Sex determination of non-model organisms in the absence of field records
using Diversity Arrays Technology (DArT) data
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 determination is
costly and often 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 accurately determined 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
determination 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.