Biology subjects

Thomas, W. K.

Publications and source records attributed to Thomas, W. K..

3 recordsLinked to original sources

bioRxiv2025

A Single Cell Atlas of the Newt Iris During Lens Regeneration

Iris pigmented epithelial (IPE) cells transdifferentiate to lens epithelial cells (LECs) during Wolffian lens regeneration in newts. Single cell RNA sequencing was used at multiple timepoints to further our understanding of this process and the cells involved in it. All major cell types present in and adjacent to the iris were identified including IPE cells, macrophages, non-pigmented ciliary epithelial cells, pigmented ciliary epithelial cells, and stroma-residing fibroblasts, endothelial cells, iridophores, and melanocytes. In the intact iris, IPE cell subpopulations were characterized by the expression of the dorsoventral genes TBX5 and VAX2, and newly identified markers LTBP2, CHRM3, and NTN1. During regeneration, IPE heterogeneity was correlated with functional states such as the cell cycle, migration, and lens vesicle formation. Pseudotime trajectory analysis revealed new insights into transcriptional and reprogramming factors during the IPE-to-LEC conversion and built a molecular and genetic blueprint of newt lens regeneration. Macrophages were identified as tissue-resident and underwent polarization from M1 early to M2 late during lens regeneration, an event that correlated temporally with the IPE-to-LEC reprogramming. Overall, this atlas provides data and analysis for iris cell types, IPE subpopulations, IPE cell states, gene expression changes as IPE cells reprogram to LECs, macrophage identity and function, and cell-to-cell interactions during newt lens regeneration. Highlights- Cell atlas identifying cells in the newt iris at multiple timepoints during lens regeneration - Intact iris contains multiple iris pigmented epithelial (IPE) cell subpopulations - Identification of IPE functional states during regeneration - Cellular trajectory analysis revealed a molecular and genetic blueprint of IPE-to-lens epithelial cell reprogramming - Identification of cell-to-cell interactions between IPE cells and other cell types - Macrophages interacting with IPE cells are tissue-resident and polarize from M1 to M2 subtypes during lens regeneration Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/692619v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1883f94org.highwire.dtl.DTLVardef@622d9org.highwire.dtl.DTLVardef@d9ed30org.highwire.dtl.DTLVardef@1631d03_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery.

Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source of assembly gaps. This makes it difficult to decipher the impact of these elements on the dynamics of genome evolution. The increased capacity of long-read sequencing technologies to span highly repetitive regions of the genome should provide novel insights into patterns of TE diversity. Here we report the generation of highly contiguous reference genomes using PacBio long read and Omni-C technologies for three species of sparrows in the family Passerellidae. To assess the influence of sequencing technology on TE annotation, we compared these assemblies to three chromosome-level sparrow assemblies recently generated by the Vertebrate Genomes Project and nine other sparrow species generated using a variety of short- and long-read technologies. All long-read based assemblies were longer in length (range: 1.12-1.41 Gb) than short-read assemblies (0.91-1.08 Gb). Assembly length was strongly correlated with the amount of repeat content, with longer genomes showing much higher levels of repeat content than typically reported for the avian order Passeriformes. Repeat content for the Bells sparrow (31.2% of genome) was the highest level reported to date for a songbird genome assembly and was more in line with woodpecker (order Piciformes) genomes. CR1 LINE elements retained from an expansion that occurred 25-30 million years ago were the most abundant TEs in the song sparrow genome. Although the other five sparrow species also exhibit evidence for a spike in CR1 LINE activity at 25-30 million years ago, LTR elements stemming from more recent expansions were the most abundant elements in these species. LTRs were uniquely abundant in the Bells sparrow genome deriving from two recent peaks of activity. Higher levels of repeat content (79.2-93.7%) were found on the W chromosome relative to the Z (20.7-26.5) or autosomes (16.1-30.9%). These patterns support a dynamic model of transposable element expansion and contraction underpinning the seemingly constrained and small sized genomes of birds. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

genomics↗

bioRxiv2023

Metagenomics for pathogen detection during a wildlife mortality event in songbirds

Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria comprising the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds, and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events. Article Summary LineThe causative agent of a mass mortality event in passerines remains inconclusive after metagenomic high-throughput sequencing with results prompting further investigation into non-pathogenic causes.

genomics↗