Characterization of the Transcriptional Complexity of the Receptive and Pre-receptive Endometria of Dairy Goats

Abstract

Endometrium receptivity is essential for successful embryo implantation in mammals. However, the lack of genetic information remains an obstacle to understanding the mechanisms underlying the development of a receptive endometrium from the pre-receptive phase in dairy goats. In this study, more than 4 billion high-quality reads were generated and de novo assembled into 102,441 unigenes; these unigenes were annotated using published databases. A total of 3,255 unigenes that were differentially expressed (DEGs) between the PE and RE were discovered in this study (P-values < 0.05). In addition, 76,729-77,102 putative SNPs and 12,837 SSRs were discovered in this study. Bioinformatics analysis of the DEGs revealed a number of biological processes and pathways that are potentially involved in the establishment of the RE, notably including the GO terms proteolysis, apoptosis, and cell adhesion and the KEGG pathways Cell cycle and extracellular matrix (ECM)-receptor interaction. We speculated that ADCY8, VCAN, SPOCK1, THBS1, and THBS2 may play important roles in the development of endometrial receptivity. The de novo assembly provided a good starting point and will serve as a valuable resource for further investigations into endometrium receptivity in dairy goats and future studies on the genomes of goats and other related mammals.

Figure 1. Size distribution of the unigenes.

Figure 2. Species distribution of the BLAST hits.

Figure 3. Histogram of unigene KOG classification.

The x-axis indicates the number of genes annotation under the group, the y-axis indicates 26 groups of KOG.

Figure 4. Histogram of the SSRs in pre-receptive and receptive endometrium.

Figure 5. Volcano plots analyses of unigenes in PE and RE.

X-axis on both panels shows base 10 logarithm of RPKM of pre-receptive endometrium. Y axis shows receptive endometrium. Red dots indicate up-regulated genes, blue was not DEG, and the green was down-regulated genes in in the receptive endometrium compared to pre-receptive phase.

Figure 6. Clustering analysis of differentially expressed unigenes.

Heat map of Pearsons correlation across the 20 most differentially expressed transcript tags, and a dendrogram of correlation between transcript tags is shown to the left of the heatmap.

Figure 7. Histogram presentation of the top 20 GO functional annotations for the DEGs.

The right x-axis indicates the number of genes in a category. The left y-axis indicates the specific category of GO.

Figure 8. Histogram presentation of the top 17 KEGG functional annotations for the DEGs.

The x-axis indicates the number of unique sequences assigned to a specific pathway, the y-axis indicates the KEGG pathway.

Figure 9. The expression levels of 18 genes exhibited significantly different expression about Calcium and Cell adhesion.