Barnett R. Schistosomiasis. (1474–547X (Electronic)).
Steinmann P, Keiser J, Bos R, Tanner M, Utzinger J. Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect Dis. 2006;6(7):411–25.
Google Scholar
Uthailak N, Adisakwattana P, Thiangtrongjit T, Limpanont Y, Chusongsang P, Chusongsang Y, et al. Discovery of Schistosoma mekongi circulating proteins and antigens in infected mouse sera. PLoS ONE. 2022;17(10):e0275992.
Google Scholar
Lin D, Zeng X, Sanogo B, He P, Xiang S, Du S, et al. The potential risk of Schistosoma mansoni transmission by the invasive freshwater snail Biomphalaria straminea in South China. PLoS Negl Trop Dis. 2020;14(6):e0008310.
Google Scholar
Barsoum RS, Esmat G, El-Baz T. Human schistosomiasis: clinical perspective: review. J Adv Res. 2013;4(5):433–44.
Google Scholar
Gordon CA, Kurscheid J, Williams GM, Clements ACA, Li Y, Zhou XN, et al. Asian schistosomiasis: current status and prospects for control leading to elimination. Trop Med Infect Dis. 2019;4(1):40.
Google Scholar
Attwood SW, Liu L, Huo GN. Population genetic structure and geographical variation in Neotricula aperta (Gastropoda: Pomatiopsidae), the snail intermediate host of Schistosoma mekongi (Digenea: Schistosomatidae). PLoS Negl Trop Dis. 2019;13(1):e0007061.
Google Scholar
Attwood SW, Fatih FA, Upatham ES. DNA-sequence variation among Schistosoma mekongi populations and related taxa; phylogeography and the current distribution of Asian schistosomiasis. PLoS Negl Trop Dis. 2008;2(3):e200.
Google Scholar
Phuphisut O, Ajawatanawong P, Limpanont Y, Reamtong O, Nuamtanong S, Ampawong S, et al. Transcriptomic analysis of male and female Schistosoma mekongi adult worms. Parasit Vectors. 2018;11(1):504.
Google Scholar
Gray DJ, Ross AG, Li YS, McManus DP. Diagnosis and management of schistosomiasis. BMJ. 2011;342:d2651.
Google Scholar
McManus DP, Dunne DW, Sacko M, Utzinger J, Vennervald BJ, Zhou XN. Schistosomiasis. Nat Rev Dis Primers. 2018. https://doi.org/10.1038/s41572-018-0013-8.
Google Scholar
Hamid HKS. Schistosoma japonicum-associated colorectal cancer: a review. Am J Trop Med Hyg. 2019;100(3):501–5.
Google Scholar
Colley DG, Bustinduy AL, Secor WE, King CH. Human schistosomiasis. Lancet. 2014;383(9936):2253–64.
Google Scholar
Schistosoma japonicum Genome S, Functional Analysis C. The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature. 2009;460(7253):345–51
Vale N, Gouveia MJ, Rinaldi G, Brindley PJ, Gartner F, da Costa JMC. Praziquantel for schistosomiasis: single-drug metabolism revisited, mode of action, and resistance. Antimicrob Agents Chemother. 2017. https://doi.org/10.1128/AAC.02582-16.
Google Scholar
Tebeje BM, Harvie M, You H, Loukas A, McManus DP. Schistosomiasis vaccines: where do we stand? Parasit Vectors. 2016. https://doi.org/10.1186/s13071-016-1799-4.
Google Scholar
Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, et al. The genome of the blood fluke Schistosoma mansoni. Nature. 2009;460(7253):352–8.
Google Scholar
Young ND, Jex AR, Li B, Liu S, Yang L, Xiong Z, et al. Whole-genome sequence of Schistosoma haematobium. Nat Genet. 2012;44(2):221–5.
Google Scholar
Stroehlein AJ, Korhonen PK, Chong TM, Lim YL, Chan KG, Webster B, et al. High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing. Gigascience. 2019. https://doi.org/10.1093/gigascience/giz108.
Google Scholar
Stroehlein AJ, Korhonen PK, Lee VV, Ralph SA, Mentink-Kane M, You H, et al. Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation. PLoS Pathog. 2022;18(2):e1010288.
Google Scholar
Luo F, Yin M, Mo X, Sun C, Wu Q, Zhu B, et al. An improved genome assembly of the fluke Schistosoma japonicum. PLoS Negl Trop Dis. 2019;13(8):e0007612.
Google Scholar
Xu X, Wang Y, Wang C, Guo G, Yu X, Dai Y, et al. Chromosome-level genome assembly defines female-biased genes associated with sex determination and differentiation in the human blood fluke Schistosoma japonicum. Mol Ecol Resour. 2023;23(1):205–21.
Google Scholar
Ohmae H, Sinuon M, Kirinoki M, Matsumoto J, Chigusa Y, Socheat D, et al. Schistosomiasis mekongi: from discovery to control. Parasitol Int. 2004;53(2):135–42.
Google Scholar
Chai JY, Jung BK. Epidemiology of trematode infections: an update. Adv Exp Med Biol. 2019;1154:359–409.
Google Scholar
Melo FL, Gomes AL, Barbosa CS, Werkhauser RP, Abath FG. Development of molecular approaches for the identification of transmission sites of schistosomiasis. Trans R Soc Trop Med Hyg. 2006;100(11):1049–55.
Google Scholar
Ruan J, Li H. Fast and accurate long-read assembly with wtdbg2. Nat Methods. 2020;17(2):155–8.
Google Scholar
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE. 2014;9(11):e112963.
Google Scholar
Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, et al. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res. 2014;24(12):2041–9.
Google Scholar
Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol. 2013;31(12):1119–25.
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinf. 2009;10:421.
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60.
Google Scholar
Laetsch D, Blaxter M. BlobTools: interrogation of genome assemblies [version 1; peer review: 2 approved with reservations]. F1000Research. 2017;6:1287.
Google Scholar
Manni M, Berkeley MR, Seppey M, Simao FA, Zdobnov EM. BUSCO Update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38(10):4647–54.
Google Scholar
Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, et al. GeSeq—versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017;45(W1):W6–11.
Google Scholar
Greiner S, Lehwark P, Bock R. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019;47(W1):W59–64.
Google Scholar
McCarthy EM, McDonald JF. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics. 2003;19(3):362–7.
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7.
Google Scholar
Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000;16(6):276–7.
Google Scholar
Mulder N, Apweiler R. InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol. 2007;396:59–70.
Google Scholar
Li L, Stoeckert CJ Jr, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13(9):2178–89.
Google Scholar
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573–80.
Google Scholar
Edgar RC, Myers EW. PILER: identification and classification of genomic repeats. Bioinformatics. 2005;21(Suppl 1):i152–8.
Google Scholar
Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21(Suppl 1):i351–8.
Google Scholar
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105–11.
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–5.
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011. https://doi.org/10.1038/nbt.1883.
Google Scholar
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003;31(19):5654–66.
Google Scholar
Stanke M, Morgenstern B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids. 2005. https://doi.org/10.1093/nar/gki458.
Google Scholar
Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997;268(1):78–94.
Google Scholar
Guigo R, Knudsen S, Drake N, Smith T. Prediction of gene structure. J Mol Biol. 1992;226(1):141–57.
Google Scholar
Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H. Interpolated Markov models for eukaryotic gene finding. Genomics. 1999;59(1):24–31.
Google Scholar
Korf I. Gene finding in novel genomes. BMC Bioinf. 2004;5:59.
Google Scholar
Almasy L, Blangero J. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet. 1998;62(5):1198–211.
Google Scholar
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 2008;9(1):R7.
Google Scholar
Nielsen H. Predicting secretory proteins with SignalP. Methods Mol Biol. 2017;1611:59–73.
Google Scholar
Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305(3):567–80.
Google Scholar
Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res. 2018;46(D1):D624–32.
Google Scholar
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):955–64.
Google Scholar
Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009;25(10):1335–7.
Google Scholar
Harris RS. Improved pairwise alignment of genomic DNA. State College: The Pennsylvania State University; 2007.
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004;14(4):708–15.
Google Scholar
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15(8):1034–50.
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.
Google Scholar
Birney E, Clamp M, Durbin R. GeneWise and genomewise. Genome Res. 2004;14(5):988–95.
Google Scholar
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74.
Google Scholar
Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357–60.
Google Scholar
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf. 2011;12(1):323.
Google Scholar
Feng J, Meyer CA, Wang Q, Liu JS, Shirley Liu X, Zhang Y. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics. 2012;28(21):2782–8.
Google Scholar
Crellen T, Allan F, David S, Durrant C, Huckvale T, Holroyd N, et al. Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. Sci Rep. 2016;6:20954.
Google Scholar
Walker AJ, Ressurreicao M, Rothermel R. Exploring the function of protein kinases in schistosomes: perspectives from the laboratory and from comparative genomics. Front Genet. 2014;5:229.
Google Scholar
Morel M, Vanderstraete M, Hahnel S, Grevelding CG, Dissous C. Receptor tyrosine kinases and schistosome reproduction: new targets for chemotherapy. Front Genet. 2014;5:238.
Google Scholar
Hambrook JR, Kabore AL, Pila EA, Hanington PC. A metalloprotease produced by larval Schistosoma mansoni facilitates infection establishment and maintenance in the snail host by interfering with immune cell function. PLoS Pathog. 2018;14(10):e1007393.
Google Scholar
El Ridi R, Tallima H, Selim S, Donnelly S, Cotton S, Gonzales Santana B, et al. Cysteine peptidases as schistosomiasis vaccines with inbuilt adjuvanticity. PLoS ONE. 2014. https://doi.org/10.1371/journal.pone.0085401.
Google Scholar
International Helminth Genomes Consortium. Comparative genomics of the major parasitic worms. Nat Genet. 2019;51(1):163–74.
Google Scholar
McKerrow JH, Caffrey C, Kelly B, Loke P, Sajid M. Proteases in parasitic diseases. Annu Rev Pathol. 2006;1:497–536.
Google Scholar
Abdulla MH, Lim KC, Sajid M, McKerrow JH, Caffrey CR. Schistosomiasis mansoni: novel chemotherapy using a cysteine protease inhibitor. PLoS Med. 2007;4(1):e14.
Google Scholar
Chakrabarti A, Narayana C, Joshi N, Garg S, Garg LC, Ranganathan A, et al. Metalloprotease Gp63-targeting novel glycoside exhibits potential antileishmanial activity. Front Cell Infect Microbiol. 2022;12:803048.
Google Scholar
Dvorak J, Mashiyama ST, Sajid M, Braschi S, Delcroix M, Schneider EL, et al. SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni. PLoS Negl Trop Dis. 2009;3(6):e449.
Google Scholar
Dietzel J, Hirzmann J, Preis D, Symmons P, Kunz W. Ferritins of Schistosoma mansoni: sequence comparison and expression in female and male worms. Mol Biochem Parasitol. 1992;50(2):245–54.
Google Scholar
Dalton JP, Clough KA, Jones MK, Brindley PJ. Characterization of the cathepsin-like cysteine proteinases of Schistosoma mansoni. Infect Immun. 1996;64(4):1328–34.
Google Scholar
Smooker PM, Jayaraj R, Pike RN, Spithill TW. Cathepsin B proteases of flukes: the key to facilitating parasite control? Trends Parasitol. 2010;26(10):506–14.
Google Scholar
Feng X, Zhu L, Qin Z, Mo X, Hao Y, Jiang Y, et al. Temporal transcriptome change of Oncomelania hupensis revealed by Schistosoma japonicum invasion. Cell Biosci. 2020;10:58.
Google Scholar
Klopfenstein DV, Zhang L, Pedersen BS, Ramirez F, Warwick Vesztrocy A, Naldi A, et al. GOATOOLS: a Python library for gene ontology analyses. Sci Rep. 2018;8(1):10872.
Google Scholar
Brookfield JF. Host-parasite relationships in the genome. BMC Biol. 2011;9:67.
Google Scholar
Ebert D, Fields PD. Host-parasite co-evolution and its genomic signature. Nat Rev Genet. 2020;21(12):754–68.
Google Scholar
Zhao QP, Gao Q, Zhang Y, Li YW, Huang WL, Tang CL, et al. Identification of Toll-like receptor family members in Oncomelania hupensis and their role in defense against Schistosoma japonicum. Acta Trop. 2018. https://doi.org/10.1016/j.actatropica.2018.01.008.
Google Scholar
Fenwick A, Utzinger J. Helminthic diseases: schistosomiasis. In: Heggenhougen HK, editor. International encyclopedia of public health. Oxford: Academic Press; 2008. p. 351–61.
Google Scholar