Hypoderaeum conoideum is a neglected but important trematode. The life cycle of this parasite is complex: snails serve as the first intermediate hosts: bivalves, fishes or tadpoles serve as the second intermediate hosts, and poultry (such as chickens and ducks) act as definitive hosts. In recent years, H. conoideum has caused significant economic losses to the poultry industry in some Asian countries. Despite its importance, little is known about the molecular ecology and population genetics of this parasite. Knowledge of mitochondrial (mt) genome of H. conoideum can provide a foundation for phylogenetic studies as well as epidemiological investigations. The entire mt genome of H. conoideum was amplified in five overlapping fragments by PCR and sequenced, annotated and compared with mt genomes of selected trematodes. A phylogenetic analysis of concatenated mt amino acid sequence data for H. conoideum, eight other digeneans (Clonorchis sinensis, Fasciola gigantica, F. hepatica, Opisthorchis felineus, Schistosoma haematobium, S. japonicum, S. mekongi and S. spindale) and one tapeworm (Taenia solium; outgroup) was conducted to assess their relationships. The complete mt genome of H. conoideum is 14,180 bp in length, and contains 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one non-coding region (NCR). The gene arrangement is the same as in Fasciola spp, with all genes being transcribed in the same direction. The phylogenetic analysis showed that H. conoideum had a relatively close relationship with F. hepatica and other members of the Fasciolidae, followed by the Opisthorchiidae, and then the Schistosomatidae. The mt genome of H. conoideum should be useful as a resource for comparative mt genomic studies of trematodes and for DNA markers for systematic, population genetic and epidemiological studies of H. conoideum and congeners.

Fischoederius elongates is an important trematode of Paramphistomes in ruminants. Animals infected with F. elongates often don’t show obvious symptoms, so it is easy to be ignored. However it can cause severe economic losses to the breeding industry. Knowledge of the mitochondrial genome of F. elongates can be used for phylogenetic and epidemiological studies. The complete mt genome sequence of F. elongates is 14,120 bp in length and contains 12 protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions (LNR and SNR). The gene arrangement of F. elongates is the same as other trematodes, such as Fasciola hepatica and Paramphistomum cervi. Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes by Maximum-likelihood and Neighbor-joining analysis method showed that F. elongates was closely related to P. cervi. The complete mt genome sequence of F. elongates should provide information for phylogenetic and epidemiological studies for F. elongates and the family Paramphistomidae.