Wen-Juan Ma's repositories
Differential_expression_associateswith_degeneration_Microbotryum_fungus
In this project, we aim to investigate the association between differential gene expression and sequence degeneration on mating-type chromosome in an anther smut fungus species Microbotryum lychnidis-dioicae. The various forms of degenerative traits we are analyzing are synonymous substitution rate (dN), transposable element insertions (TEs), premature stop codons, intron content and GC content.
Decaytrait_qtl
We are investigating the genetic architecture of decayed sexual traits in asexual females of the parasitoid wasp Asobara japonia. In particular, we conduct QTL analysis for the female functional virginity trait, which referes to asexual females resisting to mate or not fertilizing eggs after mating. In the case of A. japonica, asexual females reject mating from males resulting in complete matin failure. We detected a single QTL with large phenotypic effects underlying the female functional virginity trait. Using PacBio genome assembly and transcriptomic RNAseq datasets, we found at least 131 protein coding genes underlying the single QTL, 15 of them showed differential expression in the sexual sister species Asobara tabida.
Genome-Annotation-Pipeline
Summary of the pipeline used to generate a genome annotation
Parsing-RepeatMasker-Outputs
Few scripts facilitating the extraction of info from Repeat Masker .out files
Polyploid_speciation
This project is to assess the reproductive isolation between two hexaploid lineages in an annual plant Mercurialis annua, using common garden, phylogeny, and reciprocal crosses approaches.
Rana_Transcriptome
Sex-biased genes are central to the study of sexual selection, sexual antagonism and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with evolutionary rate.
Tvedora_dev_RNAseq
In this project, we investigate the evolution and dynamics of sex-biased genes and gene expression along the five developmental stages of the common frog Rana temporaria, in a population with proto-Y chromosomes.