11.2019: our recent paper is out in JEB
The canonical model of sex‐chromosome evolution assigns a key role to sexually antagonistic (SA) genes on the arrest of recombination and ensuing degeneration of Y chromosomes. This assumption cannot be tested in organisms with highly differentiated sex chromosomes, such as mammals or birds, owing to the lack of polymorphism. Fixation of SA alleles, furthermore, might be the consequence rather than the cause of recombination arrest. Here we focus on a population of common frogs (Rana temporaria) where XY males with genetically differentiated Y chromosomes (non‐recombinant Y haplotypes) coexist with both XY° males with proto‐Y chromosomes (only differentiated from X chromosomes in the immediate vicinity of the candidate sex‐determining locus Dmrt1) and XX males with undifferentiated sex chromosomes (genetically identical to XX females). Our study finds no effect of sex‐chromosome differentiation on male phenotype, mating success or fathering success. Our conclusions rejoin genomic studies that found no differences in gene expression between XY, XY° and XX males. Sexual dimorphism in common frogs might result more from the differential expression of autosomal genes than from sex‐linked SA genes. Among‐male variance in sex‐chromosome differentiation seems better explained by a polymorphism in the penetrance of alleles at the sex locus, resulting in variable levels of sex reversal (and thus of X‐Y recombination in XY females), independent of sex‐linked SA genes.
10.2019: our recent paper is out in MBE
Fig. 2 Large inversions on two autosomal contigs between the MvCa and MvVi Microbotryum genetic clusters and signatures of positive selection.
Nonrecombining sex chromosomes are widely found to be more differentiated than autosomes among closely related species, due to smaller effective population size and/or to a disproportionally large-X effect in reproductive isolation. Although fungal mating-type chromosomes can also display large nonrecombining regions, their levels of differentiation compared with autosomes have been little studied. Anther-smut fungi from the Microbotryum genus are castrating pathogens of Caryophyllaceae plants with largely nonrecombining mating-type chromosomes. Using whole genome sequences of 40 fungal strains, we quantified genetic differentiation among strains isolated from the geographically overlapping North American species and subspecies of Silene virginica and S. caroliniana. We inferred that gene flow likely occurred at the early stages of divergence and then completely stopped. We identified large autosomal genomic regions with chromosomal inversions, with higher genetic divergence than the rest of the genomes and highly enriched in selective sweeps, supporting a role of rearrangements in preventing gene flow in genomic regions involved in ecological divergence. Unexpectedly, the nonrecombining mating-type chromosomes showed lower divergence than autosomes due to higher gene flow, which may be promoted by adaptive introgressions of less degenerated mating-type chromosomes. The fact that both mating-type chromosomes are always heterozygous and nonrecombining may explain such patterns that oppose to those found for XY or ZW sex chromosomes. The specific features of mating-type chromosomes may also apply to the UV sex chromosomes determining sexes at the haploid stage in algae and bryophytes and may help test general hypotheses on the evolutionary specificities of sex-related chromosomes.
Co-organize Open Symposium sub-theme “Genome Evolution” at ESEB 2019 in Turku, Finland
We, with Alexander Nater, had a nice collection of Open Symposium theme on “GenomeEvolution” talks part 1 S36d, in Galleria room. The topics includes #RecombinationRate #SexChromosomes #GermLineChromosomes #epigenetics etc.
Invited for a job interview of Research Fellow at SBS at University of Aberdeen
I was lucky to be invited for a job interview for an Independent Research Fellow (tenure-track position). This was a great experience, had fun talking to various faculty members, graduates and postdocs at School of Biological Sciences.
Invited to speak at Evolution 2019 meeting
It was great to speak about the evolution of sex chromosomes and sex determination throughout frog development using RNA-seq approach, at Evolution meeting in Providence, Rhode Island in 06.2019.
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.
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!
The article in Genome Biology:
The article in Nature Communications:
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!
Excited to give a seminar 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!
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.
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.
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!
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.
Move 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)!