SEX-DETector – a probabilistic approach to study sex chromosomes in non-model organisms

Researchers from CNRS/Université Lyon have developed a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, UV). Sex chromosomes (especially the non-recombining and repeat-dense Y, W, U and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. Most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sex-linked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Tests on empirical Silene data show that this method identifies 20 to 35% more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. ~12 individuals are needed for optimal results based on simulations. For species with an unknown sex-determination system, the method can assess the presence and type (XY versus ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimised for sex chomosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organisms, including non-model ones for which nothing is known a priori, that can be bred in the lab, are suitable for this method.

The SEX-DETector pipeline: from required data to outputs.

The advised number of ospring individual to sequence was determined with simulations. Parameters of the model are written in red: the segregation type , the parents true genotype frequencies. An X/Y system is represented here but the pipeline is equivalent for a Z/W system. For a U/V system, only two individuals of each sex and one parent are advised and can be sequenced on a single Illumina Hi-seq 2000 lane. The pipeline was implemented in Galaxy for steps following trinity. Note that dierent assembler and mapper could be chosen, only the genotyper reads2snp is required to run SEX-DETector.

Availability – SEX-DETector and its implementation ina Galaxy workflow are made freely available.  http://lbbe.univ-lyon1.fr/-SEX-DETector-.html