Additional file 1 of The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors
Creators: name: Joubert, Pierre M.
name: Krasileva, Ksenia V.
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 1: Fig. S1. Degradation of linear DNA using exonuclease treatment. Fig. S2. Outward PCR validation of eccDNA forming regions. Fig. S3. Overlap in exact break points of eccDNA forming regions across samples. Fig. S4. Rarefaction analysis of sequencing coverage and eccDNA forming regions across all samples. Fig. S5. Principal components analysis of sequencing coverage between samples. Fig. S6. Overlap in eccDNA forming regions across samples, with increasing tolerance for start and end coordinates. Fig. S7. Overlap between eccDNA forming regions called using PacBio sequencing data and Illumina sequencing data. Fig. S8. Comparison between eccDNA forming regions in human samples called in this manuscript and in the original publication. Fig. S9. Comparison of eccDNA forming regions between M. oryzae and other previously studied organisms. Fig. S10. EccDNA forming regions composed of more than 90% LTR retrotransposon sequence in M. oryzae. Fig. S11. Percentage of the M. oryzae Guy11 genome made up of each LTR retrotransposon. Fig. S12. Correlation between number of LTR-LTR split reads and sequencing reads in eccDNA sequencing samples for each LTR retrotransposon in M. oryzae. Fig. S13. Correlation between number of LTR-internal split reads and sequencing reads in eccDNA sequencing samples for each LTR-retrotransposon in M. oryzae. Fig. S14. Number of LTR-LTR split reads and LTR-internal split reads in eccDNA sequencing samples for each LTR retrotransposon in M. oryzae. Fig. S15. Expected read coverage for LTR retrotransposons in M. oryzae. Fig. S16. MicroDNA enrichment and depletion in the genomes of various organisms. Fig. S17. Enrichment and depletion of microDNAs and large eccDNAs across various genomic regions in M. oryzae. Fig. S18. Correlation between gene count and junction split read count across the M. oryzae genome. Fig. S19. Correlation between junction split read count and expression for M. oryzae genes. Fig. S20. Comparison of junction split read counts between eccDNA forming regions with and without an ACS. Fig. S21. GC content and chromatin marks of eccDNA forming regions in M. oryzae. Fig. S22. Overlap between genes enriched on eccDNAs in biological replicates. Fig. S23. GO terms associated with eccDNA-associated genes. Fig. S24. GC content and chromatin marks of eccDNA-associated and eccDNA-absent genes in M. oryzae. Fig. S25. Comparison of expression data between eccDNA-associated genes and eccDNA-absent genes in M. oryzae. Fig. S26. Proximity of M. oryzae genes to repeats. Fig. S27. Proximity of M. oryzae genes to TEs. Fig. S28. Predicted effectors are prone to presence-absence variation in M. oryzae. Fig. S29. Rarefaction curves for eccDNA forming regions in M. oryzae. Fig. S30. Example of an eccDNA-mediated translocation in wine yeasts. Fig. S31. Comparison of encompassing split read counts between genes found on mini-chromosomes in M. oryzae and other genes. Fig. S32. GO terms associated with eccDNA-absent genes. Fig. S33. PCR validation of eccDNA-absent genes. Fig. S34. Effectors are enriched in eccDNAs in M. oryzae. Fig. S35. Lengths of eccDNA forming regions in M. oryzae.