Table 1

[1] We were interested in accurate comparison of the abundance of ESTs for lipid biosynthesis genes in rice (Oryza sativa) and thale crest (Arabidopsis thaliana) and took every possible precaution to avoid potential errors. This was important because all these genes are not highly expressed and the corresponding EST numbers are low.

Although in most cases ESTs are sequenced from the 5'end of the cDNA clone, some EST clones were sequenced from both ends and the corresponding sequences are in separate files in dbEST. In our catalogue the clones sequenced from both ends are labeled by blue color.

Although clones for EST sequencing are selected randomly from a cDNA library we found that in some cases due to some kind of experimental artifact clones are sequenced more than once and the resulting sequences are deposited in dbEST as separate files. This is evident because the clone IDs in some EST projects correspond to coordinates of 96-well plates used for clone storage. Comparing clone IDs we noticed that in some cases the clones encoding one and the same enzyme are clustered in the plates which is practically impossible if they were selected randomly. An extreme example is the cluster of FatB acyl-ACP thioesterase EST clones from Arabidopsis: 173C1T7, 173D2T7, 173D3T7, and 173E2T7. In such cases 5'ends of the clones are identical which is an additional proof that these clones are not independent. Clones that we believe to be not independent are labeled by red color.

A comparison of EST abundance can be made only if clones originate from non-normalized cDNA libraries and the resulting EST data are not normalized. Unfortunately for our purpose, the EST sequence data for Arabidopsis from the consortium of laboratories in France is not fully deposited in the public databases. From a certain time only unique sequences were deposited (Cooke, et al., 1996 Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J. 9:101-124). These EST files are labeled by green color.

Finally, to avoid redundant sequencing of abundant clones, the cDNA library used for the EST project at the Michigan State University was prescreened with EST clones for:

photosystem II CAB (T13913, clone 43D8T7),

CAB binding protein (T14135, clone 47H3T7),

ADP, ATP carrier protein (T14153, clone 48B2T7),

heat shock protein (T13873, clone 42F9T7),

fructose-bisphosphate aldolase (T04477, clone 36C5T7),

elongation factor TU (T04453, clone 34F5T7),

catalase (T04280, clone 35F2T7),

tonoplast intrinsic protein (T04167, clone 23H5T7),

NADH-ubiquinone oxidoreductase (T04342, clone 38C2T7),

tonoplast intrinsic protein (T04259, clone 34E6T7),

glutathione S transferase (T13961, clone 44C2T7),

glycine rich protein (T13960, clone 44C1T7),

(T.Newman, personal communication).

We did not search databases with these sequences, thus the relative EST abundance estimated in our study is not influenced by the fact that the cDNA library has been prescreened although absolute levels may be influenced slightly.

We list all lipid biosynthesis ESTs in our catalogue but do not include mentioned cases in our comparison of EST abundance.