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Abstract Allele-specific gene expression evolves rapidly on heteromorphic sex chromosomes. Over time, the accumulation of mutations on the Y chromosome leads to widespread loss of gametolog expression, relative to the X chromosome. It remains unclear if expression evolution on degrading Y chromosomes is primarily driven by mutations that accumulate through processes of selective interference, or if positive selection can also favor the down-regulation of coding regions on the Y chromosome that contain deleterious mutations. Identifying the relative rates of cis-regulatory sequence evolution across Y chromosomes has been challenging due to the limited number of reference assemblies. The threespine stickleback (Gasterosteus aculeatus) Y chromosome is an excellent model to identify how regulatory mutations accumulate on Y chromosomes due to its intermediate state of divergence from the X chromosome. A large number of Y-linked gametologs still exist across 3 differently aged evolutionary strata to test these hypotheses. We found that putative enhancer regions on the Y chromosome exhibited elevated substitution rates and decreased polymorphism when compared to nonfunctional sites, like intergenic regions and synonymous sites. This suggests that many cis-regulatory regions are under positive selection on the Y chromosome. This divergence was correlated with X-biased gametolog expression, indicating the loss of expression from the Y chromosome may be favored by selection. Our findings provide evidence that Y-linked cis-regulatory regions exhibit signs of positive selection quickly after the suppression of recombination and allow comparisons with recent theoretical models that suggest the rapid divergence of regulatory regions may be favored to mask deleterious mutations on the Y chromosome. 

Existing studies on semantic parsing focus primarily on mapping a natural-language utterance to a corresponding logical form in one turn. However, because natural language can contain a great deal of ambiguity and variability, this is a difficult challenge. In this work, we investigate an interactive semantic parsing framework that explains the predicted logical form step by step in natural language and enables the user to make corrections through natural-language feedback for individual steps. We focus on question answering over knowledge bases (KBQA) as an instantiation of our framework, aiming to increase the transparency of the parsing process and help the user appropriately trust the final answer. To do so, we construct INSPIRED, a crowdsourced dialogue dataset derived from the ComplexWebQuestions dataset. Our experiments show that the interactive framework with human feedback has the potential to greatly improve overall parse accuracy. Furthermore, we develop a pipeline for dialogue simulation to evaluate our framework w.r.t. a variety of state-of-the-art KBQA models without involving further crowdsourcing effort. The results demonstrate that our interactive semantic parsing framework promises to be effective across such models. 

Alternate isoforms are important contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five organs in threespine stickleback fish ( Gasterosteus aculeatus ), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly in which gene annotations are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq-predicted transcription start sites were more accurate and verified through ATAC-seq. We also detected many alternative splicing events between sexes and across organs. We found a substantial number of genes in both somatic and gonadal samples that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish. 

Abstract While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we assembled a highly contiguous genome of a freshwater fish from Paxton Lake. Using contigs from this genome, we were able to fill over 76.7% of the gaps in the existing reference genome assembly, improving contiguity over fivefold. Our gap filling approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish. 

Coupling between exciton states across the Brillouin zone in monolayer transition metal dichalcogenides can lead to ultrafast valley depolarization. Using time- and angle-resolved photoemission, we present momentum- and energy-resolved measurements of exciton coupling in monolayer WS2. By comparing full 4D (kx,ky,E,t) data sets after both linearly and circularly polarized excitation, we are able to disentangle intervalley and intravalley exciton coupling dynamics. Recording in the exciton binding energy basis instead of excitation energy, we observe strong mixing between the B1s exciton and An>1 states. The photoelectron energy and momentum distributions observed from excitons populated via intervalley coupling (e.g. K− → K+) indicate that the dominant valley depolarization mechanism conserves the exciton binding energy and center-of-mass momentum, consistent with intervalley Coulomb exchange. On longer timescales, exciton relaxation is accompanied by contraction of the momentum space distribution.