Abstract Detail

Comparative Genomics/Transcriptomics

Shushkov, Philip [1].

Inference of developmental trajectories from single-cell sequencing data.

Changes in transcriptional profiles are at the heart of development. Understanding transcriptional dynamics at the single-cell level is a central challenge in deciphering developmental processes. Current sequencing technologies allow the estimation of transcription profiles at unprecedented single-cell resolution but the inference of developmental progressions of cells is hampered by sampling sparsity, technological noise, and loss of spatial and temporal information. I combine noise-resilient diffusion mapping-based approaches together with Markov State Models to infer and recapitulate developmental trajectories from large single-cell datasets. Our new methods allow us to reconstruct multiple branching trajectories that occur on substantially different timescales in development and infer waves of gene expression changes along the developmental progressions. We analyze the development of vascular tissues, such as sieve elements, companion cells, and vessel elements, in different plant organs, as well as reconstruct the developmental transcriptional changes during formation of entire plant organs. We recover known regulators of vascular development that follow expected developmental dynamics based on previous studies and identify putative regulatory factors. We identify waves of gene expression changes of transcription factors and their downstream targets, which provide substantial resolution of transcriptional dynamics in vascular cell development.

1 - Tufts University, Chemistry, 62 Talbot Ave, Medford, MA, 02155, United States

Keywords:
Transcriptomics
cell type
developmental trajectory
xylem
Phloem.

Presentation Type: Oral Paper
Number: CGT5002
Abstract ID:509
Candidate for Awards:None