News

My first preprint and first paper on fungi genomics, mating-type chromosomes and differential gene expression

“Differential gene expression is associated with degeneration of mating-type chromosomes in the absence of sexual antagonism”

Figure1. Comparisons of differentially expressed (DE) versus non-differentially expressed (non-DE) genes between mating types of Microbotryum lychnidis-dioicae for various degeneration-associated traits within genomic compartments.

Figure2. Significant predictors of the degree of differential expression between mating types of Microbotryum lychnidis-dioicae testing directional effects of degeneration-associated traits.

Across kingdoms, a dominant view is DE genes on sex chr. results from sexually antagon. selection on male vs. female traits. However, the compelling logic of SA selection hasn’t been met with strong empirical evidence, alternative causes haven’t been well considered/evaluated. We tested the hypothesis that degenerative mutations, which also characterize sex chr. evolution, are responsible for differential gene expression. We did so using a model system where sexual antagonism does not occur as a confounding factor (i.e. the isogamous fungus).

Our genomic and gene expression analyses reveal that DE between haploid fungal mating types were enriched only on the old regions of the mating-type chromosomes with most ancient recombination suppression, associated with multiple signatures of sequence degeneration, including dN substitution rates, indels and premature stop codons, transposable element insertions, altered intron & GC content. The findings strongly indicate degen. mutations are important in the evolution of DE expression in non-recombining regions on mating-type/sex chromosomes.

We show that DE should not be taken as necessarily arising from antagonistic selection, and that mutations with degenerative effects must to be considered wherever reproductive compatibility or sex is determined by genes located in regions of recombination suppression.

Departmental seminar on ‘Evolution of Homomorphic Sex Chromosomes, Sex-biased Gene Expression in the Common Frog’ at Amherst College

10 Dec.2018: Today I gave a Departmental seminar on ‘Evolution of Homomorphic Sex Chromosomes, Sex-biased Gene Expression in the Common Frog’, was super fun to discuss my previous postdoc work in my current institute, at Amherst College. There were quite interesting questions regarding fitness of males with various Y-chromosome differentiation levels, and how do frogs main homomorphic sex chromosomes etc. I also brief talked about my current projects questions and some preliminary results on degeneration of non-recombining mating-type chromosomes in anther smut Microbotryum fungi. Many thanks for the invitation by Michael Hood.

Moved to the NEW Science Center Building 

06.Oct.2018: Since 01.Sep. 2018, the whole Biology Department moved to a brand new Science Center Building (25 East Drive, Amherst, MA 01002) in Amherst College. This new building is built on the basis of high energy sustainability with modern design style.

Science Centre under beautiful blue sky!
The inside view of highly energy saving design using natural light through giant windows!

A happy coincidence of my two papers are online on the same day 05 Oct. 2018

05. Oct. 2018: What a happy coincidence today! Thrilled to see our two frog sex chromosome evolution papers are out today! 🙌 🙌

Good chance to know more about evolution of sex-biased gene expression in early stage of sex chromosome evolution, and a crazy fast rate of sex chromosome turnover in true frogs. Check them out!

and

The article in Nature Communications:
https://www.nature.com/articles/s41467-018-06517-2

Two months of productive collaborations: fly back to Amherst College, MA

02.Oct.2018: I took the flight back to Amherst, MA, USA, after a fantastic and productive two months period in Prof. Tatiana Giraud lab. Thanks very much, Tatiana Giraud and the whole team for hosting me! I had a really fantastic time and stimulating visit for the past two months. Looking forward to our further collaborations!

The lab building when I left on 02. Oct. 2018, with the beautiful autumn colours!

Excited to give a seminar to present my work on frog sex chromosome evolution at Department of Genetics and Ecology Evolution, Université Paris-Sud

21 Sep. 2018: Thanks so much for the opportunity! Thanks for the hosting by Tatiana Giraud and the whole team members. I am every excited to share and discuss my work on evolution of frog homomorphic sex chromosomes and sex-biased gene expression, at Seminaires IDEEV, department of Genetics and Ecology Evolution, Université Pairs-Sud. Thanks for the great discussions. Photo credit: Jade Bruxaux.

Attending fantastic Joint ESEB-Evolution conference in Montpellier, France

The joint conference of European Society of Evolutionary Biology (ESEB) and Evolution conference of America was held in Montpellier, France this year, between 18 Aug. -22 Aug. There are over 2,700 evolutionary biologists from all over the world attending this largest conference (so far) in evolutionary biology, to present and discuss their works and exchange ideas. This conference helps promotes collaborations among people sharing similar topic interests. It was a great success due to the enormous efforts from the organisers. A huge thanks for the organizers!

Presenting my work on frog sex chromosome evolution during the conference
A very successful and fantastic joint ESEB and Evolution conference held in Montpellier, France, in total >2700 evolutionary biologists from all over the world attended.
Great place to host a conference dinner and party in a Middle Ages church/castle, we had fantastic time! Thanks for the efforts and thoughtfulness of the organisers!

 

Visiting our collaborator Prof. Tatiana Giraud lab at Université Paris-Sud in Orsay, France

I am currently visiting Tatiana’s lab and will stay in Orsay, France for Aug. and Sep. 2018. Many thanks for both Michael and Tatiana’s arrangement to make this happen, Tatiana for providing the invitation letter and hosting me. I am very excited for our various collaborations!

Great thanks for all awesome summer interns of Hood lab

July 31: Thanks for all summer interns of Hood lab, who did great jobs in contributing to various projects running in the Hood lab. The projects include disease ecology, genomics and degeneration of mating-type chromosomes etc. Photo credits: Sarah Gayer.

Hood lab photo with all the summer interns, it was great fun to work with you! Thank you all again for your hard work and substantial contributions. See you in the Fall! From left to right: Sangmin Song, James Colwell, Irish Amundson, Kelley Baumann, myself, and Sarah Gayer.

My manuscript on plant polyploidy is submitted today

Today is a happy day overall: my manuscript on a new polyploid Mercurialis annua species inferring from functional divergence in inflorescence morphology, hybrid sterility and patterns of introgression has been submitted! The ms reads very nicely, hopefully the reviewers will like it too.

We had delicious Thai dish, Pad Thai and Phanaeng curry, to celebrate a ms submission!

MinION long-reads sequencing of Microbotryum fungi

July 15th 2018 – today I launched another MinION sequencing run for one of the anther smut Microbotryum fungi species. We had successfully retained high yield of DNA from ligation sequencing protocol, with home made and tested modifications for certain steps (contact me if you have problem to retain enough DNA sample to run a flow cell, will be happy to share my experiences and modified protocol). I am excited to observe the live sequencing and very looking forward to the results and genome assembly!

MinION sequencing device is on the run now! 07.2018

This shows the MinION flow cell total 512 channels panel status, green denotes sequencing and active pores, dark blue is recovering pores, light blue is inactive ones, 07.2018.

This image shows the number of active, inactive channel used overtime through the sequencing run, 07.2018.

Moving to Amherst, Massachusetts, USA

Since 05.2018, I moved oversea from University of Lausanne (Lausanne, Switzerland) to Amherst College (Amherst, Massachusetts, USA) and join Michael Hood lab with genomics of fungi mating-type chromosomes (sex chromosomes)!

Our lab MinION long reads sequencing device (loading HMW DNA samples), 06.2018.
The window view from my new office at Amherst College, 05.2018.
The Mead Art Museum tower at Amherst College, 05.2018.
Graduation weekend of Amherst College, 05.2018.