Generating de novo genome assemblies for sex-based population analysis

In order to analyze per-population coverage differences between the sexes, we generated de novo draft genome assemblies for each sex and each population. To guarantee sufficient coverage, sequencing reads of two randomly selected individuals per sex for the 11 A. burtoni populations were combined as input for these 22 de novo draft genome assemblies. Assemblies were generated as previously described (Malmstrøm et al. 2017 (link); Böhne et al. 2019 (link)) using Celera Assembler V8.3 (Myers et al. 2000 (link)) and indexed with BWA V0.7.13 (Li and Durbin 2009 (link)). We aligned the draft assemblies against the Nile tilapia reference genome (refseq accession number GCF_001858045.2_O_niloticus_UMD_NMBU) using LAST V861 and lastal (Kiełbasa et al. 2011 (link)) to infer chromosomal locations of draft genome scaffolds.

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Lichilín N., Salzburger W, & Böhne A. (2023). No evidence for sex chromosomes in natural populations of the cichlid fish Astatotilapia burtoni. G3: Genes|Genomes|Genetics, 13(3), jkad011.

Publication 2023

Chromosomal Genome Nile tilapia Populations

Corresponding Organization :

Other organizations : University of Vienna, University of Basel, Zoological Research Museum Alexander Koenig

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Variable analysis

independent variables

Populations of A. burtoni
Sex (male and female)

dependent variables

Per-population coverage differences between the sexes

control variables

Sequencing reads of two randomly selected individuals per sex for the 11 A. burtoni populations were combined as input for the de novo draft genome assemblies
Draft genome assemblies were generated using the same methods as previously described (Malmstrøm et al. 2017; Böhne et al. 2019)

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