Transcriptome analysis and identification of differentially expressed genes between early and mature ovarian stages in the female mantis shrimp (Harpiosquilla raphidea) using RNA-Seq

Harpiosquilla raphidea, the largest of the mantis shrimps, is a commercially important crustacean species widely distributed in many countries of the Pacific Ocean. However, no data are currently available regarding the molecular mechanisms that regulate reproduction in this species. To address this knowledge gap, we performed transcriptome sequencing (RNA-Seq) of previtellogenic and vitellogenic ovaries of female H. raphidea, and compared the expression patterns of transcripts from the two resulting libraries to identify genes involved in ovarian development. A total of 418,635,748 clean reads were retrieved after removing adapter sequences and filtering out low-quality data. The reads were assembled into 242,861 unigenes with an average length of 585.27 base pairs (bp) and an N50 of 829 bp. A search of all unigenes against the NR (non-redundant protein), SwissProt, KEGG, GO, and COG databases yielded 53,111; 25,460; 27,255; 26,793; and 3838 unigene matches, respectively). Of the 53,111 unigenes identified in the NR database, 30,441 could be functionally annotated, 59.49% of which were significantly matched with the transcripts of L. vannamei. A total of 13,867 full-length transcripts and 11,441 partial transcripts were retrieved. In addition, using all-unigenes as a reference, a total of 12,765 simple sequence repeats (SSRs) were identified. DESeq2 analysis identified a total of 962 differentially expressed genes (DEGs) between previtellogenic and vitellogenic ovaries, 456 of which were upregulated and 506 downregulated. Five unigenes were validated by quantitative real-time PCR (qPCR). The results of both the RNA-Seq and qPCR analysis revealed that the H. raphidea vitellogenin gene (HrVtg) was upregulated in vitellogenic ovaries. The open reading frame of HrVtg was found to be 7455 bp long, corresponding to a polypeptide of 2485 amino acids. The important functional genes and pathways identified here provide a valuable dataset for understanding the molecular mechanisms controlling ovarian development in H. raphidea.