spp. are platyhelminth (flatworm) parasites responsible for schistosomiasis, a tropical disease endemic in sub-tropical regions of Africa, Brazil, Central America, regions of China and Southeast Asia, which causes serious morbidity, mortality and economic loss. An estimated 779 million people are at risk of infection and more than 200 million are infected 
The paired adult males and females of S. mansoni
reside in the hepatic portal vasculature, each female depositing 200–300 eggs per day near the intestinal wall. These eggs either pass into the gut lumen to be voided in the faeces and continue the life cycle or pass up the mesenteric veins and lodge in the liver, where they can cause serious pathology including granulomatous inflammation response and fibrosis. On contact with fresh water, free-living motile miracidia hatch from the eggs to infect aquatic snails (Biomphalaria
spp.), where parasites undergo two rounds of asexual multiplication and are released as infective cercariae into water. Cercariae infect the human host, by penetrating unbroken skin, and transform into schistosomula. After several days the parasites exit the cutaneous tissue via blood (or lymphatic) vessels and travel first to the lungs and onward into the systemic vasculature. They may make multiple circuits before arriving in the hepatic portal system; only then do they start to feed on blood, mature and pair up, the whole process taking approximately five weeks 
draft genomes (S. mansoni
and S. japonicum
) were recently published 
and represent the only described genomes amongst parasitic flatworms to date. Their assemblies were generated by conventional capillary sequencing but are highly fragmented (S. mansoni
, 19,022 scaffolds; S. japonicum
, 25,048 scaffolds) and severely compromise gene prediction, as well as comparative and functional genomics analyses. The transcriptome has similarly only been partially characterised by large-scale expressed sequence tag (EST) sequencing and low-resolution cDNA-based microarrays.
Second-generation sequencing technologies provide new opportunities to characterise both genomes and transcriptomes in depth. In addition to whole genome de novo
and genome improvement 
, massively parallel cDNA sequencing (RNA-seq) can identify transcriptionally active regions at base-pair resolution 
and accurately define the exon coordinates of genes 
. In addition, the quantitative nature and high dynamic range of RNA-seq allows gene expression to be scrutinised 
in a more sensitive and accurate way than other previous high-throughput methods 
In this study we systematically improved the draft genome of S. mansoni
, using a combination of traditional Sanger capillary sequencing, second generation DNA sequencing from clonal parasites and reanalysis of existing genetic markers 
. This allowed us to assemble 81% of the genome sequence into chromosomes. We have also used RNA-seq data from several life-cycle stages to refine the structures of 45% of existing genes as well as to identify new genes and alternatively spliced transcripts. In addition to cis
splicing, our data highlight extensive trans
-splicing and provide clear evidence that the latter can be used to resolve polycistronic transcripts. With RNA-seq we profiled the parasite's transcriptome during its transformation from the free-living, human-infectious cercariae to the early stages of infection and in the mature adult. As the infective form transforms into a mammalian-adapted parasite, the relative abundance of transcripts shifts markedly during a 24-hour period, from those involved in glycolysis, translation and transcription to those required for complex developmental and signalling pathways.
The improved sequence and new transcriptome data are available to the community in a user-friendly and easy to query format via both the GeneDB (www.genedb.org
) and SchistoDB (www.schistodb.net
) databases. These data demonstrate that revisiting a previously published draft genome, to upgrade its quality, is an option that should not just be reserved for model organisms.