Sex chromosomes have evolved from the same autosomes multiple times across vertebrates, suggesting that selection for recombination suppression has acted repeatedly and independently on certain genetic backgrounds. Here, we perform comparative genomics of a bird clade (larks and their sister lineage; Alaudidae and Panuridae) where multiple sex chromosome–autosome fusions appear to have formed expanded sex chromosomes. We detected the largest known avian sex chromosome (195.3 Mbp) and show that it originates from fusions between parts of four avian chromosomes: Z, 3, 4A and 5. Within these four chromosomes, we found evidence by using phylogenetic inference of five evolutionary strata where recombination had been suppressed at different time points, and showed that stratum age explained the divergence rate of Z–W gametologs. Next, we analysed chromosome content and found that chromosome 3 was significantly enriched for genes with predicted sex-related functions. Finally, we demonstrate extensive homology to sex chromosomes in other vertebrate lineages: chromosomes Z, 3, 4A and 5 have independently evolved into sex chromosomes in fish (Z), turtles (Z, 5), lizards (Z, 4A), mammals (Z, 4A) and frogs (Z, 3, 4A, 5). Our results provide insights in and support for repeated evolution of sex chromosomes in vertebrates. 

This dataset contains genome assemblies for the following species: Alauda arvensis, Alauda razae, Eremophila alpestris and Panurus biarmicus. The DNA used for these assemblies was extracted som a single adult male per species, and paired-end sequenced (150 base pairs) on an Illumina HiSeqX machine. The sequence data was assembled using Spades v3.5.0 using kmer lengths 21,33,55,77 and 127 and setting --careful. The assemblies contains scaffolds longer than 1000 base pairs. 

The data was generated for the study "Sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes" by Hanna Sigeman, Suvi Ponnikas, Pallavi Chauhan, Elisa Dierickx, M. de L. Brooke and Bengt Hansson. 

More information can be found in the manuscript. The raw reads used for the genome assemblies can be found on the NCBI Sequence Read Archive under the Bioproject accession PRJNA578893.