Schistosoma mansoni (PRJEA36577) (Smansoni_v7)

Schistosoma mansoni (PRJEA36577) Assembly and Gene Annotation

NOTE: The genome sequence and annotation for S. mansoni are updated in Ensembl Metazoa infrequently. For the latest genome and annotation, please visit WormBase ParaSite.

About Schistosoma mansoni

Schistosoma mansoni is one of a genus of trematodes that are commonly called blood-flukes, and is a significant parasite of humans and a major agent of the disease schistosomiasis. S. mansoni goes through several asexual reproductive stages in an intermediate host, a freshwater snail, from which many thousands of motile larval forms (cercaria) emerge. The cercaria can quickly penetrate human skin, and within a few days enter the circulatory system, where they feed on blood. The adult stage of S. mansoni has two sexes, in contrast to the hermaphroditic nature of most trematodes, and if a larva encounters a member of the opposite sex it develops into a sexually mature adult and the two larvae form a monogamous pairing. Females can lay hundreds of eggs per day, and these migrate to the intestines and then enter the environment in faeces, ready to hatch and infect snail hosts. In (intestinal) schistosomiasis, an immune response is initiated when eggs become trapped in the intestinal wall, or other organs such as the liver, and it is this severe immune response that underlies the disease pathology.

Assembly

The S. mansoni reference genome was sequenced by a consortium led by the Berriman lab. The reads from short and long-range paired end capillary libraries and short-range Illumina paired end libraries were mapped to assembly accession GCA_000237925.2 (Protasio et al 012; version 5.2. Mapped reads were scrutinised in GAP5 and manual edits to the assembly were made as necessary. Inspection of optical map alignments and integration of PacBio reads led to version 7, as presented here (GCA_000237925.3). This assembly has been further improved following assimilation of Oxford Nanopore, PacBio, and HiC data to create a complete telomere-to-telomere chromosome scale assembly. All improvements leading to versions 7 are described in Buddenborg et al.

Annotation

Putative gene models from the annotation accompanying previous assembly GCA_000237925.2 (Protasio et al 2012) and predictions using RNASeq data were resolved through manual curation using Apollo as a platform. For unchanged gene models, previous gene identifiers have been preserved Buddenborg et all.

References

  1. The genome of the blood fluke Schistosoma mansoni.
    Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD et al. 2009. Nature. 460:352-358.
  2. A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.
    Protasio AV, Tsai IJ, Babbage A, Nichol S, Hunt M, Aslett MA, De Silva N, Velarde GS, Anderson TJ, Clark RC et al. 2012. PLoS Neglected Tropical Diseases. 6:e1455.
  3. SchistoDB: a Schistosoma mansoni genome resource.
    Zerlotini A, Heiges M, Wang H, Moraes RL, Dominitini AJ, Ruiz JC, Kissinger JC, Oliveira G. 2009. Nucleic Acids Research. 37:D579-82.
  4. Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system.
    Sarah K Buddenborg, Alan Tracey, Duncan J Berger, Zhigang Lu, Stephen R Doyle, Beiyuan Fu, Fengtang Yang, Adam J Reid, Faye H Rodgers, Gabriel Rinaldi, Geetha Sankaranarayanan, Ulrike Böhme, Nancy Holroyd, Matthew Berriman. 2021. bioRxiv 2021.08.13.456314

Picture credit (public domain): Uniformed Services University of the Health Sciences 2006


Statistics

Summary

AssemblySmansoni_v7, INSDC Assembly GCA_000237925.3,
Database version107.1
Golden Path Length409,579,008
Genebuild byWellcome Sanger Institute
Genebuild methodImport
Data sourceWellcome Sanger Institute

Gene counts

Coding genes10,144
Pseudogenes28
Gene transcripts14,528