Repositioning of centromere-associated repeats during karyotype evolution in Oryzias fishes

The karyotype, which is the number and shape of chromosomes, is a fundamental characteristic of all eukaryotes. Karyotypic changes play an important role in many aspects of evolutionary processes, including speciation. In organisms with monocentric chromosomes, it was previously thought that chromosome number changes were mainly caused by centric fusions and fissions, whereas chromosome shape changes, that is changes in arm numbers, were mainly due to pericentric inversions. However, recent genomic and cytogenetic studies have revealed examples of alternative cases, such as tandem fusions and centromere repositioning, found in the karyotypic changes within and between species. Here, we employed comparative genomic approaches to investigate whether centromere repositioning occurred during karyotype evolution in medaka fishes. In the medaka family (Adrianichthyidae), the three phylogenetic groups differed substantially in their karyotypes. The Oryzias latipes species group has larger numb..., De novo assembly of Oryzias celebensis genome
For reference genome assembly of O. celebensis with improved continuities, PacBio continuous long reads (CLRs) (PacBio RSII with P6/C4v2 chemistry; 7.5 million reads; 88.1 Gb; ~110x coverage; PacBio, Menlo Park, CA, USA) (DRX230016) acquired in our previous study (Ansai et al., 2021) were assembled using NextDeNovo 2.5.2 (Hu et al., 2023). The assembled contig sequences were then polished with the PacBio reads used for the assembly and the Illumina short reads (Illumina HiSeq 2500; 2 x 250 bp; 296 millions reads; 148Gb; ~185x coverage; San Diego, CA, USA) (DRX230015) using NextPolish 1.4.1 (Hu et al., 2020).
              To scaffold the contigs into chromosome-level assemblies, a linkage map was constructed using an F2 family obtained by crossing an O. celebensis female with a male of a closely-related species O. woworae (2n = 42; (Myosho et al., 2018)) generated in a previous study (Ansai et al., 2021). Genotypes of the F2 family, consisti..., , # Repositioning of centromere-associated repeats during karyotype evolution in Oryzias fishes

Authors: Satoshi Ansai, Atsushi Toyoda, Kohta Yoshida, Jun Kitano

## Description of the data and file structure

#### OryCel\_1.2.fasta.gz

A fasta file containing new reference genome sequences of *Oryzias celebensis* assembled in this study.