Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly.

Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.

Comparing the inverted internal limiting membrane flap with autologous blood technique to internal limiting membrane insertion for the repair of refractory macular hole.

PURPOSE: To compare the anatomical and functional outcomes of the inverted internal limiting membrane (ILM) flap technique and the autologous blood clot (ABC) to ILM insertion technique for the repair of refractory macular hole (RMH). METHODS: Fifty-two consecutive patients (52 eyes) diagnosed with RMH with a minimum diameter more than 700 µm were enrolled. All patients underwent vitrectomy and gas tamponade. Of these, 25 patients undergo inverted ILM flap combination with ABC (Group A). The remaining 27 patients underwent ILM insertion (Group B). The main outcome measures were macular hole (MH) closure, foveal configuration, logarithm of the minimum angle of resolution (logMAR), best-corrected visual acuity (BCVA), superficial foveal avascular zone (FAZ) and superficial parafoveal vessel density. RESULTS: Three months post-operation, MH was successfully anatomic closed in 24 of 25 eyes (96%) in Group A and 25 of 27 eyes (92.5%) in Group B (P = 0.599). A concave foveal configuration of MH closure was observed in 23 of 25 eyes (92%) in Group A and 2 of 27 eyes (7.4%) in Group B (P < 0.001). Mean BCVA (logMAR) had improved from 1.31 ± 0.61 to 0.68 ± 0.40 in Group A (P < 0.001) and from 1.34 ± 0.39 to 1.29 ± 0.62 in Group B (P = 0.584) at 3 months. Average superficial FAZ area and superficial parafoveal vessel density were 0.29 ± 0.08 mm2 and 51.41 ± 2.79% in Group A and 0.73 ± 0.15 mm2 and 43.77 ± 2.71% in Group B, respectively. There was a significant difference in both the average superficial FAZ area and parafoveal vessel density between Groups A and B (P < 0.001 for both). CONCLUSION: Anatomical foveal configuration, mean BCVA (logMAR), mean superficial FAZ and parafoveal vessel density outcomes for the inverted ILM flap combined with ABC approach were better than the outcomes obtained with ILM insertion in the treatment of RMH. This approach may promote better long-term, vision function outcomes for patients diagnosed with RMH.