Whole-genome in-silico subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: The example of Schistosoma mansoni

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Portela, Julien ^a   Grunau, Christoph ^a   Cosseau, Céline ^a   Beltran, Sophie ^a   Dantec, Christelle ^b   Parrinello, Hugues ^b   Boissier, Jérôme ^a  

^a UNIVERSITÉ DE PERPIGNAN   (France)

^b INSTITUT DE GÉNOMIQUE FONCTIONNELLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; DNA;

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DNA EXTRACTION; FEMALE; GENETIC SELECTION; GENOME ANALYSIS; GENOTYPE; LARVAL STAGE; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITE ISOLATION; PATHOTYPE; POLYMERASE CHAIN REACTION; PSEUDOGENE; SCHISTOSOMA MANSONI; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEX CHROMOSOME; SEX DETERMINATION; SEX DIFFERENCE; SUBTRACTIVE HYBRIDIZATION; WHOLE GENOME IN SILICO SUBTRACTIVE HYBRIDIZATION; ANIMAL; DNA SEQUENCE; GENETICS; GENOME; GENOMICS; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE REPEAT; SEXUAL DEVELOPMENT;

SCHISTOSOMA; SCHISTOSOMA MANSONI; SCHISTOSOMATIDAE;

ANIMALS; DNA; FEMALE; GENOME; GENOMICS; MALE; NUCLEIC ACID HYBRIDIZATION; REPETITIVE SEQUENCES, NUCLEIC ACID; SCHISTOSOMA MANSONI; SEQUENCE ANALYSIS, DNA; SEX CHARACTERISTICS;

EID: 77953679813     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-387     Document Type: Article

References (24)

1. Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, et al. Whole-genome sequencing and variant discovery in C. elegans. Nature Methods 2008, 5(2):183-188. 10.1038/nmeth.1179, 18204455.
2. Short RB. Presidential address: Sex and the single schistosome. Journal of parasitology 1983, 69(1):3-22.
3. Grevelding CG. Genomic instability in Schistosoma mansoni. Molecular and Biochemical Parasitology 1999, 101(1-2):207-216. 10.1016/S0166-6851(99)00078-X, 10413055.
4. Boissier J, Mone H. Experimental observations on the sex ratio of adult Schistosoma mansoni, with comments on the natural male bias. Parasitology 2000, 121(Pt 4):379-383. 10.1017/S0031182099006393, 11072900.
5. Cosseau C, Azzi A, Smith K, Freitag M, Mitta G, Grunau C. Native chromatin immunoprecipitation (N-ChIP) and ChIP-Seq of Schistosoma mansoni: Critical experimental parameters. Molecular and Biochemical Parasitology 2009, 166(1):70-76. 10.1016/j.molbiopara.2009.02.015, 19428675.
6. Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, et al. The genome of the blood fluke Schistosoma mansoni. Nature 2009, 460(7253):352-358. 10.1038/nature08160, 2756445, 19606141.
7. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 2008, 24(15):1729-1730. 10.1093/bioinformatics/btn305, 2638869, 18599518.
8. Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Backman TW, Givan SA, et al. Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 2009, 15(5):992-1002. 10.1261/rna.1473809, 2673065, 19307293.
9. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 1999, 27(2):573-580. 10.1093/nar/27.2.573, 148217, 9862982.
10. Zerlotini A, Heiges M, Wang H, Moraes RL, Dominitini AJ, Ruiz JC, Kissinger JC, Oliveira G. SchistoDB: a Schistosoma mansoni genome resource. Nucleic Acids Research 2009, (37 Database):D579-582. 10.1093/nar/gkn681, 2686589, 18842636.
11. Webster P, Mansour TE, Bieber D. Isolation of a female-specific, highly repeated Schistosoma mansoni DNA probe and its use in an assay of cercarial sex. Molecular and Biochemical Parasitology 1989, 36(3):217-222. 10.1016/0166-6851(89)90169-2, 2797060.
12. Drew AC, Brindley PJ. Female-specific sequences isolated from Schistosoma mansoni by representational difference analysis. Molecular and Biochemical Parasitology 1995, 71(2):173-181. 10.1016/0166-6851(95)00048-6, 7477099.
13. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714. 10.1093/bioinformatics/btn025, 18227114.
14. Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G. PASS: a program to align short sequences. Bioinformatics 2009, 25(7):967-968. 10.1093/bioinformatics/btp087, 19218350.
15. Beltran S, Galinier R, Allienne JF, Boissier J. Cheap, rapid and efficient DNA extraction method to perform multilocus microsatellite genotyping on all Schistosoma mansoni stages. Memorias do Instituto Oswaldo Cruz 2008, 103(5):501-503.
16. Jeffreys AJ, Neumann R, Wilson V. Repeat unit sequence variation in minisatellites: a novel source of DNA polymorphism for studying variation and mutation by single molecule analysis. Cell 1990, 60(3):473-485. 10.1016/0092-8674(90)90598-9, 2406022.
17. DeMarco R, Kowaltowski AT, Machado AA, Soares MB, Gargioni C, Kawano T, Rodrigues V, Madeira AM, Wilson RA, Menck CF, et al. Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni. Journal of Virology 2004, 78(6):2967-2978. 10.1128/JVI.78.6.2967-2978.2004, 353769, 14990715.
18. Staelens J, Rombaut D, Vercauteren I, Argue B, Benzie J, Vuylsteke M. High-density linkage maps and sex-linked markers for the black tiger shrimp (Penaeus monodon). Genetics 2008, 179(2):917-925. 10.1534/genetics.107.080150, 2429885, 18558652.
19. Grevelding CG. The female-specific W1 sequence of the Puerto Rican strain of Schistosoma mansoni occurs in both genders of a Liberian strain. Molecular and Biochemical Parasitology 1995, 71(2):269-272. 10.1016/0166-6851(94)00058-U, 7477111.
20. Quack T, Doenhoff M, Kunz W, Grevelding CG. Schistosoma mansoni: the varying occurrence of repetitive elements in different strains shows sex-specific polymorphisms. Experimental Parasitology 1998, 89(2):222-227. 10.1006/expr.1998.4293, 9635446.
21. Chen J, Wang Y, Yue Y, Xia X, Du Q, Chang Z. A novel male-specific DNA sequence in the common carp, Cyprinus carpio. Molecular and cellular probes 2009, 23(5):235-239. 10.1016/j.mcp.2009.04.004, 19401231.
22. Horng YM, Huang MC. Male-specific DNA sequences in pigs. Theriogenology 2003, 59(3-4):841-848. 10.1016/S0093-691X(02)01150-0, 12517387.
23. Scribner KT, Petersen MR, Fields RL, Talbot SL, Pearce JM, Chesser RK. Sex-biased gene flow in spectacled eiders (Anatidae): inferences from molecular markers with contrasting modes of inheritance. Evolution; international journal of organic evolution 2001, 55(10):2105-2115.
24. Yannic G, Basset P, Hausser J. Phylogeography and recolonization of the Swiss Alps by the Valais shrew (Sorex antinorii), inferred with autosomal and sex-specific markers. Molecular ecology 2008, 17(18):4118-33. 10.1111/j.1365-294X.2008.03888.x, 19238709.