PMC

DIC microscopy on 21 deletion mutants for lipid accumulation genes. All deletion mutants (C–W) were constructed in a YKU70∆ background to enable homologous recombination at the targeted locus. Cells were grown 40 hr in low nitrogen lipid accumulation media. DIC, BODIPY 493/503 fluorescence, and composite images are shown for 23 strains. (A) R. toruloides IFO 0880 (WT). (B) RTO4_11920∆ ortholog of YKU70. (C) RTO4_11272∆ ortholog of ALG12. (D) RTO4_8709∆ ortholog of MET14. (E) RTO4_12031∆ ortholog of A. nidulans CysB. (F) RTO4_16215∆ similar to H. sapiens GNAI1. (G) RTO4_14088∆ ortholog of H. sapiens RAC1. (H) RTO4_10371∆ similar to H. sapiens KDELC1. (I) RTO4_16644∆ ortholog of BMH1. (J) RTO4_16731∆ ortholog of ERP2. (K) RTO4_9026∆ ortholog of UBP13. (L) RTO4_15890∆ similar to H. sapiens MYCL. (M) RTO4_8506∆ ortholog of CCC1. (N) RTO4_12817∆ ortholog of NCS6. (O) RTO4_10764∆ ortholog of NCS2. (P) RTO4_9970∆ ortholog of LDB17. (Q) RTO4_13598∆ ortholog of ATG2. (R) RTO4_16381∆ similar to H. sapiens PLIN1. (S) RTO4_12154∆ ortholog of GPD1. (T) RTO4_11043∆ similar to H. sapiens BSCL2. (U) RTO4_12121∆ ortholog of PMT4. (V) RTO4_10302∆ similar to C. neoformans CMT1. (W) RTO4_11380∆ ortholog of PPZ1.

qRT-PCR was used to investigate the differential expression of 17 genes in strawberry cultivars Taoyuan 3 and Superjumbo at 6, 12, 24 and 48 hr after SA treatment. FaActin was an internal control. FaSD: shikimate dehydrogenase (gene22236 ortholog); FaSK: shikimate kinase (gene31604 ortholog); FaCM: chorismate mutase (gene15010 ortholog); FaF3D: flavanone 3-dioxygenase (gene12448 ortholog); FaNPRL-1 (gene20070 ortholog); FaTGA6 (gene14220 ortholog); FaGrxC9 (gene29769 ortholog); FaWRKY51 (gene22024 ortholog); FaWRKY70 (gene13547 ortholog); FaWRKY1 (gene07210 ortholog); FaPR1 (gene01774 ortholog); FaPR5 (gene32421 ortholog); FaRGA1: resistance gene analog 1 (gene15044 ortholog); FaIL7R: interleukin-7 receptor (gene25131 ortholog); FaBIRK1: brassinosteroid insensitive 1-associated receptor kinase (gene23070 ortholog); FaPT5: patatin T-5 (gene09059 ortholog); FaH6DO: hyoscyamine 6-dioxygenase (gene01857 ortholog). The experiment was conducted in two independent trials each containing 3–4 plants per treatment per trial. Relative gene expression was measured in three technical repeats with pooled RNA from 3–4 plants. Results from two independent trials showed a similar trend, and representative data (mean ± SEM) from one trial are presented here.

The snapshots of the ortholog gene web interface of PlantOrDB. Panel a: Expandable Pairwise Ortholog Tree Viewer. Panel b: Gene and Its RBH Ortholog Genes. Panel c: Pairwise Ortholog Path Viewer. Panel d: Pairwise Ortholog Gene Details

Comparison of ortholog assignments made by Ensembl, MSOAR and MSOAR 2.0 for the two segments of human chromosome 2 (178,123,219 bp-178,685,428 bp) and mouse chromosome 2 (75,773,906 bp-76,192,000 bp). Among the 7 pairs of genes illustrated in the figure, only (TTC30B, Ttc30b) and (PDE11A, Pde11a) are known one-to-one ortholog pairs according to gene symbols, as indicated by solid lines. Since the Ensembl ortholog database includes many-to-many relationship, it outputs 7 ortholog pairs, i.e., (TTC30B, Ttc30b), (TTC30B, Ttc30a2), (TTC30B, Ttc30a1), (TTC30A, Ttc30b), (TTC30A, Ttc30a2), (TTC30A, Ttc30a1), and (PDE11A, Pde11a), introducing 5 false ortholog pairs, as indicated by dashed lines. MSOAR assigns three one-to-one ortholog pairs as indicated by the arrows in the figure, i.e., (TTC30B, Ttc30b), (TTC30A, Ttc30a1), and (PDE11A, Pde11a), including one false one-to-one ortholog pair. MSOAR 2.0, however, identifies TTC30A as an inparalog of TTC30B on the human genome and Ttc30a2 and Ttc30a1 as inparalogs of Ttc30b on the mouse genome during the phylogenetic analysis of TAGs, and removes them before invoking MSOAR. Thus, MSOAR 2.0 only outputs two one-to-one ortholog pairs, i.e., (TTC30B, Ttc30b) and (PDE11A, Pde11a), both of which are true positives.