Biology subjects

Yan, E.

Publications and source records attributed to Yan, E..

4 recordsLinked to original sources

bioRxiv2025

Dynamic changes in mRNA isoform usage during human retinal development

BackgroundAlternative mRNA splicing is a key mechanism for generating isoform diversity in eukaryotic cells. However, the extent of the splicing changes that occur during complex regulatory processes like neurodevelopment are still incompletely characterized. ResultsWe performed nanopore-based long-read RNA sequencing on differentiating human stem cell-derived retinal organoids to identify temporal patterns of isoform usage across developmental stages. We found that retinal organoids undergo dynamic shifts in isoform usage throughout differentiation, which were not necessarily accompanied with changes in overall gene expression, as was observed for many genes involved in the regulation of mRNA splicing itself. Further analysis of human stem cell-derived retinal ganglion cells uncovered neuron-specific splicing signatures. Additionally, allele-specific gene expression analysis revealed extensive allelic imbalance in induced pluripotent stem cell-derived organoid cultures. ConclusionsBy combining direct long-read RNA sequencing with human stem cell retinal models we were able to develop a comprehensive database of isoform-level changes in differentiating human retinal cells during development. These results uncovered dynamic shifts in transcript usage during retinal differentiation, adding to our knowledge base of post-transcriptional RNA processing in the developing central nervous system and human in vitro culture systems.

molecular biology↗

bioRxiv2024

Genome and tissue-specific transcriptome of the tropical milkweed (Asclepias curassavica)

Tropical milkweed (Asclepias curassavica) serves as a host plant for monarch butterflies (Danaus plexippus) and other insect herbivores that can tolerate the abundant cardiac glycosides that are characteristic of this species. Cardiac glycosides, along with additional specialized metabolites, also contribute to the ethnobotanical uses of A. curassavica. To facilitate further research on milkweed metabolism, we assembled the 197 Mbp genome of a fifth-generation inbred line of A. curassavica into 619 contigs, with an N50 of 10 Mbp. Scaffolding resulted in 98% of the assembly being anchored to 11 chromosomes, which are mostly colinear with the previously assembled common milkweed (A. syriaca) genome. Assembly completeness evaluations showed that 98% of the BUSCO gene set is present in the A. curassavica genome assembly. The transcriptomes of six tissue types (young leaves, mature leaves, stems, flowers, buds, and roots), with and without defense elicitation by methyl jasmonate treatment, showed both tissue-specific gene expression and induced expression of genes that may be involved in cardiac glycoside biosynthesis. Expression of a CYP87A gene, the predicted first gene in the cardiac glycoside biosynthesis pathway, was observed only in the stems and roots and was induced by methyl jasmonate. Together, this genome sequence and transcriptome analysis provide important resources for further investigation of the ecological and medicinal uses of A. curassavica.

plant biology↗

bioRxiv2023

Latitudinal scaling of aggregation with abundance and its consequences for coexistence in species rich forests

The search for simple principles underlying the complex spatial structure and dynamics of plant communities is a long-standing challenge in ecology1-6. In particular, the relationship between the spatial distribution of plants and species coexistence is challenging to resolve in species-rich communities7-9. Analysing the spatial patterns of tree species in 21 large forest plots, we find that rare species tend to be more spatially aggregated than common species, and a latitudinal gradient in the strength of this negative correlations that increases from tropical to temperate forests. Our analysis suggests that latitudinal gradients in animal seed dispersal10 and mycorrhizal associations11,12,13 may jointly generate this intriguing pattern. To assess the consequences of negative aggregation-abundance correlations for species coexistence, we present here a framework to incorporate the observed spatial patterns into population models8 along with an analytical solution for the local extinction risk14 of species invading from low abundances in dependence of spatial structure, demographic parameters, and immigration. For example, the stabilizing effect of the observed spatial patterns reduced the local extinction risk of species when rare almost by a factor of two. Our approach opens up new avenues for integrating observed spatial patterns into mathematical theory, and our findings demonstrate that spatial patterns, such as species aggregation and segregation, can contribute substantially to coexistence in species-rich communities. This underscores the need to understand the interactions between multiple ecological processes and spatial patterns in greater detail.

ecology↗

bioRxiv2021

Early evolution of beetles regulated by the end-Permian deforestation

The end-Permian mass extinction (EPME) led to a severe terrestrial ecosystem collapse. However, the ecological response of insects--the most diverse group of organisms on Earth--to the EPME remains poorly understood. Here, we analyse beetle evolutionary history based on taxonomic diversity, morphological disparity, phylogeny, and ecological shifts from the Early Permian to Middle Triassic, using a comprehensive new data set. Permian beetles were dominated by xylophagous stem groups with a high diversity and disparity, which probably played an underappreciated role in the Permian carbon cycle. Our suite of analyses shows that Permian xylophagous beetles suffered a severe extinction during the EPME largely due to the collapse of forest ecosystems, resulting in an Early Triassic gap of xylophagous beetles. New xylophagous beetles appeared widely in the early Middle Triassic, which is consistent with the restoration of forest ecosystems. Our results highlight the ecological significance of insects in deep-time terrestrial ecosystems.

paleontology↗