Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans

Abstract

SUMMARY We compare whole-animal RNA-seq transcriptomes for C. elegans males and hermaphrodites from the late L3 larval stage to young adulthood. During this interval, male sexual structures develop, including extensive neurogenesis and synaptogenesis that nearly doubles the size of the nervous system. Previous genome-wide expression studies in C. elegans have usually focused on only one sex—the hermaphrodite—and there are a relatively large number of genes that remain without meaningful annotation. In the present study, differential expression analysis of the RNA-seq data revealed 1,751 genes expressed at a higher level in the male. By differential expression and co-expression analyses, we identified transcription factors required for differentiation of male genital structures, semen proteins, and candidates for components of synapse function. Comparison with other prediction tools suggests that our dataset can expand gene predictions. The results validate the dataset as a rich resource for future gene discovery in C. elegans.

Spatial transcriptomics ofC. elegansmales and hermaphrodites identifies novel fertility genes

“…To further investigate if there are sex-specific differences in the expression of the germline pattern genes, we examined differential gene expression in the pooled male and hermaphrodite datasets using DESeq2 (Love et al, 2014). We found that 1274 genes were >2 fold enriched in hermaphrodites (adjusted p value < 0.1) and 3895 genes in males, which corresponds well with bulk RNA sequencing data (Kim et al, 2016). We found that 789 of the germline pattern genes were >2 fold enriched in hermaphrodites, 211 (27%) of which were only identified in the hermaphrodite expression maps (Fig.…”

“…We could detect an average of 16394 genes in hermaphrodites and 16994 in males, with a total 18778 and 19241 genes in the combined datasets, respectively. This represents 93% and 95.3% of genes that were detected in a recent study using bulk RNA sequencing of young adult hermaphrodites and males (Kim et al, 2016).…”

“…Genome-wide expression studies in C. elegans have mostly focused on the hermaphrodite, while the male transcriptome has remained relatively understudied (Kim et al, 2016).…”

“…Neurons such as the male specific CEM and MCM neurons in the head as well as mechanosensory and chemosensory neurons in the tail are required for detecting the hermaphrodite and locating the vulva (Sammut et al, 2015;Wang et al, 2014), while coupling to the vulva is mediated through the specialized structure of the male tail (Liu and Sternberg, 1995). Furthermore, sperm storage and ejaculation is dependent on parts of the male reproductive tract (including the seminal vesicle and vas deferens), which are also responsible for producing seminal fluid and the activation of spermatids prior to injection into the uterus of the hermaphrodite (Ellis and Stanfield, 2014;Kim et al, 2016;Palopoli et al, 2008;Smith and Stanfield, 2011).…”

“…Moreover, since most gene expression studies have focused on the hermaphrodite, expression patterns in the male are still largely uncharacterized (Kim et al, 2016).…”