Abstract
Litopenaeus vannamei is one of the most important shrimp species for worldwide aquaculture. Despite this, little genomic information is available for this penaeid and other closely related taxonomic crustaceans. Consequently, genes, proteins and their respective polymorphisms are poorly known for these species. In this work, we used the RNA sequencing technology (RNA-seq) in L. vannamei shrimp evaluated for growth performance, and exposed to the White Spot Syndrome Virus (WSSV), in order to investigate the presence of Single Nucleotide Polymorphisms (SNPs) within genes related to innate immunity and growth, both features of great interest for aquaculture activity. We analyzed individuals with higher and lower growth rates; and infected (unhealthy) and non-infected (healthy), after exposure to WSSV. Approximately 7,000 SNPs were detected in the samples evaluated for growth, being 3,186 and 3,978 exclusive for individuals with higher and lower growth rates, respectively. In the animals exposed to WSSV we found about 16,300 unique SNPs, in which 9,338 were specific to non-infected shrimp, and 7,008 were exclusive to individuals infected with WSSV and symptomatic. In total, we describe 4,312 unigenes containing SNPs. About 60% of these unigenes returned GO blastX hits for Biological Process, Molecular Function and Cellular Component ontologies. We identified 512 KEGG unique KOs distributed among 275 pathways, elucidating the majority of metabolism roles related to high protein metabolism, growth and immunity. These polymorphisms are all located in coding regions, and certainly can be applied in further studies involving phenotype expression of complex traits, such as growth and immunity. Overall, the set of variants raised herein enriches the genomic databases available for shrimp, given that SNPs originated from nextgen are still rare for this relevant crustacean group, despite their huge potential of use in genomic selection approaches.
Highlights
One of the central challenges in shrimp farming is to avoid economical loss due to animal growth limitations and even population death (Jung et al, 2013; Chen et al, 2015) commonly caused by pathogens
Shrimps evaluated for growth performance For this approach, we used pleopod samples from Specific Pathogen Free (SPF) L. vannamei genetically improved through a selective breeding program conducted for rapid growth performance and good survival rates in a Brazilian shrimp breeding company
The 24 libraries constructed from higher growth samples had 831,930,442 mapped reads, whilst 796,126,113 reads were mapped for the 24 libraries from lower growth samples (96% of the 1,697,401,992 filtered reads)
Summary
One of the central challenges in shrimp farming is to avoid economical loss due to animal growth limitations and even population death (Jung et al, 2013; Chen et al, 2015) commonly caused by pathogens. In an attempt of stop pathogen propagation, the organism goes into a severe oxidative metabolic stress yielding many Reactive Oxygen Species (ROS), which may cause cell and DNA structural damages, leading to apoptosis, and to animal death (Rewitz et al, 2006; Qian et al, 2014). It is widely known that viral infection and proliferation induces apoptosis in shrimp (Leu et al, 2013; Wang & Wang, 2013a; Wang et al, 2014). In this way, energy that could be being spent in growth is required by shrimp immunity when exposed to pathogens (Lv et al, 2014; Rao et al, 2016). External factors, including temperature and inefficient food supply significantly influences growth performance (Jindra, Palli & Riddiford, 2013), leading to a not profitable scenario to aquaculture
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