Summer Grill Heave Of Ou Lab (SGHOOL) and families!

Using TESS and parameter sweep, we were able to approximate the TE dynamics of these three rust fungus genomes, revealing the two-stage evolution of myrtle rust (A. psidii), with a long-lasting genome expansion transitioned to aggressive contraction ~1.2 million generations ago.

We selected three extreme cases, being fast insertion/fast deletion/stable genome (Cronartium ribicola), slow insertion/slow deletion/stable genome (Puccinia coronata), and fast insertion/slow deletion/obese genome (Austropuccinia psidii), typical of eukaryotic genome dynamics.

What can TESS achieve? We used it to study the genome evolution dynamics of Pucciniomycotina, a subdivision of rust fungi with 58 high-quality genomes available and sizes varying from 20 Mb to 1018 Mb, mostly due to TE dynamics!

The PrinTE component of TESS makes genomes live on silicon chips! It can simulate TE insertions and deletions at any rates and dynamics, including complete deletions or creation of solo LTRs, and allow genomes to evolve forward in time. Here is one simulation of a digital genome:

The third mode of TEgenomeSimulator can simulate genomes with almost identical size, TE content, TE length distribution, and a normalized TE divergence (for ease of modeling) to real genomes - essentially digital replicas. This powerful mode allows in-silico genome evolution!

The TEgenomeSimulator component has three modes, which can simulate genomes representing snapshots of TE evolution at different stages: ancient expansion, recent expansion, long-lasting burst, and short burst.

The RandSeqInsert component can simulate TIR transposon insertions using a live-updated, high-performance AVL tree structure. It takes user-provided TIR libraries and allows setting varying lengths of target site duplications and nested insertions that mimic true TE insertions.

I want to share our latest work on a forward simulation framework on transposable element evolution. The TE Evolution Simulation Suite, or TESS, contains three components that can simulate many scenarios of genome evolution under the impact of TEs.

Hello bluesky world! Newbee here! I have a postdoc position immediately available in my lab. It will focus on identifying high-quality transposons in many genomes and finding their impacts in evolution and traits. Most works, including EDTA2 development and annotation of 400+ genomes, are done! 1/n