Comprehensive Genome-Wide Analysis of Wnt Gene Family and Expression Profiling during Limb Regeneration in Portunus trituberculatus

Abstract

Wnt genes encode a family of secretory glycoproteins that are involved in various stages of organ development through regulation of cell proliferation, differentiation, and growth. Recently, Wnt genes have been shown to play an important role in regeneration processes. However, there have been no previous genome-wide analyses of the Wnt gene family members in crab species. In this study, a total of 13 Wnt family genes were identified from the genome of the swimming crab Portunus trituberculatus and classified into three main groups based on the conserved domain, protein sequence, and motifs. Chromosome location analysis showed that tandem duplication may have resulted in the expansion of the PtWnt gene family. RNA-seq results indicated that most PtWnt genes had a higher Fragments Per Kilobase of transcript sequences per Million base pairs (FPKM) value in the regenerating limb bud muscle than in the normal limb muscle, and the genes were enriched in a number of pathways that had biological functions underlying limb regeneration such as the cell surface receptor signaling pathway, the hippo signaling pathway, receptor binding, and basal cell carcinoma. Moreover, quantitative real-time PCR (RT-qPCR) analysis confirmed that the expression levels of nine PtWnts except for PtWnt1, PtWnt2, and PtWnt6 had a consistently increasing trend during limb regeneration. PtWnt1, PtWnt2, and PtWnt6 exhibited significantly up- or down-regulated expression at different limb regeneration stages. These results provide valuable information for further evolutionary and functional characterization of PtWnt genes and indicate the complexity and specialized mechanism of the Wnt signaling pathway regulating regeneration in crustaceans.

Whole-Genome Identification and Characterization of the DKK Gene Family and Its Transcription Profiles: An Analysis of the Chinese Soft-Shell Turtle (Pelodiscus sinensis)

“…We downloaded Hidden Markov Model (HMM) files for the DKK gene (IPR039863) from the Pfam Protein Family Database ( , accessed on 10 July 2023). The HMMER 3.0 software [ 32 ] was employed to identify members of the DKK gene family within the P. sinensis genome. Subsequently, the candidate sequences were validated and redundant ones were eliminated through detailed analysis using the NCBI Conserved Domain tool ( , accessed on 17 July 2023) [ 33 ] and SMART database ( , accessed on 20 July 2023) [ 34 ].…”