Open Access Highly Accessed Research article

Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus

Yun Bai1, Zhuangzhi Zhang2, Lei Jin1, Hui Kang1, Yongqiang Zhu1, Lu Zhang1, Xia Li1, Fengshou Ma1, Li Zhao2, Baoxin Shi2, Jun Li3, Donald P McManus4, Wenbao Zhang3* and Shengyue Wang1*

Author Affiliations

1 Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, 250 Bibo Road, Shanghai 201203, China

2 Veterinary Research Institute, Xinjiang Academy of Animal Sciences, 151 East-Kelamayi Street, Urumqi, Xinjiang 830000, China

3 State Key Laboratory Incubation Base of Xinjiang Major Diseases Research, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, No. 1 Liyushan Road, Urumqi, Xinjiang 830054, China

4 Molecular Parasitology Laboratory, QIMR Berghofer Institute of Medical Research, Brisbane, QLD, Australia

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BMC Genomics 2014, 15:736  doi:10.1186/1471-2164-15-736

Published: 29 August 2014

Abstract

Background

MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotes. The cestode Echinococcus granulosus has a complex life-cycle involving different development stages but the mechanisms underpinning this development, including the involvement of miRNAs, remain unknown.

Results

Using Illumina next generation sequencing technology, we sequenced at the genome-wide level three small RNA populations from the adult, protoscolex and cyst membrane of E. granulosus. A total of 94 pre-miRNA candidates (coding 91 mature miRNAs and 39 miRNA stars) were in silico predicted. Through comparison of expression profiles, we found 42 mature miRNAs and 23 miRNA stars expressed with different patterns in the three life stages examined. Furthermore, considering both the previously reported and newly predicted miRNAs, 25 conserved miRNAs families were identified in the E. granulosus genome. Comparing the presence or absence of these miRNA families with the free-living Schmidtea mediterranea, we found 13 conserved miRNAs are lost in E. granulosus, most of which are tissue-specific and involved in the development of ciliated cells, the gut and sensory organs. Finally, GO enrichment analysis of the differentially expressed miRNAs and their potential targets indicated that they may be involved in bi-directional development, nutrient metabolism and nervous system development in E. granulosus.

Conclusions

This study has, for the first time, provided a comprehensive description of the different expression patterns of miRNAs in three distinct life cycle stages of E. granulosus. The analysis supports earlier suggestions that the loss of miRNAs in the Platyhelminths might be related to morphological simplification. These results may help in the exploration of the mechanism of interaction between this parasitic worm and its definitive and intermediate hosts, providing information that can be used to develop new interventions and therapeutics for the control of cystic echinococcosis.

Keywords:
Echinococcus granulosus; microRNA; Deep sequencing; Differential expression; Life cycle stage development