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Genomic sequencing of African Jewelfish

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Project Investigators: Margaret Hunter, Pam Schofield

Project Start Date: 2014 End Date: 2015

Recent Funding: (FY14) USGS GE PES


We plan to develop Restriction site Associated DNA (RAD) markers using Next generation sequencing to conduct high-throughput and efficient screening of sex-linked DNA markers.

If a large proportion of the genomic DNA sequence of male and female African Jewelfish was available, it could allow a more efficient screen for sex-linked DNA markers, reducing the number of primers to be screened and shortening the time required to identify a sex-specific marker. By comparing the male genomic sequence to the female genomic sequence using DNA analysis software, all the sequences that are common to both sexes could be eliminated as a source of DNA sequences for the design of new PCR primers. Instead of generating random primer sequences, primers could be designed from DNA sequences that are found only in the genomic DNA sequences of males. It would thus be advantageous to obtain sex-specific genomic DNA sequences for African jewelfish in order to enhance the screening efforts for sex-specific DNA markers and increase the likelihood of success.

The technology of genomic DNA sequencing has greatly advanced. Large number of genomic loci can be sequenced rapidly at a relatively low cost. Next generation sequencing using the Illumina MiSeq will rapidly produce male and female sex-specific genomic DNA sequences for African jewelfish. This produces thousands of sequences at a coverage level sufficient to provide the resolution of sex-specific sequences, if present, and distinguishing those differences from individual DNA sequence variation. If possible, sequencing will be conducted in collaboration with a USGS genetics laboratory.

Work Plans


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