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Genomic tools and sex determination in the extremophile brine shrimp Artemia franciscana

(2014)
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Abstract
The aim of this study was the construction of a genomic Artemia toolkit. Sex-specific AFLP-based genetic maps were constructed based on 433 AFLP markers segregating in a 112 full-sib family, revealing 21 male and 22 female linkage groups (2n = 42). Fifteen putatively homologous linkage groups, including the sex linkage groups, were identified between the female and male linkage maps. Eight sex-linked markers, heterozygous in female animals, mapped to a single locus on a female linkage group, supporting the hypothesis of a WZ/ZZ genetic sex-determining system and showing primary sex determination is likely directed by a single gene. To fine-map the sex locus, bulked segregant analysis was performed. Candidate primary sex-determining genes were identified, including Cytochrome P450 which, through transcriptomic studies, is already known as a candidate sex-determining gene for Macrobrachium nipponense. The 1,310-Mbp Artemia draft genome sequence (N50 = 14,784 bp; GC-content = 35%; 176,667 scaffolds) was annotated, predicting 188,101 genes with an average length of 692 bp. Ninety-two percent of the transcriptome reads of Artemia in different conditions were present in the Artemia genome, indicating that the functional part of the genome under the RNAseq sampling conditions is virtually fully represented in the assembly. Several steps were taken in this study to introduce Artemia as a new genomic model for crustaceans. Although the functional part of the Artemia genome under the RNAseq sampling conditions is virtually fully represented in the assembly, thus making it useful for qualitative research, genome finishing strategies will still be necessary to complete the genome project. The further development of genomic resources for Artemia will add a completely new dimension to Artemia research and its use as live food in aquaculture.
Keywords
Brine Shrimp, artemia, aquaculture

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Citation

Please use this url to cite or link to this publication:

Chicago
De Vos, Stephanie. 2014. “Genomic Tools and Sex Determination in the Extremophile Brine Shrimp Artemia Franciscana”. Ghent, Belgium: Ghent University. Faculty of Bioscience Engineering.
APA
De Vos, Stephanie. (2014). Genomic tools and sex determination in the extremophile brine shrimp Artemia franciscana. Ghent University. Faculty of Bioscience Engineering, Ghent, Belgium.
Vancouver
1.
De Vos S. Genomic tools and sex determination in the extremophile brine shrimp Artemia franciscana. [Ghent, Belgium]: Ghent University. Faculty of Bioscience Engineering; 2014.
MLA
De Vos, Stephanie. “Genomic Tools and Sex Determination in the Extremophile Brine Shrimp Artemia Franciscana.” 2014 : n. pag. Print.
@phdthesis{5674181,
  abstract     = {The aim of this study was the construction of a genomic Artemia toolkit. Sex-specific AFLP-based genetic maps were constructed based on 433 AFLP markers segregating in a 112 full-sib family, revealing 21 male and 22 female linkage groups (2n = 42). Fifteen putatively homologous linkage groups, including the sex linkage groups, were identified between the female and male linkage maps. Eight sex-linked markers, heterozygous in female animals, mapped to a single locus on a female linkage group, supporting the hypothesis of a WZ/ZZ genetic sex-determining system and showing primary sex determination is likely directed by a single gene. To fine-map the sex locus, bulked segregant analysis was performed. Candidate primary sex-determining genes were identified, including Cytochrome P450 which, through transcriptomic studies, is already known as a candidate sex-determining gene for Macrobrachium nipponense. The 1,310-Mbp Artemia draft genome sequence (N50 = 14,784 bp; GC-content = 35\%; 176,667 scaffolds) was annotated, predicting 188,101 genes with an average length of 692 bp. Ninety-two percent of the transcriptome reads of Artemia in different conditions were present in the Artemia genome, indicating that the functional part of the genome under the RNAseq sampling conditions is virtually fully represented in the assembly. Several steps were taken in this study to introduce Artemia as a new genomic model for crustaceans. Although the functional part of the Artemia genome under the RNAseq sampling conditions is virtually fully represented in the assembly, thus making it useful for qualitative research, genome finishing strategies will still be necessary to complete the genome project. The further development of genomic resources for Artemia will add a completely new dimension to Artemia research and its use as live food in aquaculture.},
  author       = {De Vos, Stephanie},
  isbn         = {9789059897175},
  language     = {eng},
  pages        = {XX, 153},
  publisher    = {Ghent University. Faculty of Bioscience Engineering},
  school       = {Ghent University},
  title        = {Genomic tools and sex determination in the extremophile brine shrimp Artemia franciscana},
  year         = {2014},
}