Abstract
As an important tool for systematic analysis, genome-scale metabolic network (GSMN) model has been widely used in various organisms. However, there are few reports on the GSMNs of aquatic crustaceans. Litopenaeus vannamei is the largest and most productive shrimp species. Feed improvement is one of the important methods to improve the yield of L. vannamei and control water pollution caused by the inadequate absorption of feed. In this work, the first L. vannamei GSMN named iGH3005 was reconstructed and applied to the optimization of feed. iGH3005 was reconstructed based on the genomic data. The model includes 2,292 reactions and 3,005 genes. iGH3005 was used to analyze the nutritional requirements of five different L. vannamei commercial varieties and the genes influencing the metabolism of the nutrients. Based on the simulation, we found that tyrosine-protein kinase src64b like may catalyze different reactions in different commercial varieties. The preference of carbohydrate utilization is different in various commercial varieties, which may due to the different expressions of some genes. In addition, this investigation suggests that a rational and targeted modification in the macronutrient content of shrimp feed would lead to an increase in growth and feed conversion rate. The feed for different commercial varieties should be adjusted accordingly, and possible adjustment schemes were provided. The results of this work provided important information for physiological research and optimization of the components in feed of L. vannamei.
Highlights
Litopenaeus vannamei, known as South American white-leg shrimp, is naturally distributed in the pacific coastal waters from northern Peru to Mexico
Using enzyme number as a bridge, the genes of L. vannamei were matched to the reactions, and the information of pathway and subsystem was integrated to each reaction, which composed the draft reconstruction of L. vannamei genome-scale metabolic network (GSMN)
By searching the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found that their corresponding enzyme was tyrosine-protein kinase src64b like, which means that this enzyme in different commercial varieties of L. vannamei has different expression levels and catalyzes different reactions
Summary
Litopenaeus vannamei, known as South American white-leg shrimp, is naturally distributed in the pacific coastal waters from northern Peru to Mexico. Various substances have been tried as feed additives to test their effects on improving the growth performance of L. vannamei, including butonlin onion extract (Munaeni et al, 2019), succinic acid (Duan et al, 2018), β-glucan (Li et al, 2019), yeast hydrolysate (Jin et al, 2018), and large seaweeds (Niu et al, 2018). These studies focus on some specific compounds but lack systematic analysis, which limit the comprehensive exploration and analysis of the nutritional requirements of L. vannamei
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