Joint profiling of gene expression and chromatin accessibility during amphioxus development at single-cell resolution

Area of Science:

• Evolutionary developmental biology
• Genomics
• Chordate biology

Background:

• Vertebrate evolution involved whole-genome duplication events, leading to complex regulatory and gene expression patterns.
• Amphioxus, a basal chordate, serves as a crucial model for understanding vertebrate origins due to its slow evolutionary rate.
• Single-cell sequencing has enabled detailed developmental atlases in various vertebrate and invertebrate species.

Purpose of the Study:

• To construct a comprehensive developmental cell atlas for amphioxus using single-nucleus RNA sequencing (snRNA-seq) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq).
• To elucidate cell fate commitment and lineage specification during amphioxus embryogenesis and in adult tissues.
• To identify key regulators and genetic regulatory networks governing amphioxus development and evolution.

Main Methods:

• Single-nucleus RNA sequencing (snRNA-seq) across different developmental stages and adult tissues of amphioxus.
• Single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) to map regulatory elements.
• Bioinformatic analysis to construct a developmental tree and identify gene regulatory networks.

Main Results:

• Construction of a detailed developmental tree for amphioxus cell fate commitment and lineage specification.
• Characterization of key regulatory genes and genetic networks underlying developmental processes.
• Generation of high-resolution single-cell data covering embryogenesis and adult tissues.

Conclusions:

• The study provides unprecedented insights into the developmental mechanisms of amphioxus, a key model for vertebrate evolution.
• The identified regulatory networks and cell lineages offer a foundation for comparative genomics and evolutionary studies.
• Publicly available data on the AmphioxusAtlas platform facilitates future research into chordate development and evolution.