Transcriptome analysis of the Sepia pharaonis: Identification of low salinity stress-related information and microsatellite markers

Highlights

• Explore osmoregulation in Sepia pharaonis by transcriptome sequencing;

• Reveal key insights into the genetic markers of salt stress in Sepia pharaonis.

• Discovery useful microsatellites for genetic linkage mapping

Abstract

Sepia pharaonis has great commercial value for aquaculture. However, it is sensitive to salinity fluctuations and lacking in genomic information. The present work utilized high-throughput transcriptome sequencing to assess the effect of low salinity (22.0 ppt) on gills of S. pharaonis. 6153 genes were identified as differentially expressed (p < 0.05), of which 3340 were increased and 2813 were decreased in low salinity group (22.0 ppt) relative to the control group (29.0 ppt). Subsequently, these DEGs were allocated to 226 KEGG pathways and 491 GO terms. Analysis of the transcriptome sequences and DEGs identified several unigenes and pathways involved in salt stress regulation. Moreover, the S. pharaonis carried 101,576 simple sequence repeats (SSRs). This is the first time osmoregulation in S. pharaonis has been explored by transcriptome sequencing. The data presented here reveals key insights into the genetic markers of salt stress in S. pharaonis.

Introduction

Sepia pharaonis is commonly located in the Red Sea and Persian Gulf, from northern Australia to Gulf of Thailand and Japan, and from the Indian Ocean to the Andaman Sea (Roper et al., 2005). Being a giant cuttlefish species, it can grow to 42 cm in mantle length and 5 kg in weight. The feeding habits, resistance to disease, tolerance to crowding and handling, short life span, and rapid growth makes this species an ideal commercially viable mariculture (Minton et al., 2001).

Among the key factors that determine the stable growth and well-being of many aquaculture species in salinity. Thus, the level of salinity should be optimized for effective artificial propagation of S. pharaonis. During culture, S. pharaonis often experiences significant chances in salinity caused by heavy rainfalls, and this may lead to high mortality and farm productivity. Osmoregulation is the most direct response to salinity change. Then physiological functions of immune, digestion system will be affected, causing growth and survival threat.

Several types of research about the effect of salinity to S. pharaonis have been done. Le et al. (2014) found the suitable salinity of S. pharaonis larvae was from 24 ppt to 33 ppt, and the most appropriate salinity was 27 ppt, by researching the impact of salinity on survival and growth similar to the finding of Dai et al. (2012). Huang et al. (2012) studied the effects of salinities (15.0, 18.0, 21.0, 24.0, 27.0, 30.0 and 33.0) on fertilized egg hatching and survival activity index (SAI) of the larvae of S. pharaonis in the laboratory at 22 ± 1 °C. Wen et al. investigated the effects of salinity on survival and behavior in juvenile S. pharaonis in a laboratory (Wen et al., 2011). Except for suitable salinity for fertilized egg, larvae and juvenile, the effects of abrupt and gradual changes of salinity on survival rate, specific growth rate, weight gain rate, hepatosomatic index, and enzyme activity (superoxide dismutase, glutamic-pyruvic transaminase, glutamic oxaloacetic transaminase, alkaline phosphatase) were explored as well (Kexin et al., 2015). However, current researchers focus on tolerance and general physiology to the salinity of this species, and the molecular mechanism is little to be understood.

Currently, unlike many other species for which genomic sequences are available, such sequences are unavailable for sepia and this have substantially limited the exploration of its physiological regulation. To overcome this challenge, researchers have employed next-generation sequencing approach to characterize the molecular process of this species efficiently at low cost (De Vos et al., 2019). Transcriptome sequencing yields double-stranded cDNA which are annotated in relevant databases (Ma et al., 2019). This has expanded our understanding and accelerated the identification of new genes networks, for many organisms for which the genomes are yet to be fully elucidated (Mardis, 2008). Additionally, the widespread application of next-generation sequencing has also led to the discovery and characterization of SSRs for many aquaculture species. This is because its time-saving (Jia et al., 2019). SSRs are important factors used in breeding and genetic studies.

In the present work, Illumina Hiseq2500 tool was employed to map the gill transcriptome of S. pharaonis. Genes related to salinity stress were identified. Furthermore, we uncovered and characterized SSR elements in the transcriptome for the first time in S. pharaonis which helps to understand its genetic information and osmoregulation.