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Additional file 2: Supplementary Fig. 1. Mitogenome structure of seven sorghum accessions whenusing 10G of CLR data. Supplementary Fig. 2. Mitogenome structure of seven sorghum accessions when using all available CLR data. Supplementary Fig. 3. Example of the final mitogenome conformation process. The conformation is from the mitogenome assembled by SPAdes using corrected CLR reads of IS929, the color-coded portion is contig-01 of IS929 assembled by Flye using 10G CLR, which were compared to the conformation, from red to pink, representing the continuity of the contig. Supplementary Fig. 4. PCR amplification to check the 12 linkages of IS929(Type I) in PI525695(Type II) and PI536008(Type III). The colors and labels in a and b show the same connections of contigs of IS929 in PI525695 and PI536008. The red marked labels in c are corresponding to the connections in a and b. Supplementary Fig. 5. The location of forward repeats(F), reversed repeats(R) and P palindromic repeats(P) in the contig-01 of seven sorghum mitogenomes. Supplementary Fig. 6. The location of forward repeats (F), reversed repeats (R) and P palindromic repeats (P) in the contig-02 of seven sorghum mitogenomes. Supplementary Fig. 7. The location of forward repeats (F), reversed repeats (R) and P palindromic repeats (P) in the contig-03 of seven sorghum mitogenomes. Supplementary Fig. 8. The location of forwardrepeats (F), reversed repeats (R) and P palindromic repeats (P) in the contig-04 of seven sorghum mitogenomes. Supplementary Fig. 9. The location of forward repeats (F), reversed repeats (R) and P palindromic repeats (P) in the contig-05 of seven sorghum mitogenomes. Supplementary Fig. 10. The location of forward repeats (F), reversed repeats (R) and P palindromic repeats (P) in the contig-06 of seven sorghum mitogenomes. Supplementary Fig. 12. The location of forward repeats (F), reversed repeats(R) and P palindromic repeats (P) in seven sorghum plastid genomes. Supplementary Fig. 13. Location of a 12.4 kbp repeat sequence from sorghum reference genome NC_008360.1 in each of three structural types. Supplementary Fig. 14. Location of a 3.6 kbp repeat sequence from sorghum reference genome NC_008360.1 in each of three structural types. Supplementary Fig. 15. Location of a 4 kbp repeat sequence from sorghum reference genome NC_008360.1 in each of three structural types. Supplementary Fig. 16. Location of a 33 kbp repeat sequence from sorghum reference genome NC_008360.1 in each of three structural types. Supplementary Fig. 17. GC content of fragments transferred from sorghum organelles to the nucleus. a: GC content of NUMTs with different levels of sequence identity; b: GC content of NUPTs with different levels of sequence identity. Supplementary Fig. 18. The GC content of transfer fragment flanking sequences a: The GC content of NUMT flanking sequences. b: The GC content of NUPT flanking sequences. Supplementary Fig. 19. The full-length original gel of Figure 1d.

Additional file 1: Supplementary Figure 1. Scatter plot representing DA loading of Ugandan accessions based on races. (a) and (b) are replicate 2 and 3 respectively. Each dot represents an individual and the colour code is displayed in the index.

Additional file 2: Supplementary Figure 2. Topographic map of Uganda showing the elevation.

This is the accepted manuscript version of the work published in its final form as Zhi, X., Tao, Y., Jordan, D., Borrell, A., Hunt, C., Cruickshank, A., Potgieter, A., Wu, A., Hammer, G., George-Jaeggli, B., & Mace, E. (2022). Genetic control of leaf angle in sorghum and its effect on light interception.Journal of Experimental Botany,73(3), 801-816. https://doi.org/10.1093/jxb/erab467 Deposited by shareyourpaper.org and openaccessbutton.org. We've taken reasonable steps to ensure this content doesn't violate copyright. However, if you think it does you can request a takedown by emailing help@openaccessbutton.org. &nbsp

This is the accepted manuscript version of the work published in its final form as Tirfessa, A., Mclean, G., Mace, E., Oosterom, E., Jordan, D., & Hammer, G. (2020). Differences in temperature response of phenological development among diverse ethiopian sorghum genotypes are linked to racial grouping and agroecological adaptation.Crop Science,60(2), 977-990. https://doi.org/10.1002/csc2.20128 Deposited byshareyourpaper.organdopenaccessbutton.org. We've taken reasonable steps to ensure this content doesn't violate copyright. However, if you think it does you can request a takedown by emailinghelp@openaccessbutton.org.

Spontaneous sequence changes and the selection of beneficial mutations are driving forces of gene diversification and key factors of evolution. In highly dynamic co-evolutionary processes such as plant-pathogen interactions, the plant's ability to rapidly adapt to newly emerging pathogens is paramount. The hexaploid wheat gene Lr34, which encodes an ATP-binding cassette (ABC) transporter, confers durable field resistance against four fungal diseases. Despite its extensive use in breeding and agriculture, no increase in virulence towards Lr34 has been described over the last century. The wheat genepool contains two predominant Lr34 alleles of which only one confers disease resistance. The two alleles, located on chromosome 7DS, differ by only two exon-polymorphisms. Putatively functional homoeologs and orthologs of Lr34 are found on the B-genome of wheat and in rice and sorghum, but not in maize, barley and Brachypodium. In this study we present a detailed haplotype analysis of homoeologous and orthologous Lr34 genes in genetically and geographically diverse selections of wheat, rice and sorghum accessions. We found that the resistant Lr34 haplotype is unique to the wheat D-genome and is not found in the B-genome of wheat or in rice and sorghum. Furthermore, we only found the susceptible Lr34 allele in a set of 252 Ae. tauschii genotypes, the progenitor of the wheat D-genome. These data provide compelling evidence that the Lr34 multi-pathogen resistance is the result of recent gene diversification occurring after the formation of hexaploid wheat about 8,000years ago