Sex determination is roughly known in ~90% of animal species. In less than 1% of the 15.000 dioecious plants (species with male and female individuals), we know that sex chromosomes determine sex. To fill this gap, we have been deploying different strategies to study plant sex chromosomes. One of them rely on applying SEX-DETector, a new method that we have developed (see below) to several dioecious plants.

We have been focusing on:

1. -Silene latifolia and other dioecious silene species, Silene is a model genus to study plant sex chromosomes
   

2. -Amborella trichopoda, the sister species of all extent angiosperms, which is dioecious
   

3. -Coccinia grandis, a dioecious cucurbit in which in the monoecious close relatives melon and cucumber, genes controlling monoecy have been identified (some of which could be the sex-determining genes in dioecious species)
   

4. -Cannabis sativa, in which developing genetic markers to sex seedlings is of economical importance
   

5. -Vitis sylvestris to understand sex determination in grapevine and how grapevine reverted to hermaphroditism during its domestication
   

- and other dioecious plants...

Meiotic recombination rates vary along the chromosomes and biologists in many different fields are interested in getting estimates of these variations. The Marey map approach is a graphical method that compares a genetic and a physical maps of a chromosome to get the local recombination rates. It is a very popular method but no generic tool existed before we developed MareyMap (Rezvoy et al. 2007). MareyMap is a R package that can be installed on the computer’s user. We have recently developed a web service for an easier use of MareyMap (Siberchicot et al. 2018).

More information about MareyMap here

Y chromosomes are notoriously difficult to sequence with conventional strategies to sequence genomes and very few well-assembled Y chromosomes are available. Recently, alternatives have been developed. One of them relies on performing segregation analysis to identify sex-linked SNPs.  In collaboration with statisticians, we have developed three methods relying on mathematical models and using statistics to infer sex-linkage:

- SEX-DETector, which takes RNA-seq-derived genotyping data from a family as input

- SD++, an ultrafast version of SEX-DETector in c++ to analyze genomic-derived genotyping data of a family

- SDpop, which takes all kind of genotyping data from male and female individuals sampled in the field

More information about the SEX-DETector suite here

The genomic changes underlying the transition from the gymnosperm reproductive cones to the angiosperm flower are still poorly understood. We want to use a genomic/transcriptomic/molecular evolution approach to address this question. We have recently embarked in a project coordinated by Charlie Scutt on using Amborella, a basal angiosperm, and gymnosperms to reconstruct ancestral regulators and identify neo-functionalization processes that were directly responsible for the origin of the carpel. Through this approach, we expect to provide a molecular explanation for the origin of the carpel and thereby contribute to an understanding of the origin of the flowering plants: the still unresolved question, famously described by Charles Darwin as “an abominable mystery”.