On the Origin and Evolution of Drosophila New Genes during Spermatogenesis

1. Introduction

The origin of new genes is one of the fundamental processes underlying the production of functional novelties and organismal diversity [1,2]. This process is inevitably shaped by pre-existing regulatory differences between organs of the individual [3], and those between autosomes and sex chromosomes in the genome [4]. Extensive case and large genomic studies in Drosophila and mammals discovered two surprisingly convergent patterns between the two distantly related phyla. First, testes, compared with other organs, seem to play a more important role in permitting the nascent new genes to originate, and to subsequently adopt novel functions in other tissues by evolutionary time (the ‘out of the testis’ hypothesis) [5]. New genes, especially those of young ages (e.g., species-specific new genes) are more likely to have a testis-biased expression pattern than the other ‘older’ new genes (new genes that are shared by multiple species) or single-copy genes [6,7,8]. This is probably because intensive sperm competition and sexual conflict drive testes to evolve overall a more rapidly evolving transcriptomic environment than other organs that may accommodate new genes. In addition, during mammalian spermatogenesis, meiotic and postmeiotic cells (spermatocytes and spermatids) were reported to confer a more permissive open chromatin state that may allow and expose more promiscuous expression of nascent new gene copies to natural selection [9,10]. These new gene copies are either to be purged by natural selection, or to be fixed within the population if they confer novel beneficial functions.

A second general pattern regarding the birth of new genes is that the X chromosome seems to be producing an excess of testis-biased new genes that are relocated onto the autosomes in both Drosophila and mammals [11,12]. This ‘out of the X’ pattern has been found for the new genes generated by retrotransposition or DNA-based duplications [7], suggesting that this is not impacted by the mechanism of how new genes were generated, but by the complex different molecular and evolutionary factors acting on the X chromosome vs. autosomes [4]. Such factors include meiotic sex chromosome inactivation (MSCI), a process that was well documented in mammals with both X and Y chromosomes forming a heterochromatic ‘XY body’ in spermatocytes [13]. More specifically, the ‘out of the X’ pattern for retrogenes was found to be only started after eutherian lineages were split, which was taken as evidence for the origin of MSCI in the eutherian ancestor [14]. Similar patterns of precocious silencing of X-linked genes in spermatocytes have also been reported in C. elegans [15] and Drosophila [16] by cytogenetic or transgenic studies. A second factor is the sexually antagonistic selection that is also expected to drive nascent male-biased genes off the female-biasedly transmitted X chromosome [17]. These factors, together with the lack of canonical dosage compensation of X chromosome in the male germline [18], lead to an underrepresentation of male-biased genes on the X chromosome, i.e., demasculinization of the X [19].

Previous studies of new genes used the whole-testis RNA-seq [19,20], or different manually dissected parts of Drosophila testis that are enriched for different stages of cells in spermatogenesis for microarray [21]. Direct cell-level evidence for MSCI driving the new gene out of the X chromosome is still lacking. In addition, debates about whether there is MSCI in Drosophila [22,23] have lasted until very recently. A new single-cell RNA-seq (scRNA-seq) study of larvae testes of D. melanogaster provided novel cell-level expression evidence and resolution of distinctive nuclear features of X chromosome vs. autosomes that supported the existence of MSCI of some but not all X-linked genes [24]. This study also uncovered that the gene-poor dot chromosome, a former X chromosome in non-Drosophila Diptera species [25], exhibited a similar dynamic expression pattern with that of X chromosome during spermatogenesis, probably due to their close nuclear territory that subjects them to the same regulatory program. Another scRNA-seq of adult testes found that de novo genes, which originated from non-coding DNA sequences, showed a distinct cell type distribution across expressed testis cell types between segregating vs. fixed de novo genes [26]. This work revealed a dynamic cell-level expression pattern of X-linked genes vs. autosomal genes, or that of de novo genes vs. other genes in the testes; and also offered a great resource to re-examine several hypotheses regarding the new gene evolution in testes which previously cannot be precisely addressed due to the relatively lower resolution of bulk RNA-seq or microarray data. Here, we reanalyze the testis scRNA-seq data, with the focus on comparing the expressed cell types or stages during spermatogenesis between the new gene and its parental gene. Our aim is to reveal how the age, origination mechanisms, and chromosome location impact the evolution of new genes across different testis cell types. Specifically, if MSCI exists in Drosophila and drives the relocation of X-borne new genes onto the autosomes, we would expect that a shift of autosomal new genes to be expressed toward the middle or late spermatogenesis (e.g., in spermatocytes or spermatids after spermatogenesis enters meiosis) stages, relative to their parental genes that are expressed in the early spermatogenesis (mitotic) stage (e.g., spermatogonia). Test of this hypothesis is to provide mounting evidence for MSCI in Drosophila, and provide more insights into the molecular driving forces of new gene evolution in testes.

2. Results

2.1. Comparing the Expression Patterns of Genes between Chromosomes during Spermatogenesis

In order to compare the new gene and parental gene, and test the aforementioned hypothesis about MSCI, we first prepare two datasets: one is the identified new genes and their parental genes among different Drosophila lineages from GenTree (http://gentree.ioz.ac.cn/, accessed on 1 March 2021) [27], with the information of age and origination mechanisms of new genes’ annotated (Figure 1a). In general, new genes tend to show a shorter gene length, and less exons (p < 0.05, Wilcoxon rank sum test) compared with their parental genes (Figure S1), because many new genes were produced by retrotransposition without any introns (hence a shorter gene length), or partial gene duplications. For the chromosomal location, younger new genes (branch 5,6) are enriched (p < 0.05, Fisher’s exact test) on the X chromosome, whereas older new genes (branch1) are enriched on autosomes, which is consistent with the reported result [6]. There does not seem to be a significant difference in distance to nearby meiotic recombination hotspots [28], nor the distance to the nearby transposable elements between the new genes and the genomic background (Figure S2). The new gene’s age is inferred based on the presence or absence of the focal new gene in D. melanogaster or multiple Drosophila species including D. melanogaster, i.e., in the ancestor of all these species. Additionally, the origination mechanisms were divided into DNA-based duplication, RNA-based duplication (retrotransposition), or de novo evolution [1,29], based on their possibly different patterns emerging from later expression comparison between parental vs. new genes. For example, new genes produced by retrotransposition or located on a different chromosome compared with the parental genes are more likely to share different cis-regulatory elements with those of their parental genes and evolved novel expression patterns. In particular, de novo genes have been recently analyzed with the Drosophila adult testis scRNA-seq dataset and are not the focus of this study, nor they help to clarify the role of MSCI during new gene evolution [26]. A second dataset is that we use the scRNA-seq of adult testes of D. melanogaster and annotate every gene for their major expressed stages during spermatogenesis. We use the adult testis data because some new or parental genes in the following analyses may be expressed in the post-meiotic cells that are underrepresented in the larvae testes.

After estimating the average expression level (Figure 1b) and the percentage of expressed cells (Figure S3) within each type of cell for each gene, we annotate each gene as one of the five cell categories. According to unsupervised clustering, mitotic genes refer to those that are predominantly expressed in spermatogonia; meiosis genes refer to those that are predominantly expressed in spermatocytes, and post-meiosis genes refer to those that are predominantly expressed in spermatids. There are also some genes that span two adjacent stages or developing cell types (Figure 1b, e.g., ‘meiosis and mitosis’ genes that are expressed in both spermatogonia and spermatocytes). Overall, mitotic genes comprise the largest category (over 50% of the 15,189 genes expressed in the germline) among all five types of genes, with 6431 (42.3%) genes expressed in spermatogonia, and 1300 (8.6%) non-overlapping genes expressed in both spermatogonia and early spermatocytes, whereas genes predominantly expressed in spermatids comprise the smallest part, with only 690 genes (4.5%). Our division of genes according to their expressed cell types or stages is consistent with their respective enrichment of gene ontology (GO) terms (Figure S4). For example, mitotic genes are enriched for GOs of ‘mitotic cell cycle process’, ‘mitotic nuclear division’, etc., and post-meiotic genes are enriched for GOs of ‘spermatid development’ and ‘sperm motility’, etc.

Comparing with the autosomes excluding the dot chromosome, we found a significant (p < 0.05, Fisher’s test) enrichment of mitotic genes, but a significant (p < 0.05, Fisher’s test) underrepresentation of meiotic/post-meiotic genes, on both X chromosome and dot chromosome of D. melanogaster. This pattern is consistent with the results previously reported on the mouse X chromosome [30]. For the Y chromosome, over 50% of the genes are not expressed in any cell types, and it in contrast shows an underrepresentation of mitotic genes (Figure 1c,d) relative to the autosomes. A similar enrichment or under-representation pattern of certain testis genes on the X chromosome can be also observed, if we divide the genes according to the percentage of cells that they are expressed, among each cell type (Figure S3), suggesting our results are robust to the different methods of categorizing the genes. These patterns indicate a distinctive chromosomal composition of genes expressed in different testis cell types. They are consistent with the previous analyses using the larvae scRNA-seq data [24], which suggested that the dramatic reduction in X-linked gene expression starting from early until late primary spermatocytes, and a deficiency of X-linked meiotic genes is more likely to be caused by MSCI rather than lack of dosage compensation in meiotic cells. They are also consistent with the probably shared expression regulatory mechanism of X- and dot-linked genes during spermatogenesis [24].

2.2. New Genes of Different Ages or Produced by Different Mechanisms Have a Different Expression Pattern across Testis Cells

A large portion of functional new genes that become fixed in the population are usually expected to have evolved a diverged expression pattern from their parental genes to avoid functional redundancy [1]. After annotating the major expressed cell type(s) of each gene, we set out to compare between new vs. parental genes for their major expressed testis cell types to test this hypothesis. Our previous study comparing different age groups of new vs. parental genes uncovered the fact that new genes have gradually acquired active histone modification by their ages [8]. Consistent with this, the percentage of new genes expressed within at least one type of testis cells has increased by new gene age (Figure 2a, the parts that are not black). Additionally, the percentage of parental–new gene pairs that are expressed within completely non-overlapping cell types of testes becomes higher in the older groups of new genes (32~39%) than the new genes of younger ages (24% or 25% of group 5 or 6 genes, Figure 2a). Overall, new genes are significantly (p < 0.05, Fisher’s test) more enriched for meiosis or post-meiosis genes in the testis, but deficient for mitotic genes, compared with their parental genes (Figure 2a). The pattern of different expressed testis cell types is mainly attributed to those new genes that are of relatively older age (age group 1–3). These single-cell level expression patterns support the notion that new genes gradually acquired novel functions and diverge their expression patterns from their parental copies within testes during evolution.

Particularly, there is a significant enrichment (p < 0.05, Fisher’s test) of mitotic genes among the parental genes of very young genes (age group 5 and 6 combined), which are specific to D. melanogaster or shared by D. melanogaster and D. simulans, relative to the genomic background (Figure 2a,c). We previously showed that these two groups of young genes are also more enriched for testis-specific genes relative to other age groups, whereas the ‘older’ new genes are more enriched for house-keeping genes [8]. These results together indicate that mitotic genes, or genes expressed in spermatogonia, have a disproportionately large role in producing the ‘out of the testis’ pattern of Drosophila new genes.

When we divided the new genes according to their origination mechanisms, namely DNA-based duplication, RNA-based duplication (retrotransposition) and de novo evolution from non-coding genomic DNAs, and also divided them by whether the parental and new gene copies reside on the same chromosome (intra-chromosomal) or not (inter-chromosomal); different categories of parental–new gene pairs show different expression patterns across testis cells. The differences of expressed testis cell types between parental and new genes are much larger for the new genes produced by retrotransposition compared with those produced by DNA-based duplication (Figure 2b), whereas there does not seem to be a pronounced difference between new genes produced by inter- or intra-chromosomal DNA duplications. Additionally, de novo genes also show a significantly different expression pattern across the testis cell types compared with the genomic background (Figure 2c). These patterns can be explained by the fact that retrogenes and de novo genes are much more likely to acquire novel cis-regulatory elements than DNA-based new gene duplications [1,2]. In particular, both new retrogenes and de novo genes exhibit an enrichment of meiosis or post-meiosis genes, i.e., genes expressed in spermatocytes and spermatids (‘into the meiosis’), and correspondingly an underrepresentation of mitosis genes (expressed in spermatogonia) compared with their progenitors or the genomic background (Figure 2b,c). Genes expressed in late spermatogenesis stages may be more frequently exposed to sperm competition than those expressed in spermatogonia, which probably accounts for the fixation of these new genes in the population.

2.3. MSCI Plays an Important Role in ‘out of the X’ Pattern of New Genes

Having discovered an ‘into the meiosis’ pattern for retrotransposed new genes and de novo genes, we further examine the parental–new genes pairs that are divided according to their chromosomal distributions. We hypothesize that if MSCI drives an ‘out of the X’ pattern of new genes, we expect to find an enrichment of meiosis genes for the new genes on the autosomes, whereas an underrepresentation of meiosis genes for their progenitors located on the X chromosome. This is indeed the case (Figure 3a, Table S1, Table S2e): among 68 pairs of X-linked parental genes that produce an autosome new gene (‘X to A’, 41 pairs by DNA-based duplication, 27 pairs by retroposition), there are 42 autosomal new genes expressed in cells of meiosis or post-meiosis stages, in contrast to only 16 X-linked parental genes that are expressed at the same stages. Compared with the parental genes, the ‘X to A’ new genes are significantly (p < 0.05, Fisher’s test) enriched for meiosis and postmeiosis genes, but significantly deficient for mitotic genes. Such a significantly complementary expression pattern between parental and new genes is not found for other inter-chromosomal parental–new gene pairs between autosomes (‘A to A’) or from autosomes to X chromosome (‘A to X’) and provides direct evidence for MSCI in Drosophila (Figure 3a).

To further delineate the direction of, and measure the extent of germline cell type changes of each new gene compared with its parental gene, we labelled the four germline cell categories or their combinations (‘mitosis’, ‘mitosis and meiosis’, ‘meiosis’, ‘meiosis and postmeiosis’ in Figure 1b) as 1 to 4. For example, if a parental gene predominantly expressed in spermatogonial or mitotic cells (cell type 1) produces a new gene predominantly expressed in spermatids or meiotic/postmeiotic cells (cell type 4), such a gene pair is annotated with an ‘into the meiosis’ change of 3. Any positive values of cell type change for a parental gene expressed in the mitotic cells (cell type 1 or 2) are defined with an ‘into the meiosis’ change, vice versa for the ‘into the mitosis’ change with negative values, or others with no or minor changes as ‘within the meiotic cells’ or ‘within the mitotic cells’. In general, new genes are always much more likely to show a propensity of ‘into the meiosis’ change than the opposite direction of ‘into the mitosis’ change when being compared with their parental genes, except for DNA-based new gene duplications between autosomes. Additionally, retrotransposed new genes are more likely to show an ‘into the meiosis’ change relative to DNA-based new gene duplication of the same inter-chromosomal gene duplication category. For example, there is about 1.5-fold (59.2% vs. 40.5%) more ‘X to A’ retrogenes that exhibit a ‘into the meiosis’ change than the ‘X to A’ DNA-based new gene duplicates. In fact, ‘X to A’ retrotransposed new genes exhibit the highest percentage of ‘into the meiosis’ change among all types of inter-chromosomal gene duplications (Figure 3b). These data together support the notion that MSCI drives the ‘out of the X’ pattern of new genes in Drosophila [7,11].

2.4. New Gene Cases of ‘into the Meiosis’

We finally examine the parental–new gene pairs that have been previously studied for their functions, in order to elucidate the evolutionary forces driving their expression divergence across different testis cells (Table S3). Among the ‘X to A’ parental–new gene pairs that exhibit the ‘into the meiosis’ trend, we find nuclear transport factor 2 (Ntf-2) and its retroposed new gene Ntf-2r that was identified nearly 20 years ago as one of the first reported retroposed new genes [31]. The coding sequence of Ntf-2r has been characterized to have undergone positive selection relative to its parental copy, and its promoter was inferred to drive a late testis-specific expression similar to that of beta-2 tubulin. This is indeed the case: while Ntf-2 concentrates its expression within the spermatogonia, the expression of Ntf-2r has the highest level within early spermatocytes and extends further into spermatids (Figure 4). A second case is sex lethal (Sxl) and its duplicated gene copy CG5213 or maca. Maca has been recently reported to be critical for the proper splicing of Y-linked genes kl-2, kl-3 and kl-5 with gigantic introns, and the maca mutant exhibits a failure in the sperm individualization process and thus male sterility [32]. This is also consistent with maca’s expression concentrated within the early spermatocytes, compared with Sxl that is predominantly expressed in spermatogonia. Among the ‘A to A’ genes that exhibit a ‘into the meiosis’ trend, we found two cases of proteasome new genes Prosalpha4T1 and Prosalpha3T that have been proposed to be important for sperm tail elongation. The parental genes of both cases are housekeeping genes that are expressed in most tissues, and in testes, predominantly in spermatogonia, whereas the two new genes are exclusively expressed during late spermatogenesis, and in few or no other adult tissues. Mutants of Prosalpha4T1 have been recently shown to cause male sterility [33]. These cases indicate that many new genes have acquired novel functions through evolving divergent cell-level expression from their parental genes in testes.

We do notice that there are also cases of ‘into the meiosis’ among the ‘A to X’ genes (Figure 3b); this suggests that the MSCI does not impact all the genes located on the X chromosome, particularly those whose expression is required for spermatogenesis. Although underrepresented, there are still many X-linked genes expressed during meiosis (Figure 1b). Among all the identified cases of ‘A to X’ genes with the ‘into the meiosis’ change (Figure S5), we have not found cases whose functions have been studied in detail. However, ‘A to X’ duplicated new genes, or tandem gene duplications on the X chromosomes that show predominant expression within meiotic cells for both parental and new gene copies can provide us some insights. Among these cases, we found the X-linked xmas-1, whose parental gene Mmp2 is located on the autosomes. Mmp2 is an important developmental gene related to metamorphosis and is biasedly expressed in pupae but has a low expression level in testes [34]. Interestingly, it is also required for ovulation and specifically expressed in follicle cells [35,36], whereas xmas-1 encodes a hydrophilic protein required for spermatogenesis and oogenesis and one of its mutant lines shows male sterility [37]. This probably represents another case of gene duplication that evolved to resolve sexual conflict [38], in addition to the recently reported case of Apollo and Artemis gene duplication pair [39], whereas the tandemly duplicated genes of Sdic family on the X chromosome are mainly expressed in meiotic cells (Figure 4), and have been suggested to be important for sperm competition by influencing the sperm motility [40]. These cases together suggest that, besides the selection of MSCI against meiotic genes to be located on the X chromosome, sperm competition and sexual conflict may nevertheless fix some X-linked new genes that are expressed during meiosis. More future functional studies into these ‘A to X’ new genes that show meiotic gene expression (Table S3, Figure S5) can test this hypothesis.

3. Discussion

Here, we harness the recently published scRNA-seq data of D. melanogaster and address several important questions on the origin and evolution of new genes in testes, in the context of distinct regulatory programs of X chromosome vs. autosomes. In somatic cells of male Drosophila, male-specific lethal (MSL) protein complex specifically targets the X chromosome and results in a balanced expression level between the single-copied X chromosome vs. the autosomes with two copies [41]. Such a canonical dosage compensation mechanism is absent in the male germline cells, and seems to be replaced by a non-canonical dosage compensation whose mechanism is still unclear, in spermatogonia [42]. Previous transcriptomic and epigenetic studies of enriched spermatogonia cells of bam mutant flies [43,44] showed an overall enrichment of chromatin remodelling factors, and a distinct histone modification pattern from mammalian embryonic stem cells on genes related to cell differentiation. These factors may explain genes predominantly expressed in spermatogonia are most abundant among all genes compared with those expressed in other testis cells (Figure 1), suggesting a more permissive transcriptional environment in spermatogonia than other testis cells. It may also explain that mitotic genes act as an important source for generating the young genes and contributing to the ‘out of the testis’ pattern of new gene origination in Drosophila. Particularly, mitotic genes are enriched on the Drosophila X chromosome (Figure 1), and this has been also reported on the mouse X chromosome [30,45]. The convergent accumulation of male germline mitotic genes on the two independently evolved X chromosomes probably reflects the ‘fast-X evolution’ effect, that male recessive beneficial alleles are expected to be fixed at a faster rate on the X chromosome than the autosomes [46,47].

On the other hand, the general deficiency of male meiotic genes on the X, and consistently, an excess of X-borne new genes onto the autosomes (‘X to A’ genes) that are predominantly expressed in the male meiotic cells (Figure 3), demonstrate the effect of MSCI in Drosophila. Again, a similar underrepresentation of male meiotic genes on the mouse X chromosome has also been reported before [30]. Such similar patterns of the X chromosomes of mouse and Drosophila indicate the selection of MSCI against X-linked genes that are specifically expressed during meiosis. This does not preclude some X-linked new genes that evolved novel or necessary functions during meiosis to be fixed in population (e.g., Sdic gene family), driven by either sperm competition or sexual conflict, which is expected to be more intense during late spermatogenesis. In mammals, the contrasting forces of ‘fast-X evolution’ and MSCI together resulted in an excess of genes duplicated onto the X chromosome, as well as an excess of genes relocated from the X chromosome (the ‘gene traffic’ pattern) [12]. The development of scRNA-seq data atlas of different organs of both Drosophila and mammals [48], as well as future functional studies into the parental–new gene pairs that have been annotated for their divergent expressed testis cell types in this study (Figure S5), provide more insights into the complex molecular and evolutionary factors acting on the X chromosome, and the evolutionary trajectories of new genes.

4. Materials and Methods

4.1. Datasets of New Genes and scRNA-seq

The new gene dataset of Drosophila is derived from GenTree [27]. We only used those identified de novo genes or new genes with clearly defined parental genes with respective age information. Among these, there are 565 new genes produced by gene duplication (464 from DNA-based duplication and 101 from RNA-based duplication) and 140 de novo genes. These new genes are divided into 6 age groups based on their origination time, with the youngest group only restricted to Drosophila melanogaster and labeled as branch 6 and so on (Figure 1a). For duplication pairs, the new genes were shorter than their parental genes in gene length, and have less exons than their parental genes, especially for RNA-level duplicated new genes, as retrogenes were generated from mRNA and had no introns (Figure S1). Additionally, for the chromosomal location of new genes, it seems not having specificity in a chromosome or distance to TE (Figure S2). It was reported that new genes in Drosophila have an ‘out of X’ pattern. For our new gene set, the inter-chromosomal RNA-level duplication new genes indeed have an ‘out of X’ pattern, showing an excess of new genes retroposed from X to autosomes (X-squared = 5.7022, p-value = 0.01694) when being compared with the expected ratio (calculated basing on gene number of source chromosome, chromosome size of targeted chromosome and frequency of retroposition to a given chromosome [7]) (Table S4).

We used previously published scRNA-seq data of adult D. melanogaster testes from 2 different strains [26]. Reads were aligned and filtered based on the FlyBase dmel_r6.15 reference genome with Cellranger 4.0.0 [49], and count matrices were generated. Potential doublets were detected using DoubletFinder [50] and removed. R package Seurat 4.0.2 [51] was used for single-cell downstream analysis. First, genes expressed in at least 3 cells and cells with at least 200 genes expressed were kept. Remaining cells were normalized by SCTransform [52] with default parameters. A total of 2000 variable features were selected in each dataset, and 2 datasets were integrated using the canonical correlation analysis (CCA) method implemented in Seurat by default augments. After integration, FindNeighbors and FindClusters were performed with 30 PCs and the resolution was 2. Cells were visualized with Uniform Manifold Approximation and Projection (UMAP). We annotated 7 cell types, including 4 germline cell types and 3 somatic cell types with markers used in [26]. We used AGO3 and Aub as markers for spermatogonia. Clusters with high expression of CycB and fzo were annotated as early spermatocytes and clusters expressing twe but not fzo were identified as late spermatocytes. Spermatids were identified by soti, boly and p-cup. Clusters enriched in tj and eya are cyst cells. Hub cells are marked by Fas3 and zfh1. Cells expressing MtnA but not zfh1 are epithelial cells. Average expression levels (log2(CPM + 1)) for each cell type were calculated. Since germline somatic cells are of relatively low numbers, we focused our study on germ cells.

4.2. Defining the Major Expressed Cell Type of Drosophila Genes

For all the genes annotated in Flybase (r6.15), 15,189 genes were expressed in germline cells, 30 genes were only detected in somatic cell types, and the other 2508 genes were not expressed in testis. We used the 15,189 germline expressing genes (log2(CPM + 1)) to generate a row-scaled heatmap with the ComplexHeatmap (version 2.6.2 [53]) package in R, using hierarchical clustering (hclust in r, the complete linkage method) and cutting the generated dendrogram tree into 7 clusters (cutree function called by color_branches from dendextend package in r) basing on the gene expression pattern (the blank lines in Figure 1b are the borders of the clusters). Based on the development of the germline cells and clustering patterns, we divided 7 clusters into 5 categories, genes enriched in spermatogonia were defined as mitosis genes, genes enriched in spermatocytes were defined as meiosis genes, genes enriched in spermatids were defined as post-meiosis genes. We further defined those enriched in both spermatogonia and early spermatocytes as mitosis and meiosis genes, and those enriched in spermatocytes and spermatids as meiosis and post-meiosis genes. Since the post-meiosis stage contains very few genes in the clustering result, we combined the meiosis and post-meiosis stage together. To verify our categorization of genes, we not only clustered the expressional level using row-scaled log2(CPM + 1) value of each gene in every cell type, but also used the percentage of expressed cells in each cell type to carry out hierarchical clustering. The overall pattern of different types of genes across different chromosomes stayed the same, regardless how we clustered the genes (Figure S3).

4.3. Comparing the Percentage of Genes in Different Stages between Chromosomes

To find out if there was enrichment of genes in different stages in each chromosome, first we showed the distribution of different categories of genes in autosomes, 4, X and Y chromosomes, and compared whether the difference of percentage for genes in each stage between other chromosomes (4,X,Y) and autosomes were significant (Figure 1c). The gene numbers in each chromosome in each stage were shown in Supplementary Table S5a.

For the calculation method of the ratio in Figure 1d, we first normalized the gene numbers in each stage with the gene numbers in each chromosome and obained the normalized numbers in different stages in each chromosome (Figure 1c, Table S5b), then calculated the ratio between other chromosomes vs. autosomes based on the normalized numbers in each stage of each chromosome (Figure 1d, Table S5c).

4.4. Comparing the Expressed Cell Types between the New and Parental Genes

To measure the stage shift between the new and parental genes, we proposed a calculation method. From spermatogonia to spermatids, corresponding to numbers 1 to 4, the difference between child value and parent value is the pairs’ stage shift condition. The negative number means the child stage is before the parent stage, and a positive number means the child stage is after the parent stage, thus we obtained a value by which to measure the stage shift condition. All the significant tests in main figures were performed using the Fisher test in R (Table S2). For duplicated new genes, the tests were checked between parent and child. For de novo new genes, the tests were checked between de novo new genes and all annotated genes. We used Flybase (http://flybase.org/, accessed on 4 May 2021) to manually check individual genes’ expression patterns across different tissues or stages, based on the modENCODE transcriptome data [54,55].

5. Conclusions

In conclusion, we provide cell-level evidence for MSCI driving the new genes off the X chromosome to be relocated onto the autosome in Drosophila, and uncovered the different expression patterns of new genes across testis cells compared to their progenitors.