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Type: Journal article
Title: Sex assignment in a non-model organism in the absence of field records using Diversity Arrays Technology (DArT) data
Author: Onley, I.R.
Austin, J.J.
Mitchell, K.J.
Citation: Conservation Genetics Resources, 2021; 13(3):255-260
Publisher: Springer (part of Springer Nature)
Issue Date: 2021
ISSN: 1877-7252
Statement of
Isabelle R. Onley, Jeremy J. Austin, Kieren J. Mitchell
Abstract: Conservation genomics research often relies on accurate sex information to make inferences about species demography, dispersal, and population structure. However, field determined sex data are not always available and can be subject to human error, while laboratory sex assignment methods such as PCR assays can often be costly and challenging for non-model species. Conservation genomics programs increasingly use reduced-representation genome sequencing to assess neutral and functional genetic diversity, population structure, gene flow and pedigrees in threatened species. Here we demonstrate that sex can be determined from reduced-representation sequencing data produced by the increasingly popular Diversity Arrays Technology sequencing workflow (DArT-seq) using a program originally designed for application to shotgun data. This program—sexassign—compares the “dosage” of sequencing reads mapping to autosomes versus the X chromosome. In the present study, sexassign was used to identify the sex of 60 field-collected Greater Stick-Nest Rat (Leporillus conditor) samples, despite the absence of an annotated reference genome for the species. This “read-dosage” approach is not only more accurate and affordable than traditional sex assignment methods, but can be applied to any diploid organism with a heterogametic sex determination system—including non-model and understudied species of conservation importance—by using FASTQs generated by DArT.
Keywords: Conservation genomics; Sex assignment; Bioinformatics; DArT-seq
Description: Published online: 09 March 2021.
Rights: © The Author(s), under exclusive licence to Springer Nature B.V. 2021
DOI: 10.1007/s12686-021-01203-w
Appears in Collections:Aurora harvest 8
Australian Centre for Ancient DNA publications

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