A total of 106 group faecal samples of different wild birds from Kamal Nehru Zoo, Ahmedabad and Sayyajibaug Zoo, Vadodara, were examined. Out of this 51 (48.11%) were found positive for parasitic infection. Eggs of Ascaris and Capillaria species were observed in 22 (20.75%) and 14 (13.2%) group faecal samples respectively, while the oocyst of Coccidia (Eimeria species) were observed in 19 (17.92%) group faecal samples. Ascardia galli and Cotugnia digonopora were recovered during postmortem of three hariyal pigeon, while only Ascaridia galli was observed in a postmortem of parrot, peacock and cockatiel.

Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create an NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest trematode mitochondrial genome sequenced to date. The noncoding control regions are separated into two parts by the tRNA-Gly gene and don’t contain either tandem repeats or secondary structures, which are typical for trematode control regions. The gene content and arrangement are identical to that of F. hepatica. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The mtDNA for the intestinal fluke is reported herein for the first time by our group that would help investigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data. More so, it would serve as a resource for comparative mitochondrial genomics and systematic studies of trematode parasites.

No abstract

Opisthorchiasis is a public health problem in South-East Asian countries and Eastern Europe. The infection implicates mainly two species of Opisthorchis, namely O. viverrini and O. felineus, that occur mostly in fish-eating mammals and humans, although there are rare reports of human cases involving two other species, O. noverca and O. guayaquilensis. Opisthorchis noverca has been reported frequently in dogs and pigs from the Indian subcontinent, with rare reports from cattle and human subjects. With a view to supplementing morphology-based identification of this species, the present study aimed to provide molecular characterization of O. noverca, using rDNA internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome oxidase I (mt COI) markers so as to determine its genetic correlation with other species of Opisthorchiidae, and also to generate a taxon-specific molecular marker based on the ITS2 region. The phylogenetic relationship between O. noverca and other species of the genus was determined using molecular sequence data. To strengthen the result, secondary structure sequence analyses of ITS2 with hemi-compensatory base changes (hCBCs), and amino acid sequence analyses, were also evaluated. Our results confirm that O. noverca is a distinct and valid species.

An integrated pipeline for NGS and annotation of the complete mitochondrial genomeAsia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies 57 now provide opportunities for high throughput sequencing, assembly and annotation within a 58 short span of time. Herein, we describe a high-throughput sequencing and bioinformatics 59 pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms 60 such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome 61 using innovative approaches for PCR primer design as well as assembly. We took advantage 62 of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison 63 with available data for the Fasciola hepatica mtDNA as the reference genome for design of 64 precise and specific primers for amplification of mt genome sequences from F. buski. A long-65 range PCR was carried out to create a NGS library enriched in mt DNA sequences. Two 66 different NGS platforms were employed for complete sequencing, assembly and annotation 67 of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke 68 comprise 14,118 bp and is thus the shortest trematode mitochondrial genome sequenced to 69PeerJ PrePrints | https://peerj.com/preprints/58v2/ | v2 received: 4