A Populus EST resource for plant functional genomics

Abstract

Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

Fig. 1.

Relation between sequence length of Populus contigs and similarity to the best scoring Arabidopsis sequence. AFC Populus sequences (4,166) were compared by using blastx with the Arabidopsis proteome, and the score for each sequence was plotted against sequence length.

Fig. 2.

Homologs to most Arabidopsis gene families are represented in populusdb. The cumulative curve indicates the percentage of genes in the Arabidopsis genome that has sequence similarity better than the value given to a sequence in populusdb. For example, 50% of the genes have a hit with an E value <10^–38 and 75% have a hit with an E value <10^–10.

Fig. 3.

Functional classification of the Populus EST data set according to the Umeå Plant Science Center-MIPS classification schedule

Fig. 4.

Relative abundance of clones in functional classes (excluding clones without significant homology to a protein with a predicted function (classes 98 and 99) in the different libraries.

Fig. 5.

Dendrogram representation of the similarities in expression profiles for the Populus libraries, based on a clustered correlation map calculated according to Ewing et al. (16).

Fig. 6.

The complete clustered correlation map calculated according to Ewing et al. (16). Only clusters with >10 ESTs were included.

Fig. 7.

Subsection of the clustered correlation map, showing a cluster mainly containing genes encoding histone and ribosomal proteins.

Fig. 8.

Subsection of the clustered correlation map, showing a cluster mainly containing genes encoding photosynthetic proteins.