RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus.

Ying Dong,Zhong Chen,Zunchun Zhou,Aifu Yang,Yongjia Pan,Shan Gao,Hongjuan Sun,Jingwei Jiang,Xiaoyan Guan

doi:10.1186/s12864-016-2810-3

Ying Dong, Zhong Chen + Show 7 more

Open Access

https://doi.org/10.1186/s12864-016-2810-3

Copy DOI

Abstract

BackgroundSea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. In this study, we characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression.ResultsRNA sequencing of 21 cDNA libraries from various tissues and developmental stages of SUS-affected A. japonicus yielded 553 million raw reads, of which 542 million high-quality reads were generated by deep-sequencing using the Illumina HiSeq™ 2000 platform. The reference transcriptome comprised a combination of the Illumina reads, 454 sequencing data and Sanger sequences obtained from the public database to generate 93,163 unigenes (average length, 1,052 bp; N50 = 1,575 bp); 33,860 were annotated. Transcriptome comparisons between healthy and SUS-affected A. japonicus revealed greater differences in gene expression profiles in the body walls (BW) than in the intestines (Int), respiratory trees (RT) and coelomocytes (C). Clustering of expression models revealed stable up-regulation as the main pattern occurring in the BW throughout the three stages of SUS progression. Significantly affected pathways were associated with signal transduction, immune system, cellular processes, development and metabolism. Ninety-two differentially expressed genes (DEGs) were divided into four functional categories: attachment/pathogen recognition (17), inflammatory reactions (38), oxidative stress response (7) and apoptosis (30). Using quantitative real-time PCR, twenty representative DEGs were selected to validate the sequencing results. The Pearson’s correlation coefficient (R) of the 20 DEGs ranged from 0.811 to 0.999, which confirmed the consistency and accuracy between these two approaches.ConclusionsDynamic changes in global gene expression occur during SUS progression in A. japonicus. Elucidation of these changes is important in clarifying the molecular mechanisms associated with the development of SUS in sea cucumber.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2810-3) contains supplementary material, which is available to authorized users.

Highlights

Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious
It is noteworthy that the numbers of differentially expressed genes (DEGs) in the body walls (BW) were higher in SUS-affected samples compared to those in healthy samples (I-SUS-BW vs. HBW 9,854, II-SUS-BW vs. H-BW 10,182, III-SUS-BW vs. H-BW 9,726 and I-N-BW vs. H-BW 9,607, II-N-BW vs. HBW 9,670, III-N-BW vs. H-BW 9,570 DEGs), but lower when SUS-affected samples obtained at the three infection stages were compared to each other (619, 514, and 946 in the SUS groups and 732, 499, and 961 in the normal groups)
When the stage II SUS samples were compared to healthy samples, small numbers of DEGs were found in the Int (1,718), respiratory trees (RT) (3,279) and C (1,847), while more were found in the BW (II-SUS-BW vs. H-BW 10,182 and II-NBW vs. H-BW 9,670)

Summary

Introduction

Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. We characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression. Unlike the genome, which is roughly fixed for a certain cell type, the transcriptome is considered to be highly dynamic [2,3,4,5,6,7]. These transcriptomic changes are the prelude to the impact of protein translation on the phenotype of the organism. Other studies have focused on whole transcriptome analysis to provide an improved understanding of the processes of tumorigenesis and cancer metastasis in human [19, 20]

Methods

Results

Conclusion