Identifying the Centromeric Repeats and Full-Length LTR-RTs (flLTR-RTs).

The TRASH pipeline was used to identify CentGm91, CentGm92, CentGm413, CentGm273, and CentGm444 satellites in soybean centromeres, and the StainedGlass package was used to generate sequence identity heat maps. For the analysis of RepeatExplorer, a total of 10 million randomly selected sequence reads from the input control were analyzed using Web-based Galaxy RepeatExplorer software (https://repeatexplorer-elixir.cerit-sc.cz/galaxy/). To identify repeats associated with CENH3 nucleosomes, the CENH3-ChIP-seq and input reads were subjected to BLAST analysis against the cluster repeats with the parameters “-outfmt 6 -evalue 1e-8 -num_alignments 500.” The flLTR-RTs were identified using LTRharvest (76), where LTR_finder (77) and LTRharvest (78) were employed to identify flLTR-RTs based on the principle of structure ab initio. The following parameter settings were used: “ltr_finder -D 25000 -d 3000 -L 2000 -l 100 -p 20 -C -M 0.85” and “ltrharvest -overlaps best -seed 30 -minlenltr 100 -maxlenltr 2000 -mindistltr 3000 -maxdistltr 25000 -similar 85 -mintsd 4 -maxtsd 20 -motif tgca -motifmis 1 -vic 60 -xdrop 5 -mat 2 -mis -2 -ins -3 -del -3,” respectively. LTR_retriever was then used to integrate both candidates.