Table 1.
The 50 most stable Eucalyptus genes selected from microarray data analysis employing the SDMA and the SAM statistical algorithms
| Gene name | EUCAGEN scaffold | Gene ID | BLAST annotation | e-Value | SDMA |
SAM |
|||
|---|---|---|---|---|---|---|---|---|---|
| SD | Ranking | Fold change | Score (d) | Ranking | |||||
| Eucons01 | 4 | emb|CAY47298.1| | Serine transporter (Pseudomonas fluorescens SBW25) | 2e-94 | 0.000082 | 1 | 0.999995685 | 0.00661473 | 48 |
| Eucons02 | 1,599 | No hit | 0.00029 | 2 | 1.000005363 | 0.007716502 | 23 | ||
| Eucons03 | 7 | gb|EEY18801.1| | DNA damage checkpoint protein rad24 (Verticillium alboatrum VaMs.102) | 7e-44 | 0.000365 | 3 | 0.999993841 | 0.008958654 | 41 |
| Eucons04 | 88 | gb|EEF43392.1| | Cdk8, putative (Ricinus communis) | 2e-49 | 0.000461 | 4 | 1.000006755 | 0.009261212 | 21 |
| Eucons05 | 332 | No hit | 0.000509 | 5 | 1.000008973 | 0.010259132 | 46 | ||
| Eucons06 | 134 | gb|EEF44719.1| | Plastidic ATP/ADP-transporter, putative (R. communis) | 5e-20 | 0.000549 | 6 | 1.000009876 | 0.012322456 | 40 |
| Eucons07 | 515 | gb|EEF03117.1| | ABC transporter family protein (Populus trichocarpa) | 7e-29 | 0.000561 | 7 | 1.000010164 | 0.01241657 | 8 |
| Eucons08 | 2 | gb|EEF33688.1| | Transcription elongation factor s-II, putative (R. communis) | 1e-25 | 0.000582 | 8 | 1.000013416 | 0.012556064 | 15 |
| Eucons09 | 6 | gb|EEF42371.1| | Nucleic acid binding protein, putative (R. communis) | 1e-18 | 0.000665 | 9 | 1.000015637 | 0.013553234 | 9 |
| Eucons10 | 369 | gb|ACG37397.1| | Anther-specific proline-rich protein APG (Zea mays) | 3e-42 | 0.000678 | 10 | 1.000018989 | 0.015574381 | 2 |
| Eucons11 | 1 | No hit | 0.000694 | 11 | 1.0000296 | 0.016330796 | 44 | ||
| Eucons12 | 2,755 | No hit | 0.000694 | 12 | 0.999973005 | 0.016437714 | 7 | ||
| Eucons13 | 288 | No hit | 0.000732 | 13 | 0.999966 | 0.016807148 | 17 | ||
| Eucons14 | 899 | gb|AAM52237.1| | Senescence/dehydration-associated protein-related (Arabidopsis thaliana) | 8e-14 | 0.000734 | 14 | 1.000035875 | 0.017118153 | 36 |
| Eucons15 | 2 | emb|CAA65477.1| | Lipid transfer protein (Prunus dulcis) | 7e-35 | 0.000785 | 15 | 1.000039015 | 0.018024764 | 5 |
| Eucons16 | 6,792 | gb|EEF44560.1| | F-box and wd40 domain protein, putative (R. communis) | 5e-19 | 0.000791 | 16 | 0.999960301 | 0.01818155 | 35 |
| Eucons17 | 62 | No hit | 0.000794 | 17 | 1.000045767 | 0.020617825 | 34 | ||
| Eucons18 | 6 | No hit | 0.000800 | 18 | 0.999960851 | 0.021328632 | 4 | ||
| Eucons19 | 9 | No hit | 0.000821 | 19 | 1.000046587 | 0.021445011 | 1 | ||
| Eucons20 | 175 | gb|EEE97842.1| | Chromatin remodeling complex subunit (P. trichocarpa) | 6e-47 | 0.000879 | 20 | 1.000054302 | 0.021978112 | 14 |
| Eucons21 | 1,753 | gb|EEF48129.1| | Aspartyl-tRNA synthetase, putative (R. communis) | 2e-42 | 0.000913 | 21 | 0.99994759 | 0.022500691 | 6 |
| Eucons22 | 584 | No hit | 0.000931 | 22 | 1.000052414 | 0.02331048 | 28 | ||
| Eucons23 | 180 | dbj|BAB02414.1| | Chloroplast nucleoid DNA binding protein-like (A. thaliana) | 2e-53 | 0.000970 | 23 | 1.000055076 | 0.02331048 | 3 |
| Eucons24 | 15 | gb|EEF45372.1| | Conserved hypothetical protein (R. communis) | 5e-44 | 0.000992 | 24 | 0.999948713 | 0.024728932 | 10 |
| Eucons25 | 531 | No hit | 0.001028 | 25 | 0.999941348 | 0.024874888 | 19 | ||
| Eucons26 | 95 | gb|EEF45384.1| | Vacuole membrane protein, putative (R. communis) | 3e-15 | 0.001030 | 26 | 1.000068819 | 0.024983297 | 11 |
| Eucons27 | 743 | gb|EEF44734.1| | Peroxisome biogenesis factor, putative (R. communis) | 2e-51 | 0.001063 | 27 | 1.000059599 | 0.025183557 | 16 |
| Eucons28 | 87 | No hit | 0.001085 | 28 | 0.999931481 | 0.025250589 | 13 | ||
| Eucons29 | 6 | gb|EER99842.1| | Hypothetical protein SORBIDRAFT_02g041780 (Sorghum bicolor) | 4e-13 | 0.001158 | 29 | 0.999914659 | 0.025278616 | 12 |
| Eucons30 | 173 | gb|EEF45541.1| | Sentrin/sumo-specific protease, putative (R. communis) | 4e-46 | 0.001175 | 30 | 1.000062543 | 0.025638209 | 20 |
| Eucons31 | 842 | emb|CAP42856.1| | SsrA-binding protein (Bordetella petrii) | 8e-43 | 0.001175 | 31 | 0.999931592 | 0.02654049 | 50 |
| Eucons32 | 8 | gb|EDS90429.1| | Nitrogen regulation protein NR(II) (Escherichia albertii TW07627) | 6e-34 | 0.001181 | 32 | 1.000079957 | 0.026547459 | 18 |
| Eucons33 | 1,056 | No hit | 0.001189 | 33 | 1.000081012 | 0.026669523 | 26 | ||
| Eucons34 | 1,034 | gb|EEE90904.1| | Predicted protein (P. trichocarpa) | 5e-18 | 0.001256 | 34 | 1.000078558 | 0.026841264 | 30 |
| Eucons35 | 349 | No hit | 0.001257 | 35 | 1.000079192 | 0.027114749 | 37 | ||
| Eucons36 | 52 | ref|NP_565080.1| | Mitochondrial transcription termination factor-related/mTERF-related (A. thaliana) | 3e-45 | 0.001263 | 36 | 0.999911838 | 0.027388068 | 38 |
| Eucons37 | 229 | No hit | 0.001273 | 37 | 0.999915438 | 0.027861819 | 24 | ||
| Eucons38 | 447 | emb|CAN64407.1| | Hypothetical protein (Vitis vinifera) | 8e-25 | 0.001276 | 38 | 0.999891043 | 0.027872741 | 45 |
| Eucons39 | 1,208 | No hit | 0.001286 | 39 | 0.99990712 | 0.028070603 | 25 | ||
| Eucons40 | 570 | No hit | 0.001293 | 40 | 0.999908155 | 0.028195758 | 33 | ||
| Eucons41 | 720 | No hit | 0.001303 | 41 | 1.000098979 | 0.028550233 | 32 | ||
| Eucons42 | 4 | No hit | 0.001361 | 42 | 0.999893249 | 0.028605047 | 29 | ||
| Eucons43 | 482 | gb|EEF46905.1| | Serine/threonine-protein kinase PBS1, putative (R. communis) | 6e-35 | 0.001365 | 43 | 1.000105741 | 0.028682612 | 27 |
| Eucons44 | 228 | gb|EEF48108.1| | Pollen specific protein sf21, putative (R. communis) | 3e-42 | 0.001378 | 44 | 1.000117513 | 0.030661159 | 43 |
| Eucons45 | 10,041 | No hit | 0.001385 | 45 | 0.9999055 | 0.030782861 | 42 | ||
| Eucons46 | 485 | gb|ACM45716.1| | Class IV chitinase (Pyrus pyrifolia) | 2e-61 | 0.001428 | 46 | 1.000104153 | 0.031264117 | 49 |
| Eucons47 | 175 | gb|EEE86166.1| | F-box family protein (P. trichocarpa) | 4e-31 | 0.001432 | 47 | 1.00010279 | 0.031514942 | 22 |
| Eucons48 | 873 | No hit | 0.001613 | 48 | 1.00012433 | 0.031516084 | 39 | ||
| Eucons49 | 359 | gb|EEF03628.1| | Predicted protein (P. trichocarpa) | 9e-25 | 0.001848 | 49 | 0.999886858 | 0.031626533 | 47 |
| Eucons50 | 30 | No hit | 0.001303 | 50 | 1.000098979 | 0.031987517 | 31 | ||
Gene names and the identity of E. grandis genomic (EUCAGEN) scaffolds where sequences are located, as well as the EMBL or GenBank accession codes (Gene ID) and putative functional identity of sequences based on BLAST analysis are indicated along with the estimated (e) value. Results of the statistical analysis performed are indicated: standard deviations (SD) for the SDMA method, and fold change and final score (d) of the SAM method. Genes were ranked from highest to lowest stability for both methods. Lines shaded in gray represent genes selected for validation via RT–qPCR analysis.