Parasites infection in Black-necked Cranes Revealed by Piloting High-throughput Sequencing of V4 and V9 Regions of 18S rDNA

Abstract

Abstract Illumina high-throughput sequencing is a representative tool for understanding the diversity of eukaryotic community. We compared the parasites diversity of 24 fecal samples from the wintering black-necked cranes in Caohai wetland using the Illumina sequencing of 18S rDNA V4 and V9 regions. Globally, 237 operational taxonomic units (OTUs) and 197 OTUs were detected using the V4 and V9 primer sets, respectively. Taxonomic analyses of these OTUs revealed that the number of phyla, families, genera and species in V4 datasets were higher than V9 datasets and at the level of class and order was lower than V9 datasets. The alpha diversity index for V4 were all higher than V9, which also illustrates that datas from the V4 region are more rich. However, the V9 datasets detected Echinostoma caproni which was a common parasite in birds while the V4 datasets were failed, so we strongly recommend both V4 and V9 regions be used to assess the diversity within the parasites in fecal samples. After in-depth discussion on the species level and phylogenetic analysis of parasites, we finally confirmed that the black-necked cranes were infected with E. reichenowi, E. gruis, C. struthionis and E. caproni. Among them, E. caproni was a zoonotic parasite, C. struthionis had unknown pathogenicity, and E. reichenowi and E. gruis had the greatest threat to the health of black-necked cranes. These four parasites should be given great attention and sustained attention in the follow-up study. The results enriched the application of high-throughput sequencing technology in bird parasite detection.