De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski

• Published in: PloS one 2018-10, Vol.13 (10), p.e0205570-e0205570
• Main Authors: Biswal, Devendra Kumar, Roychowdhury, Tanmoy, Pandey, Priyatama, Tandon, Veena
• Format: Article
• Language: English
• Subjects: Analysis; Animals; Annotations; Biochemistry; Biodiversity; Bioinformatics; Biology and Life Sciences; Data processing; Deoxyribonucleic acid; Diagnostic systems; DNA; DNA sequencing; Energy metabolism; Fasciolidae - genetics; Fasciolidae - metabolism; Fasciolopsis buski; Fluke infections; Gene expression; Gene Expression Profiling; Gene sequencing; Genetic aspects; Genome, Helminth; Genomes; Genomics; Health aspects; Helminth Proteins - genetics; Helminth Proteins - metabolism; Hemoglobin; Hogs; Humans; Infections; Intestine; Kinases; Long Interspersed Nucleotide Elements; Metabolism; Mitochondrial DNA; Next-generation sequencing; Organismal biology; Organisms; Parasites; Phylogeny; Protein kinase; Proteins; Public health; Research and Analysis Methods; Ribonucleic acid; Ribosomal DNA; Risk factors; RNA; RNA-mediated interference; Sequence Homology; Short Interspersed Nucleotide Elements; Sus scrofa; Transcriptome; Transposons; Tropical diseases
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0205570

Many trematode parasites cause infection in humans and are thought to be a major public health problem. Their ecological diversity in different regions provides challenging questions on evolution of these organisms. In this report, we perform transcriptome analysis of the giant intestinal fluke, Fasciolopsis buski, using next generation sequencing technology. Short read sequences derived from polyA containing RNA of this organism were assembled into 30,677 unigenes that led to the annotation of 12,380 genes. Annotation of the assembled transcripts enabled insight into processes and pathways in the intestinal fluke, such as RNAi pathway and energy metabolism. The expressed kinome of the organism was characterized by identifying all protein kinases. A rough draft genome assembly for Fasciolopsis buski is also reported herewith with SRA accessions for crosschecking the findings in the analyzed transcriptome data. Transcriptome data also helped us to identify some of the expressed transposable elements. Though many Long Interspersed elements (LINEs) were identified, only two Short Interspersed Elements (SINEs) were visible. Overall transcriptome and draft genome analysis of F. buski helped us to characterize some of its important biological characteristics and provided enormous resources for development of a suitable diagnostic system and anti-parasitic therapeutic molecules.