Amphioxus Genomics

Cephalochordates, commonly known as lancelets or amphioxus, represent an ancient chordate lineage falling at the boundary between invertebrates and vertebrates. They are considered the best living proxy for the common ancestor of all chordate animals and hold the key for understanding chordate evolution. As a result, they have gradually become popular as emerging model organisms in developmental biology during the past decade. There are three genera of cephalochordates: Branchiostoma, Epigonichthys, and Asymmetron. To date, studies on cephalochordates are almost exclusively limited to the Branchiostoma genus, leaving the other two genera largely unexplored. As the most distant related cephalochordate genus relative to Branchiostoma, Asymmetron occupies a basal position in the cephalochordate phylogeny and diverges from the Branchiostoma genus 120-160 mya. Morphologically, the most striking difference between Asymmetron and Branchiostoma lies in that Asymmetron has gonads only on the right side whereas Branchiostoma has gonads on both sides.

Starting from my PhD, we set out to develop transcriptomic and genomic resources for a representative species from the Asymmetron genus, Asymmetron lucayanum, by both RNA-seq and whole-genome shotgun (WGS) sequencing. By comparing its transcriptomic and genomic sequences with those of distantly related amphioxus species from the Branchiostoma genus, as well as with several representative vertebrate species, many aspects of genome biology for amphioxus were illuminated. Amongst the findings are a seemingly slow lineage-specific molecular evolutionary rate, observed sets of fast-evolving genes, a new calibration of molecular and fossil data describing the evolution of this lineage, a first pass description of conserved non-coding elements, a collection of genes potentially specific to germline development, and the evolution of genes encoding green fluorescent proteins (GFPs) in amphioxus. These findings lay a good foundation for functional studies on this important organisms. Recently, through an international collaboration, we started to work on producing a high quality genome assembly for Asymmetron lucayanum by combining long-read sequencing and chromosome conformation capture technologies, which will greatly help us to better understand the biology and evolution of Asymmetron amphioxus.

Yeast Genomics

Baker’s yeast, Saccharomyces cerevisiae, is a leading biological model system with great economic importance in food, medicine, and biotechological industries. Discoveries in S. cerevisiae have helped shed light on almost every aspect of molecular biology and genetics. It was the first eukaryote to have its genome sequence, population genomics and genotype–phenotype map extensively explored.

In 2015-2016, we applied deep long-read sequencing to 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its closest wild relative Saccharomyces paradoxus. We performed end-to-end complete genome assembly for their nuclear and mitochondrial genomes. The thorough comparison of these genomes coupled with full-fledged genomic feature annotation, explicit nuclear chromosomal partitioning (into internal cores, interstitial subtelomeres and terminal chromosome-ends) and well-resolved phylogenetic relationship enabled us to generate a comprehensive view of structural dynamics in the genome evolution of both species with unparalleled resolution. The striking contrast of such structural dynamics between S. cerevisiae and S. paradoxus highlighted the influence of human activity on structural genome evolution. This study brings long-read sequencing technologies to the field of population genomics, studying genome evolution using multiple reference-quality genome sequences. A dedicated website for this project can be accessed via this link. Along with this study, we further developed a streamlined, modular, and automated computational framework “LRSDAY“, which enables high-quality genome assembly and annotation production with minimal manual intervention required. In one follow-up study, we are working on applying long-read sequencing technology to selected groups of S. cerevisiae strains to perform in-depth examination on the impacts of structural variation in yeast domestication. Also, we are interested in the functional impact of structural variation on important cellular processes such as meiotic recombination. We are currently working on a project to quantitatively measure such effect using ~12,000 meiotic spores. These spores come from six crossing pairs of four parental yeast strains with well-cataloged structural variants (SVs) by our previous study.

Last updates: Aug 22, 2017