De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome

Abstract

The black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally; however, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date based on nine adult tissues and eight early life-history stages (BUSCO - Complete: 98.2% [Duplicated: 51.3%], Fragmented: 0.8%, Missing: 1.0%). The assembly resulted in 236,388 contigs, which were then further segregated into 99,203 adult tissue specific and 58,678 early life-history stage specific clusters. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. Transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.

Figure 1

Species distribution of successfully annotated sequences across the top 29 species using the SwissProt (A) and arthropod subsection of the non-redundant (B) database.

Figure 2

Distribution of sequence annotations based on the SWISS-PROT database across the top 20 GO terms at level 2. Determined across the entire dataset for Biological Process (BP, green), Molecular Function (MF, blue), and Cellular Component (CC, yellow).

Figure 3

Principal component analysis showing the top most highly differentially expressed transcripts of (A) nine tissue types (top 1,000) and (B) eight early life-history stages (top 500). PC = principal component, PL = post-larvae.

Figure 4

Heatmap and hierarchical grouping of the top 2,000 differentially expressed genes in the nine different tissue types. A darker colour indicates a higher expression level. Gene expression patterns (rows) were grouped into nine expression groups based on Pearson’s correlation and the three replicates of each tissue type (columns) into nine tissue groups based on Euclidean distance. EY – eyestalk; FG – female gonad; GI – gill; HL – hemolymph; HP – hepatopancreas; LO – lymphoid organ; MG – male gonad; MU – muscle; ST – stomach.

Figure 5

Heatmap and hierarchical grouping of the top 500 differentially expressed genes in the eight larval and post-larval stages examined. A darker colour indicates a higher expression level. Gene expression patterns in each larval/post-larval stage (row) were grouped into nine expression groups based on Pearson’s correlation.

Figure 6

Presence of mRNA contigs that encode for RNA polymerase subunits based on KEGG pathway analysis^–. Green shading highlights the presence of gene orthologs in the P. monodon transcriptome.

Figure 7

Presence of eukaryotic basal transcription factor sequences based on KEGG pathway analysis^–. Green shading highlights the presence of gene in the P. monodon transcriptome.