WARNING: Preliminary Analysis

Neo X Gene Movement

We are interested in the evolutionary impact of X inactivation. There are several hypotheses about why the X would evolve MSCI during spermatogenesis. Here we focus on the idea that genes important for spermatogenesis will move off of the X to avoid silencing. To investigate this question we look at gene movement off of the Neo X chromosome in D. pseudoobscura and D. willistoni. In this group, the Muller element A (X) fused with Muller element D (3L) (Figure 1). We expect that genes important for spermatogenesis, on Muller element D, will move to another chromosome or be lost.

First, we need to characterize gene movement in the Drosophila genus. Then we can look for enrichment of gene movement off of Muller D in genes up regulated in primary spermatocytes. To characterize gene movement we look at gene localization in a subset of the Drosophila genus. We focused on 5 members of the genus: D. pseudoobscura, D. melanogaster, D. willistoni, D. mojavensis, and D. virilis. I downloaded updated gene annotations and ortholog mappings from GSE99574. I supplemented these ortholog mappings with those provided by FlyBase. We selected a set of 13,473 orthologous genes present in D. melanogaster and at least one of the other species. Using these gene locations we can determine how the gene is behaving in D. pseudoobscura and D. willistoni.

Methods

Identification of orthologs

The quality of assemblies and annotations are highly variable across the Drosophila genus. Genes from D. willistoni, D. mojavensis, and D. virilis are currently mapped to scaffolds instead of chromosome arm. We used annotations from D. melanogaster to assign Muller element to each of these scaffolds using a consensus approach. For each scaffold, with > 20 genes, we looked where the orthologs were located in D. melanogaster. We assigned the Muller element using majority rule. To validate our approach, we did this same process for D. pseudoobscura which has chromosomal annotation. We achieved 100% agreement with D. pseudoobscura annotation.

Classification of evolutionary state

We classified each gene as conserved, gene_death, moved_on, or moved_off based on localization across the genus (Table 1). For example, if a gene is located on Muller D in all species then it is conserved (Table 1a). Similarly, recent_conserved genes were on Muller D in Sophophora branch, but were elsewhere in D. virilis and D. mojavensis. To determine movement in D pseudoobscura we did the following. If the gene was on Muller D in all species, but not found in D. pseudoobscura then it was considered gene_death. If the gene was on Muller D in all species, but on another Muller element in D. pseudoobscura then it was considered moved_off. We used the same logic for D. willistoni. We then furthered grouped genes as selection favoring a gene remaining where it is (conserved, moved_on) or selection against where it is (gene_death, moved_off).

Table 1a. Classification of genes on Muller element D.

Table 1b. Classification of genes on Muller element E.

Results

Ortholog selection

Yang et al. only generated orthologs based on genes expressed in their data. There were a number of FlyBase annotated orthologs that were excluded from their list. The majority of orthologs present in both data sets were mapping to the same Muller element (Table 2a). While the similarity of missing orthologs was very different (Table 2a). I merged these ortholog sets by updating the FlyBase annotation using Yang et al. mappings (Table 2a). The number of genes present on each Muller element is similar across species with most elements having ≤ 175 different (Table 2b).

Table 2a. Similarity of Yang et al. vs FlyBase.

^†Adj. Rand Score.

Table 2b. Number of genes per muller element.

Gene movement classification

For gene movement results browse to the respective page either using the links below or the side bar.

Table 3. D. pseudoobscura movement classes.

Table 4. D. willistoni movement classes.

Gene movement cell type enrichment

D. pseudoobscura

• SP vs Primary Spermatocytes
• SP vs EPS
• SP vs PS
• EPS vs PS

D. willistoni

• SP vs Primary Spermatocytes
• SP vs EPS
• SP vs PS
• EPS vs PS