Abstract
The Mozambique tilapia (Oreochromis mossambicus) is a fascinating taxon for evolutionary and ecological research. It is an important food fish and one of the most widely distributed tilapias. Because males grow faster than females, genetically male tilapia are preferred in aquaculture. However, studies of sex determination and sex control in O. mossambicus have been hindered by the limited characterization of the genome. To address this gap, we assembled a high-quality genome of O. mossambicus, using a combination of high coverage of Illumina and Nanopore reads, coupled with Hi-C and RNA-Seq data. Our genome assembly spans 1,007 Mb with a scaffold N50 of 11.38 Mb. We successfully anchored and oriented 98.6% of the genome on 22 linkage groups (LGs). Based on re-sequencing data for male and female fishes from three families, O. mossambicus segregates both an XY system on LG14 and a ZW system on LG3. The sex-patterned SNPs shared by two XY families narrowed the sex determining regions to ∼3 Mb on LG14. The shared sex-patterned SNPs included two deleterious missense mutations in ahnak and rhbdd1, indicating the possible roles of these two genes in sex determination. This annotated chromosome-level genome assembly and identification of sex determining regions represents a valuable resource to help understand the evolution of genetic sex determination in tilapias.
Highlights
Sex determination, the process by which a sexually reproducing organism initiates differentiation as a male or female, is triggered either by genetic factors on sex chromosomes or environmental factors (Capel, 2017)
This genome sequence will contribute to the development of technologies to produce all male populations of O. mossambicus for commercial aquaculture, and may help us to better understand the unusual diversity of sex chromosomes in tilapias
Recent genome assemblies from a female O. niloticus Japanese strain and male O. aureus Wuxi strain generated from 100X Nanopore reads by us were 1,005 Mb and 1,006 Mb, respectively (Tao et al, 2021)
Summary
The process by which a sexually reproducing organism initiates differentiation as a male or female, is triggered either by genetic factors on sex chromosomes or environmental factors (Capel, 2017). Cytological analysis can only distinguish highly divergent sex chromosomes with significant differences in morphology (Wright et al, 2016; Palmer et al, 2019). The sex chromosome systems of mammals and birds are highly conserved, with cytologically differentiated sex chromosomes that have lost many ancestral genes and gained a large number of repetitive sequences. Fishes display a diversity of sex determining systems, from environmental to genetic. Most fish have homomorphic sex chromosomes which are indistinguishable by shape (Devlin and Nagahama, 2002; Bachtrog et al, 2014). Sex chromosomes have been characterized in a wide variety of fishes based on both chromosome-level genome assemblies generated from long read sequence data, as well as re-sequencing of male and female genomes using short read sequencing technology (Dixon et al, 2019; Pan et al, 2019; Li et al, 2020; Peichel et al, 2020; Wen et al, 2020; Einfeldt et al, 2021; Li et al, 2021; Nakamoto et al, 2021; Tao et al, 2021; Xue et al, 2021)
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