In this study we generated four haploid genome assemblies derived from two interspeicifc hybrids. The scripts can be found in Assembly. The details of the methods are avaiable in the supplementary methods.
We used RNA-seq (short read) and Iso-Seq (long read) to annotate the transcripts. Together with the protein sequences of the published amphioxus genomes, we annotated the coding genes in the amphixous genomes produced in this study. The scripts are availabe in Annotation.
We used individually re-sequenced data of male and female population to identify the sex-linked regions. The sex-linked regions show the higherst levels of population differentiation between males and females. The scripts used for those analyses are available in Sex chromosome.
This study also includes analyses of segmental duplications, TADs, Hox gene evolution.
The annotation files are available from this link: https://www.dropbox.com/scl/fo/7es66dlyocuwmvhx5kv0s/h?dl=0&rlkey=awb9n16f1smehkxkyuy36wa2g