DOI: 10.5061/dryad.280gb5mwf
title: Data from: Repositioning of centromere-associated repeats during karyotype evolution in Oryzias fishes

description: 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 numbers of chromosome arms than the other groups, with most
 chromosomes being metacentric. The O. javanicus species group has similar
 numbers of chromosomes to the O. latipes species group, but smaller arm
 numbers, with most chromosomes being acrocentric. The O. celebensis
 species group has fewer chromosomes than the other two groups and several
 large metacentric chromosomes that were likely formed by chromosomal
 fusions. By comparing the genome assemblies of O. latipes, O. javanicus,
 and O. celebensis, we found that repositioning of centromere-associated
 repeats might be more common than simple pericentric inversion. Our
 results demonstrated that centromere repositioning may play a more
 important role in karyotype evolution than previously appreciated.
description: <strong>De novo assembly of <em>Oryzias
 celebensis</em> genome</strong> For
 reference genome assembly of <em>O. celebensis</em> 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 F<sub>2</sub> family obtained by crossing an <em>O. celebensis</em> female with a male of a closely-related species <em>O. woworae</em> (2n = 42; (Myosho et al., 2018)) generated in a previous study (Ansai et al., 2021). Genotypes of the F<sub>2</sub> family, consisting of two grandparents and 164 F<sub>2</sub> fish, were determined using double digest restriction site-associated DNA sequencing (ddRAD-seq) (DRA010679). The ddRAD-seq reads were trimmed using Trim Galore 0.4.3 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with cutadapt 1.12 (Martin, 2011) and mapped to the assembled contigs using BWA-backtrack 0.7.17 (Li & Durbin, 2009). The polymorphisms in the RAD tags were called using Stacks Version 2.64 (Rochette et al., 2019). A linkage map was constructed using 3,757 informative markers in lep-map3 (Rastas, 2017). After calling the parental genotypes using the <em>ParentCall2</em> module, markers with high segregation distortion (dataTolerance=0.001) and an excess number of missing genotypes (&gt;10% of individuals; missingLimit=0.1) were removed using the <em>Filtering2</em> module. The 1,756 markers were assigned to 18 linkage groups (LGs) by grouping the markers with pairwise LOD score higher than 10 (lodLimit=10) using the <em>SeparateChromosomes2</em> module, resulting in the total number of LGs equal to the haploid chromosome number of <em>O. celebensis</em> (n = 18). The order of the markers within each LG was determined by maximizing the likelihood of 50 iterations for each LG (numMergeIterations=50) using the <em>OrderMarkers2</em> module.               Based on the linkage map, three contigs in which four or more markers were aligned to two different linkage groups were split into two different contigs. Their breakpoints were determined based on a cross-species synteny map between <em>O. celebensis</em> and <em>O. latipes</em> by aligning the cDNA sequences of <em>O. latipes</em> (Ensembl Release 104; http://www.ensembl.org/) to the reassembled contigs of <em>O. celebensis</em> using minimap2-2.24 (r1122) (Li, 2018). Finally, chromosomal sequences were reconstructed using the positional information of 1,755 markers of the genetic map with ALLMAPS in JCVI utility libraries v1.2.7 (Tang et al., 2015). The number of LG was determined based on the syntenic chromosomes of <em>O. latipes</em>. The names of the fused chromosomes correspond to all syntenic chromosomes (e.g., LG1_19_17 is syntenic to LG1, LG19, and LG17 of the <em>O. latipes</em> chromosomes).
description: # 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.