The data contained in this directory were generated using the methods described below. Detailed information will be published in a forthcoming paper.

Mice
We resequenced genomic DNAs from FLS/Shi, JF1/Ms, MSM/Ms, NC/Nga, and STR/OrtCrlj. FLS/Shi, NC/Nga, and STR/OrtCrlj are maintained as pedigreed breeding stocks at the RIKEN BRC. The genomic DNA of JF1/Ms and MSM/Ms was newly extracted in this study from cryopreserved specimens previously used in earlier publications (Takada et al., 2013). Samples used in the sequencing study are listed in Table S1.

Acquisition of new genome sequencing data by hybrid-assembly
Long-Read genomic sequencing of five mouse strains for de novo assembly was performed using PacBio Sequel II SMRT Cell system and Short-read genomic sequencing for hybrid assembly was also performed using HiSeq2500 for JF1/Ms (PE600) and NovaSeq6000 (Illumina) for FLS/Shi, MSM/Ms, NC/Nga, and STR/OrtCrlj (PE500) according to the manufacturer’s protocols. We assembled the genomes using Falcon v1.8.1 (Chin et al., 2016) and Wtdbg2 v2.5 (Ruan and Li, 2019) to create two contig sets from their long-read datasets. Parameters for Wtdbg2 were ‘-x sequel’ and ‘-g 3G’, as estimated genome size, and those of Falcon were ‘genome_size = 2800000000’, ‘seed_coverage = 60, and ‘length_cutoff = 9000’. These two contig sets were individually improved through the following process: first polished using the long-read data with Arrow (SMRT link version 2.3.3), and then polished using short-read data with NextPolish (Hu et al., 2019), and finally the haplotigs were eliminated using Purge_dups (Guan et al., 2020). These two contig sets were merged with Quickmerge (Chakraborty et al., 2016). This merged contigs were organized into chromosomal level sequences with RagTag (Alonge et al., 2022) using the mouse genome assembly GRCm39 as the reference. Their mitochondrial genomes were independently assembled using Platanus (Kajitani et al., 2019) from their short-read datasets, and then merged into this assembly, and finally the scaffolds were sorted by length. The completeness of final assemblies were evaluated by the benchmarking universal single-copy orthologs (BUSCO) v5.1.2 using the Glires data sets (glires_odb10) (Manni et al., 2021).

Repeat Masking
Repetitive sequences on the scaffolds were identified with RepeatMasker v4.1.5 (Smit et al., 2013), with the option ‘-species “Mus musculus”’. 

Variant Call
Filtering and trimming of short reads are executed with Fastp (Chen et al., 2018), mapping to the reference genome was conducted with BWA (Li and Dubin, 2010), and the genomic variants including SNPs and short indels were identified with the Genome Analysis Toolkit (GATK) (https://gatk.broadinstitute.org/hc/en-us) using these short read data sets. These genomic and structural variations were merged to create the VCF files, which were used in the database. For data acquisition for structural variation visualization, genomic structural variations between the scaffolds and the reference were detected using PAV (Ebert et al., 2021). The mouse genome assembly GRCm39 was used as the reference in these analyses. The merged VCF files (HybridVCF) were generated based small variants (less than 50 bp) from the GATK outputs and large variants (equal and greater than 50 bp) from the PAV outputs. The detection of variants in transposable elements was performed using both the variant data and repeat annotation data from RepeatMasker, and then the size distribution of insertion and deletion was evaluated as Ferrj et al., (2023).

References

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