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Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species

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Abstract

Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.

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Availability of data and material

All sequencing data is available in the NCBI BioProject database under the accession number PRJNA693418 or as supplemental files to this manuscript.

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Acknowledgements

The authors would like to thank the various aquaculture facilities for the use of their infrastructure and access to biological materials.

Funding

The South African National Research Foundation funded this research: Grant reference number: MCR180616347589.

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  1. Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa

    T. Jackson, E. Ishengoma & C. Rhode

  2. Department of Biological Sciences, Mkwawa University College of Education, University of Dar Es Salaam, P.O. Box 2329, Dar es Salaam, Tanzania

    E. Ishengoma

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Correspondence to C. Rhode.

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The experimental protocols for the collection of biological samples and handling of live animals were approved by the Stellenbosch University, Research Ethics Committee: Animal Care and Use, protocol reference numbers: SU-ACUM14-00,007 and 6569.

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Jackson, T., Ishengoma, E. & Rhode, C. Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species. Mar Biotechnol 23, 560–575 (2021). https://doi.org/10.1007/s10126-021-10046-3

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