Chromosome-level genome assembly of Oncomelania hupensis: the intermediate snail host of Schistosoma japonicum.

BACKGROUND: Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia. Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host of S. japonicum. A complete genome sequence of O. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite. Assembling a high-quality reference genome of O. hupehensis will provide data for further research on the snail biology and controlling the spread of S. japonicum. METHODS: The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences. RESULTS: A total length of 1.46 Gb high-quality O. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed that O. hupensis was separated from a common ancestor of Pomacea canaliculata and Bellamya purificata approximately 170 million years ago. Comparing the genome of O. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity. CONCLUSIONS: Integrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level of O. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.

A polymorphism within ErbB4 is associated with risk for hepatocellular carcinoma in Chinese population.

AIM: To investigate the association between hepatocellular carcinoma (HCC) susceptibility and a 12-bp insertion/deletion polymorphism (rs6147150) in the 3'UTR of ErbB4. METHODS: Using a case-control design, the rs6147150 genotypes in 270 patients with HCC and 270 healthy controls were determined by direct polymerase chain reaction and polyacrylamide gel electrophoresis. Logistic regression was used to analyze the association between the polymorphism and cancer risk. RESULTS: Computational modeling suggested that rs6147150 was located in the seed region of hsa-let-7c, a potential target sequence in ErbB4 3'UTR. Logistic regression analysis showed that, compared with individuals homozygous for wild-type, heterozygotes [adjusted odds ratio (OR) = 1.48, 95% confidence interval (CI) = 1.03-2.17, P = 0.034] and individuals homozygous for 12-bp del/del (OR = 2.50, 95% CI = 1.37-4.56, P = 0.001) were at significantly higher risk of HCC. Carriers of the "del" allele of rs6147150 had a 1.59-fold increased risk for HCC (95% CI = 1.22-2.07, P = 0.003). CONCLUSION: rs6147150 may be associated with HCC risk, in part through let-7c-mediated regulation, and may be involved in the pathogenesis of HCC in Chinese populations.