TaxGen

Background and Objective

Sexual specialization in plants has fascinated scientists for centuries. One important question is: What is the genetic basis of sex determination in different dioecious plant species? Recently, advances in high throughput sequencing provided exciting answers to this question in various dioecious angiosperm species and demonstrated that single genes may function as master regulators of sex determination (e.g., in Diospyros and Populus). These results supported one-factor models for the evolution of dioecy as an alternative to the classic two-factor model. In a recent theoretical model, it has been pointed out that “genes controlling sex expression in monoecious species may often also be involved in sex determination in related dioecious species, and vice versa“ (Renner and Mueller, Nature Plants 2021). Plant genera with monecious and dioecious species, such as the gymnosperm genus Taxus, represent excellent models to further explore this hypothesis by elucidating the genetic and molecular basis for sex determination. The project TaxGen focuses on the dioecious species Taxus baccata and thereby aims to extend the research on sex determination to conifers.

Approach

The exceptionally large and complex genomes of gymnosperms (Taxus baccata: about 11 Gb) make genome sequencing and assembly much more challenging than in angiosperms. Highly accurate long-read and Hi-C sequencing of a male and a female Taxus baccata individual will be performed at one of the DFG funded competence centres for high throughput sequencing to assemble chromosome-level reference genomes (DRESDEN-concept Genome Center). Long-read isoform sequencing data of different tissues from the reference individuals will support the annotation of the reference genomes. The heterogametic sex and the sex-determining region (SDR) will be identified in a genome-wide association study using resequencing data of 20 male and 20 female individuals. The identification of the sex-determining gene(s) will be supported by quantitative RNA sequencing of different male and female individuals. Moreover, based on genetic variants in the sex-determining region of Taxus baccata, molecular sex markers will be developed, which are of great practical importance in a species reaching sexual maturity at an age above 15 years.

The work packages include:

1. DNA and RNA sequencing of Taxus baccata individuals
2. Assembly and annotation of a male and female Taxus baccata reference genome
3. Localization, characterization and annotation of the SDR in Taxus baccata
4. Comparative genomics in the genus Taxus
5. Development of molecular sex markers for Taxus baccata and transferability tests