Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini.

Ben-Wen Li,Gary J Weil,Kong-Zhen Gu,Rahul Tyagi,Qing Ren Zeng,Samantha N Mcnulty,Bruce A Rosa,Makedonka Mitreva

doi:10.1186/s13071-016-1785-x

Abstract

BackgroundParagonimiasis is an important and widespread neglected tropical disease. Fifteen Paragonimus species are human pathogens, but two of these, Paragonimus westermani and P. skrjabini, are responsible for the bulk of human disease. Despite their medical and economic significance, there is limited information on the gene content and expression of Paragonimus lung flukes.ResultsThe transcriptomes of adult P. westermani and P. skrjabini were studied with deep sequencing technology. Approximately 30 million reads per species were assembled into 21,586 and 25,825 unigenes for P. westermani and P. skrjabini, respectively. Many unigenes showed homology with sequences from other food-borne trematodes, but 1,217 high-confidence Paragonimus-specific unigenes were identified. Analyses indicated that both species have the potential for aerobic and anaerobic metabolism but not de novo fatty acid biosynthesis and that they may interact with host signaling pathways. Some 12,432 P. westermani and P. skrjabini unigenes showed a clear correspondence in bi-directional sequence similarity matches. The expression of shared unigenes was mostly well correlated, but differentially expressed unigenes were identified and shown to be enriched for functions related to proteolysis for P. westermani and microtubule based motility for P. skrjabini.ConclusionsThe assembled transcriptomes of P. westermani and P. skrjabini, inferred proteins, and extensive functional annotations generated for this project (including identified primary sequence similarities to various species, protein domains, biological pathways, predicted proteases, molecular mimics and secreted proteins, etc.) represent a valuable resource for hypothesis driven research on these medically and economically important species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-016-1785-x) contains supplementary material, which is available to authorized users.

Highlights

Paragonimiasis is an important and widespread neglected tropical disease
A total of 27,842 transcripts from 21,586 unigenes were generated from P. westermani while 35,312 transcripts from 25,825 unigenes were generated from P. skrjabini
Fragmentation, reported as the percentage of reference genes matched to non-overlapping transcript BLAST hits, was estimated at 24.3 % for P. westermani and 26.7 % for P. skrjabini with respect to the protein coding sequences of C. sinensis

Summary

Introduction

Fifteen Paragonimus species are human pathogens, but two of these, Paragonimus westermani and P. skrjabini, are responsible for the bulk of human disease. Despite their medical and economic significance, there is limited information on the gene content and expression of Paragonimus lung flukes. When infected crustaceans are ingested by a permissive host (typically small carnivores such as canids, felids, murids, mustelids, viverrids, etc.), metacercariae migrate out of the digestive tract and into the lung, where they mature to long-lived, hermaphroditic, sexually reproducing adults within pulmonary cysts. Metacercariae ingested by a non-permissive often fail to find the lung. They remain in an immature state and migrate through abnormal tissues including the central nervous system (CNS). Paragonimus skrjabini, for example, is poorly adapted to humans and often causes these ectopic infections [3]

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