Advances in the sequencing of the genome of the adenophorean nematodeTrichinella spiralis

Abstract

SUMMARY The adenophorean nematodes are evolutionarily distant from other species in the phylum Nematoda. Interspecific comparisons of predicted proteins have supported such an ancient divergence. Accordingly, Trichinella spiralis represents a basal nematode representative for genome sequencing focused on gaining a deeper insight into the evolutionary biology of nematodes. In addition, molecular characteristics that are conserved across the phylum could be of great value for control strategies with broad application. In this review, we describe and summarize progress that has been made on the sequencing and analysis of the T. spiralis genome. The genome sequence was used in preliminary analyses for the investigation of specific questions relating to the biology of T. spiralis and, more generally, to parasitic nematodes. For instance, we evaluated an unusually large DNase II-like protein family, predicted proteins of prospective interest in the parasite-host muscle cell interaction, anthelmintic targets and prospective intestinal genes, the encoded proteins (potentially) linked to immunological control against other nematodes. The results are discussed in relation to characteristics that are broadly conserved among evolutionary distant nematodes. The results lead to expectations that this genome sequence will contribute to advances in research on T. spiralis and other parasitic nematodes.

Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction

“…4a). Trichinella spiralis contains 166 DNase II-like proteins 22,23 that include the abundant excretory-secretory protein gp43 24 . T. muris and Trichinella spiralis each encode one ortholog of the metazoan DNase II (Fig.…”

“…4a ). T. spiralis encodes 166 DNase II–like proteins 22 , 23 that include the abundant excretory-secretory protein gp43 (ref. 24 ).…”

Molecular taxonomy, phylogeny and biogeography of nematodes belonging to the Trichinella genus

“…Indeed, the most telling character, the presence or absence of a host-derived, collagen sheath around the infected muscle cell led to the conclusion that the genus could be biologically delineated into 2 distinct groups: the encapsulated and nonencapsulated clades (Zarlenga et al, 2006). These groups received heightened interest from the genome sequencing community and in 2004, a major effort was launched to sequence the complete genome of T. spiralis as a representative clade 1, encapsulated nematode (Mitreva and Jasmer, 2008). Genome sequencing efforts have since expanded to include the nonencapsulated species, T. pseudospiralis, using ''next generation'' sequencing technologies (Zarlenga et al, 2009) and T. spiralis data for comparative sequence assignment.…”

Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years

“…The smaller assembly, derived from the 60 Mbp prior, most likely resulted from excessive condensation of repetitive DNA elements. The difference between Trichinella genome assembly sizes presented here and one estimate of genome size made by flow cytometry (71 Mbp) (Mitreva and Jasmer, 2008) may reflect as-yet undetected repetitive DNA. For example, Phobos, which can detect degenerate repeats in the genome, estimated almost twice the number of simple repeats detected by RepeatMasker; this highlights the difficulty of correctly identifying, much less assembling, degenerate repetitive DNA.…”