Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

Abstract

The testis is a peculiar tissue in many respects. It shows patterns of rapid gene evolution and provides a hotspot for the origination of genetic novelties such as de novo genes, duplications and mutations. To investigate the expression patterns of genetic novelties across cell types, we performed single-cell RNA-sequencing of adult Drosophila testis. We found that new genes were expressed in various cell types, the patterns of which may be influenced by their mode of origination. In particular, lineage-specific de novo genes are commonly expressed in early spermatocytes, while young duplicated genes are often bimodally expressed. Analysis of germline substitutions suggests that spermatogenesis is a highly reparative process, with the mutational load of germ cells decreasing as spermatogenesis progresses. By elucidating the distribution of genetic novelties across spermatogenesis, this study provides a deeper understanding of how the testis maintains its core reproductive function while being a hotbed of evolutionary innovation.

A single-cell atlas of adult Drosophila ovary identifies transcriptional programs and somatic cell lineage regulating oogenesis

“…Germline 1 cells are enriched for DNA replication and repair genes, and Germline 2 cells switch to an enrichment in biosynthetic-and metabolic-pathway genes ( Fig 2D). This is strikingly similar to the recent findings in a testis scRNA-seq study, which suggest an increase in mutational load in the immature germline cells of the testis and an early expression bias for DNA repair genes [64].…”

Unraveling Stage-Dependent Expression Patterns of Circular RNAs and Their Related ceRNA Modulation in Ovine Postnatal Testis Development

“…The testis is a strongly transcriptionally active organ whose main functions is to produce sperm through spermatogenesis ( Witt et al, 2019 ). CircRNAs, as an abundant non-coding RNA in the eukaryotic transcriptome, are important modulators involved in modulating expression of genes at the transcriptional, post-transcriptional as well as translational levels and miRNA functions ( Ebbesen et al, 2017 ).…”

Combined use of feature engineering and machine-learning to predict essential genes in Drosophila melanogaster

“…From Ensembl, we obtained genomic, coding sequences (CDSs) and proteins (canonical) data. For D. melanogaster , we also obtained gene transcription data for different tissues ( 30 ); multi-cell or single-cell transcriptomic data from embryo ( 31 ), gonads (GEO accession: GSE125947), testis ( 32 ), brain ( 33 ) and wing disc ( 34 ); Ribo-seq annotations ( 35 ); proteomic data ( 36 ); ATAC-seq peaks ( 37 ), and variomic data (genome-wide SNPs) ( 13 , 38 ).…”