Whole Transcriptome Analysis Provides Insights into Molecular Mechanisms for Molting in Litopenaeus vannamei

Abstract

Molting is one of the most important biological processes in shrimp growth and development. All shrimp undergo cyclic molting periodically to shed and replace their exoskeletons. This process is essential for growth, metamorphosis, and reproduction in shrimp. However, the molecular mechanisms underlying shrimp molting remain poorly understood. In this study, we investigated global expression changes in the transcriptomes of the Pacific white shrimp, Litopenaeus vannamei, the most commonly cultured shrimp species worldwide. The transcriptome of whole L. vannamei was investigated by RNA-sequencing (RNA-seq) throughout the molting cycle, including the inter-molt (C), pre-molt (D0, D1, D2, D3, D4), and post-molt (P1 and P2) stages, and 93,756 unigenes were identified. Among these genes, we identified 5,117 genes differentially expressed (log2ratio ≥1 and FDR ≤0.001) in adjacent molt stages. The results were compared against the National Center for Biotechnology Information (NCBI) non-redundant protein/nucleotide sequence database, Swiss-Prot, PFAM database, the Gene Ontology database, and the Kyoto Encyclopedia of Genes and Genomes database in order to annotate gene descriptions, associate them with gene ontology terms, and assign them to pathways. The expression patterns for genes involved in several molecular events critical for molting, such as hormone regulation, triggering events, implementation phases, skelemin, immune responses were characterized and considered as mechanisms underlying molting in L. vannamei. Comparisons with transcriptomic analyses in other arthropods were also performed. The characterization of major transcriptional changes in genes involved in the molting cycle provides candidates for future investigation of the molecular mechanisms. The data generated in this study will serve as an important transcriptomic resource for the shrimp research community to facilitate gene and genome annotation and to characterize key molecular processes underlying shrimp development.

RNA sequencing reveals distinct gene expression patterns during the development of parasitic larval stages of the salmon louse (Lepeophtheirus salmonis)

“…Gao et al. () investigated the adult moult cycle, which means that growth and moulting are the main regulated processes, whereas in our study in L. salmonis the larvae development is also involved. As expected, similarities between these two data sets were found.…”

“…During larval moult, the transition between consecutive stages is not only accompanied by growth, but in addition by major restructuring of the body and its appendages. These strong phenotypic changes are reflected in a strong shift in the overall gene expression in arthropods (Gao et al., ; Kuballa, Holton, Paterson, & Elizur, ; White, Rifkin, Hurban, & Hogness, ).…”

Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis

“…While a sizeable microarray EST dataset does already exist for the porcelain crab Petrolisthes cinctipes ($98K ESTs; Tagmount et al 2010), the sequences generated in this study via NGS approaches nearly triple this dataset ($194K ESTs) and adds $279K sequences for the closely related species Petrolisthes manimaculis. Within just the last few years, the community of crustacean biologists have utilized NGS-powered functional genomics approaches to examine, among other topics, growth and development (lipid storage and diapause cues in Calanus finmarchicus copepods; Tarrant et al (2014); comparison of eye-development among ecotypes in the freshwater isopod, Asellus aquaticus; Stahl et al (2015)), immune and toxin responses (investigation of resistance to a delousing drug in Caligus rogercresseyi, Chávez-Mardones and Gallardo-Escárate (2015); identification of candidate genes involved in virusinduced immune response in L. vannamei; Robalino et al (2007); elucidation of differences between sexes and populations in drug resistance in the parasitic copepod L. salmonis; Poley et al (2015), regulation of molting (Y-organ molt gland profiling, Das et al (2016); global expression changes throughout the molt cycle in L. vannamei, Gao et al (2015), and responses to hypercapnia and hypoxia (characterization of a suite of hemocyanin genes involved in hypercapnic-hypoxia response in L. vannamei; Johnson et al (2015), nitrate stress (contrasting acute and chronic exposure in the river prawn Macrobrachium nipponense; Xu et al (2016), and thermal and osmotic challenges (acute and plastic heat shock responses in P. cinctipes; Teranishi and Stillman (2007); Stillman and Tagmount (2009);Ronges et al (2012); responses to acute salinity stress in L. vannamei, Wang et al (2015). Such approaches are useful in helping to develop mechanistic models of cellular processes accompanying phenotypic shifts in response to stress (phenotypic plasticity) and provide fruitful grounds for addressing hypotheses in the field of ecological physiology.…”

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

“…Domesticated shrimps could not mature well with declining growth rates over generations (Jackson & Wang, 1998). Albeit its importance, the knowledge on genes controlling shrimp’s growth remained limited partly due to the lack of the genome, thus up-to-now most growth-related genes identified in P. monodon were from L. vannamei (Gao et al, 2017; Gao et al, 2015; Santos et al, 2018).…”