Sexually biased transcripts at early embryonic stages of the silkworm depend on the sex chromosome constitution

Gene

Volumn 560, Issue 1, 2015, Pages 50-56

  Kawamoto, Munetaka ^a   Koga, Hikaru ^a   Kiuchi, Takashi ^a   Shoji, Keisuke ^a   Sugano, Sumio ^b   Shimada, Toru ^a   Suzuki, Yutaka ^b   Katsuma, Susumu ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Dosage compensation; PiRNA; Sex determination; Silkworm; Transcriptome; W chromosome

Indexed keywords

PIWI INTERACTING RNA; TRANSCRIPTOME; INSECT PROTEIN; MESSENGER RNA;

ARTICLE; BIOINFORMATICS; BOMBYX MORI; CONTROLLED STUDY; DEVELOPMENTAL STAGE; EMBRYO; EMBRYO DEVELOPMENT; FEMALE; GENE DOSAGE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; MALE; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; SEX CHROMOSOME; SEX DETERMINATION; TRANSPOSON; ANIMAL; ANIMAL EMBRYO; BOMBYX; EMBRYOLOGY; GENE EXPRESSION PROFILING; GENETICS; INSECT CHROMOSOME; MICROARRAY ANALYSIS; SEXUAL DEVELOPMENT;

BOMBYX MORI;

ANIMALS; BOMBYX; CHROMOSOMES, INSECT; EMBRYO, NONMAMMALIAN; EMBRYONIC DEVELOPMENT; FEMALE; GENE EXPRESSION PROFILING; INSECT PROTEINS; MALE; MICROARRAY ANALYSIS; RNA, MESSENGER; SEX CHARACTERISTICS; SEX CHROMOSOMES;

EID: 84923069991     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2015.01.036     Document Type: Article

References (24)

1. Abe H., Mita K., Yasukochi Y., Oshiki T., Shimada T. Retrotransposable elements on the W chromosome of the silkworm, Bombyx mori. Cytogenet. Genome Res. 2005, 110(1-4):114-151.
2. Abe H., Fujii T., Tanaka N., Yokoyama T., Kakehashi H., Ajimura M., Mita K., Banno Y., Yasukochi Y., Oshiki T., Nenoi M., Ishikawa T., Shimada T. Identification of the female-determining region of the W chromosome in Bombyx mori. Genetica 2008, 133:269-282.
3. Anders S., Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010, 11:R106.
4. Fujii T., Shimada T. Sex determination in the silkworm, Bombyx mori: A female determinant on the W chromosome and the sex-determining gene cascade. Semin. Cell Dev. Biol. 2007, 18:379-388.
5. Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N., Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29:644-652.
6. Harrison P.W., Mank J.E., Wedell N. Incomplete sex chromosome dosage compensation in the Indian meal moth, Plodia interpunctella, based on de novo transcriptome assembly. Genome Biol. Evol. 2012, 4:1118-1126.
7. Hasimoto H. The role of the W-choromosome in the sex deternination of Bombyx mori. Jpn. J. Genet. 1933, 8:245-247. (in Japanese).
8. Kawaoka S., Kadota K., Arai Y., Suzuki Y., Fujii T., Abe H., Yasukochi Y., Mita K., Sugano S., Shimizu K., Tomari Y., Shimada T., Katsuma S. The silkworm W chromosome is a source of female-enriched piRNAs. RNA 2011, 17:2144-2151.
9. Kawaoka S., Arai Y., Kadota K., Suzuki Y., Hara K., Sugano S., Shimizu K., Tomari Y., Shimada T., Katsuma S. Zygotic amplification of secondary piRNAs during silkworm embryogenesis. RNA 2011, 17:1401-1407.
10. Kim D., Pertea G., Trapnell C., Pimentel H., Kelley R., Salzberg S.L. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013, 14:R36.
11. Kiuchi T., Koga H., Kawamoto M., Shoji K., Sakai H., Arai Y., Ishihara G., Kawaoka S., Sugano S., Shimada T., Suzuki Y., Suzuki M.G., Katsuma S. A single female-specific piRNA is the primary determiner of sex in the silkworm. Nature 2014, 509:633-636.
12. Koike Y., Mita K., Suzuki M.G., Maeda S., Abe H., Osoegawa K., deJong P.J., Shimada T. Genomic sequence of a 320-kb segment of the Z chromosome of Bombyx mori containing a kettin ortholog. Mol. Genet. Genomics 2003, 269:137-149.
13. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
14. Li B., Dewey C.N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinforma. 2011, 12:323.
15. R Core Team R: A Language and Environment for Statistical Computing 2014, R Foundation for Statistical Computing, Vienna, Austria, (http://www.R-project.org/).
16. Smith G., Chen Y.R., Blissard G.W., Briscoe A.D. Complete dosage compensation and sex-biased gene expression in the moth Manduca sexta. Genome Biol. Evol. 2014, 6:526-537.
17. Suzuki M.G., Shimada T., Kobayashi M. Absence of dosage compensation at the transcription level of a sex-linked gene in a female heterogametic insect, Bombyx mori. Heredity 1998, 81:275-283.
18. Suzuki M.G., Shimada T., Kobayashi M. Bm kettin, homologue of the Drosophila kettin gene, is located on the Z chromosome in Bombyx mori and is not dosage compensated. Heredity 1999, 82:170-179.
19. Suzuki M.G., Funaguma S., Kanda T., Tamura T., Shimada T. Analysis of the biological functions of a doublesex homologue in Bombyx mori. Dev. Genes Evol. 2003, 213:345-354.
20. Suzuki M.G., Funaguma S., Kanda T., Tamura T., Shimada T. Role of the male BmDSX protein in the sexual differentiation of Bombyx mori. Evol. Dev. 2005, 7:58-68.
21. Tanaka Y. Genetic studies in the silkworm. J. Coll. Agric. Sapporo 1916, 6:1-33.
22. Walters J.R., Hardcastle T.J. Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori. Genome Biol. Evol. 2011, 3:491-504.
23. Warnes G.R., Bolker B., Bonebakker L., Gentleman R., Liaw W.H.A. gplots: Various R programming tools for plotting data. R package version 2.14.0 2014, (http://CRAN.R-project.org/package=gplots). T. Lumley, M. Maechler, A. Magnusson, S. Moeller, M. Schwartz, B. Venables (Eds.).
24. Zha X., Xia Q., Duan J., Wang C., He N., Xiang Z. Dosage analysis of Z chromosome genes using microarray in silkworm, Bombyx mori. Insect Biochem. Mol. Biol. 2009, 39:315-321.