David Swarbreck

EISCA and EISTA: Full-Spectrum Pipelines for Single-Cell and Spatial Transcriptomics Analysis

EISCA and EISTA are pipelines for single-cell and spatial transcriptomics analysis that provide standardized, modular workflows for data processing and downstream analysis.

Long-read single-cell genomics: resolving chimeras in multiple displacement amplification

The paper develops lrSAGA, a tool to improve genome assembly from long-read MDA sequencing of single cells, achieving higher completeness and fewer misassemblies.

Evolutionary Rewiring of Root Cell-Type Nitrogen Responses

The paper shows that nitrogen responses in plant roots are cell-type specific and evolve across species, with NLP7 proteins modulating these responses in Arabidopsis and tomato.

Chromosome-scale genome assembly of diploid halophyte Thinopyrum bessarabicum excludes J genome from polyploid Thinopyrum ancestry

This paper presents a chromosome-scale genome of Thinopyrum bessarabicum, showing the J genome is not part of polyploid Thinopyrum ancestry and identifies genomic features linked to salt tolerance.

Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts

The paper uses single-cell sequencing to reveal genetic diversity in Bodo flagellates and their bacterial endosymbionts, showing SSU rDNA is insufficient for species classification.

Whole genome sequencing reveals how plasticity and genetic differentiation underlie sympatric morphs of Arctic charr

The paper uses whole genome sequencing to analyze genetic differentiation and plasticity in sympatric morphs of Arctic charr across multiple lakes, revealing a polygenic basis and varying levels of reproductive isolation.

A comparison of long-read single-cell transcriptomic approaches

This study compares long-read single-cell sequencing platforms, identifying common limitations and demonstrating their utility for isoform-resolved analyses.

Leveraging existing data to maximise quality and consistency across gene model annotations: a Fusarium pan-annotation

This paper improves gene model annotations across 82 Fusarium genomes by combining existing annotations with de novo predictions, enhancing consistency and quality for comparative genomics.

High-quality genome assembly for the genetically improved Abbassa Nile tilapia enables the reconstruction of X and Y haplotypes

The paper presents a high-quality genome assembly for the GIANT Nile tilapia strain, enabling the reconstruction of X and Y haplotypes and identifying sex determination loci on LG23.

A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition

Biosynthesis and Bioactivity of Anti-Inflammatory Triterpenoids in Calendula officinalis (pot marigold)

This study identifies C16-hydroxylated triterpenoids as key anti-inflammatory compounds in Calendula officinalis and reconstructs their biosynthetic pathway for production.

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

This study presents a chromosome-scale genome assembly and annotation of Alopecurus aequalis, revealing its genetic similarity to barley and expansion of herbicide resistance genes.

Multiple Independent Genetic Code Reassignments of the UAG Stop Codon in Phyllopharyngean Ciliates

The paper identifies multiple independent reassignments of the UAG stop codon to encode amino acids in Phyllopharyngean ciliates, showing UAG as a sense codon and UAA as the fixed stop codon.

The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion.

The paper presents a reference genome assembly for the Violet Carpenter Bee, including gene annotation and mitochondrial genome, as part of the European Reference Genome Atlas.

De novo annotation of the wheat pangenome reveals complexity and diversity of the hexaploid wheat pan-transcriptome

This study annotates the wheat pan-transcriptome de novo and identifies gene diversity and expression patterns across multiple wheat cultivars and tissues.

Identification of a Non-Canonical Ciliate Nuclear Genetic Code Where UAA and UAG Code for Different Amino Acids

The paper identifies a non-canonical genetic code in a ciliate where UAA and UAG codons specify different amino acids, challenging the universality of the genetic code.

Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus

The paper presents a chromosome-level genome assembly for the GIFT tilapia strain, identifying introgressed regions from O. mossambicus associated with growth and immunity traits.

Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes

The paper uses long-read sequencing to identify novel isoforms and splicing regulators during neuronal differentiation in human neuroblastoma cells.

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

The paper presents a chromosome-scale rye genome assembly to study genomic evolution and agronomic traits in Triticeae crops.

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

The paper presents chromosome-scale genome assemblies of aphids, revealing extensive autosome rearrangements and X chromosome conservation over 30 million years.

A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume

Grass pea, a diploid legume with a 6.3 Gbp genome, gets two draft assemblies, one short-read and one Nanopore, plus 33,819 annotated genes.

An aphid host-responsive RNA transcript that migrates systemically in plants promotes aphid reproduction

The paper identifies an aphid gene family that translocates RNA into plants, promoting aphid reproduction and indicating cross-kingdom RNA deployment.

Sex-specific changes in the aphid DNA methylation landscape

This study analyzes DNA methylation and gene expression differences between male and asexual female morphs of the green peach aphid, finding sex-specific methylation patterns linked to sexual differentiation.

Genome-wide transcription during early wheat meiosis is independent of synapsis, ploidy level and the Ph1 locus

The paper analyzes RNA-Seq data from wheat and related species to show that gene expression during early meiosis is not significantly affected by synapsis, ploidy level, or the Ph1 locus.

Efficient and accurate detection of splice junctions from RNAseq with Portcullis

Portcullis filters false splice junctions from RNA-seq alignments with high accuracy and efficiency, scaling well for large datasets and fragmented genomes.

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

The paper presents an algorithm to improve transcript annotation by integrating multiple RNA-Seq assemblies and introduces an open-source tool for this purpose.

The ash dieback invasion of Europe was founded by two individuals from a native population with huge adaptive potential

The paper analyzes the genetic diversity of Hymenoscyphus fraxineus, showing the European population was founded by two divergent haplotypes with adaptive potential.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

A clonally reproducing generalist aphid pest colonises diverse host plants by rapid transcriptional plasticity of duplicated gene clusters

This study shows that the green peach aphid uses rapid transcriptional changes of duplicated genes to colonize diverse host plants without genetic specialization.

Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community.

The paper reports on a crowdsourced project analyzing ash dieback fungus data, revealing insights into its genome and biology through community contributions.