propose that infinitive wh-relatives display a maximally syncretic left periphery, whereas infinitive wh-interrogatives have a full-fledged left periphery, crucially involving ForceP, because they are selected by a higher predicate. This crucial difference between infinitive relatives and interrogatives will also be shown to be consistent with the existence of specialized complementizers for the former but not the latte

Regulation of Budding Yeast Mating-Type Switching Donor Preference by the FHA Domain of Fkh1

During Saccharomyces cerevisiae mating-type switching, an HO endonuclease-induced double-strand break (DSB) at MAT is repaired by recombining with one of two donors, HMLα or HMRa, located at opposite ends of chromosome III. MATa cells preferentially recombine with HMLα; this decision depends on the Recombination Enhancer (RE), located about 17 kb to the right of HML. In MATα cells, HML is rarely used and RE is bound by the MATα2-Mcm1 corepressor, which prevents the binding of other proteins to RE. In contrast, in MATa cells, RE is bound by multiple copies of Fkh1 and a single copy of Swi4/Swi6. We report here that, when RE is replaced with four LexA operators in MATa cells, 95% of cells use HMR for repair, but expression of a LexA-Fkh1 fusion protein strongly increases HML usage. A LexA-Fkh1 truncation, containing only Fkh1's phosphothreonine-binding FHA domain, restores HML usage to 90%. A LexA-FHA-R80A mutant lacking phosphothreonine binding fails to increase HML usage. The LexA-FHA fusion protein associates with chromatin in a 10-kb interval surrounding the HO cleavage site at MAT, but only after DSB induction. This association occurs even in a donorless strain lacking HML. We propose that the FHA domain of Fkh1 regulates donor preference by physically interacting with phosphorylated threonine residues created on proteins bound near the DSB, thus positioning HML close to the DSB at MAT. Donor preference is independent of Mec1/ATR and Tel1/ATM checkpoint protein kinases but partially depends on casein kinase II. RE stimulates the strand invasion step of interchromosomal recombination even for non-MAT sequences. We also find that when RE binds to the region near the DSB at MATa then Mec1 and Tel1 checkpoint kinases are not only able to phosphorylate histone H2A (γ-H2AX) around the DSB but can also promote γ-H2AX spreading around the RE region