Table III.
Comparison of EST data and ENC values for ORFs in the C. reinhardtii genome encoding putative proteins involved in biosynthesis of chlorophylls (1–16) or carotenoids (21–43)
C. reinhardtii EST clones deposited in GenBank (http://www.ncbi.nlm.nih.gov) were grouped into three categories: (1) unstressed (clones of projects 874, 894, and 1,024 from Shrager et al., 2003; clones whose accession begins with “AV” from Asamizu et al., 1999, 2000); (2) stressed (projects 963, 1,031, and 3,510 [=1,115] from Shrager et al., 2003; projects 832 and 833); (3) other (projects 1,030, 3,511 (=1,112), and 925 from Shrager et al., 2003; clones whose accession begins with “BP” from Asamizu et al., 2004). EST clones with more than one sequence entry in GenBank (5′- and 3′-reads) were counted only once. The detailed frequencies of EST clones in each project are available as Supplemental Tables I and II. The ENC used by each ORF was calculated according to Wright (1990). For UROD, CPX, CHLI, and CHLH, the respective isogene that is represented by the majority of EST clones in cDNA libraries generated from unstressed cells and at the same time has the lowest ENC value is in bold.
| Step
|
Gene Product
|
EST Clones
|
ENC
|
|||
|---|---|---|---|---|---|---|
| Unstressed | Stressed | Other | Total | |||
| 1 | GTS | 0 | 0 | 0 | 0 | 29.4 |
| 2 | GTR | 5 | 13 | 5 | 23 | 32.4 |
| 3 | GSA | 6 | 3 | 5 | 14 | 25.7 |
| 4 | ALAD | 24 | 7 | 13 | 44 | 28.6 |
| 5 | PBGD | 11 | 20 | 4 | 35 | 28.0 |
| 6 | UROS | 3 | 4 | 2 | 9 | 30.6 |
| 7 | UROD1 | 19 | 6 | 10 | 35 | 23.7 |
| UROD2 | 3 | 7 | 6 | 16 | 30.3 | |
| UROD3 | 9 | 8 | 2 | 19 | 34.3 | |
| 8 | CPX1 | 14 | 4 | 8 | 26 | 26.1 |
| CPX2 | 3 | 2 | 0 | 5 | 35.2 | |
| 9 | PPX | 1 | 0 | 0 | 1 | 30.5 |
| 10a | CHLD | 6 | 2 | 3 | 11 | 30.9 |
| 10b | CHLI1 | 15 | 17 | 9 | 41 | 25.8 |
| CHLI2 | 6 | 0 | 3 | 9 | 31.9 | |
| 10c | CHLH1 | 21 | 4 | 19 | 44 | 25.9 |
| CHLH2 | 0 | 0 | 0 | 0 | 33.8 | |
| 11 | PPMT | 7 | 2 | 0 | 9 | 31.2 |
| 12 | CHL27A | 18 | 71 | 17 | 106 | 28.8 |
| CHL27B | 9 | 2 | 1 | 12 | 24.8 | |
| 14 | LPOR | 7 | 16 | 7 | 30 | 23.7 |
| 15 | CAO | 13 | 5 | 10 | 28 | 31.4 |
| 16 | CHS | 8 | 3 | 3 | 14 | 28.7 |
| 21 | DXS | 22 | 12 | 12 | 46 | 31.3 |
| 22 | DXR | 1 | 3 | 1 | 5 | 27.5 |
| 23 | CMS | 3 | 1 | 1 | 5 | 38.5 |
| 24 | CMK | 1 | 3 | 0 | 4 | 35.2 |
| 25 | MCS | 6 | 1 | 0 | 7 | 34.5 |
| 26 | HDS | 12 | 0 | 3 | 15 | 25.9 |
| 27 | IDS | 16 | 4 | 7 | 27 | 28.3 |
| 28 | IDI | 1 | 0 | 0 | 1 | 33.3 |
| 29 | GGPS | 2 | 8 | 3 | 13 | 32.6 |
| 30 | PSY | 8 | 1 | 9 | 18 | 40.0 |
| 31 | PDS | 5 | 6 | 6 | 17 | 29.7 |
| 32 | ZDS | 1 | 4 | 3 | 8 | 28.8 |
| 33 | CRTISO | 0 | 0 | 0 | 0 | 30.4 |
| 34 | LCYB | 7 | 3 | 6 | 16 | 32.7 |
| 35 | LCYE | 6 | 1 | 3 | 10 | 33.5 |
| 36 | CHYB | 0 | 0 | 0 | 0 | 31.4 |
| 37 | CHYE | 0 | 0 | 0 | 0 | ? |
| 38 | ZEP | 5 | 2 | 3 | 10 | 30.3 |
| 42 | BKT | 1 | 0 | 0 | 1 | 39.5 |
| 43 | GGR | 37 | 5 | 0 | 57 | 26.5 |