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. 2021 Feb 22;11(4):jkab052. doi: 10.1093/g3journal/jkab052

Figure 4.

Figure 4

Alignment plots of large inversion regions on chromosomes 5 and 20 in the rainbow trout genome. (A) OmyA05 from this Arlee genome assembly aligned to Omy05 and showing that as oriented in the current Swanson assembly (Pearse et al. 2019) both are arranged according to the Ancestral (A) karyotype of the double inversion on chromosome 5. (B) OmyA20 aligned to chromosome Ssa28 of the Atlantic salmon genome assembly (Lien et al. 2016) showing the major inversion and indicating that the Arlee genome has the Rearranged (R) karyotype for the inversion on rainbow trout chromosome 20. c. OmyA20 aligned to Omy20 of the current Swanson assembly and showing only a small inversion close to the center of the chromosome, whereas the major inversion is aligned in the same orientation between the two rainbow trout genome assemblies. d. Canu contig tig00001481 of OmykA_1.1 assembly aligned to Omy20 of the current Swanson assembly and showing that the smaller inversion is within the boundary of the Arlee assembly contig, and hence not likely to be caused by scaffolding error in the Arlee assembly.