Info

Cladogram Figure Legend

Figure 1. An approximate cladogram showing the taxonomic relationship between plant species with more than 10,000 ESTs. The cladogram structure has been derived from the NCBI taxonomy database. The EST collections have been extracted from within the EST division of the EMBL database (release 86). Super-imposed on the figure are basic legends that identify groups of related species that are of relevance to agriculture and forestry. These clades include the gymosperms and the angiosperm clade that contains the rosids (eurosid I and eurosid II are highlighted), the asterids, the caryophyllids and the monocots. These 'rough' descriptive clades describe 80% of the species with more than 10,000 ESTs.

Figure 1. An approximate cladogram showing the taxonomic relationship between plant species with more than 10,000 ESTs. The cladogram structure has been derived from the NCBI taxonomy database. The EST collections have been extracted from within the EST division of the EMBL database (release 86). Super-imposed on the figure are basic legends that identify groups of related species that are of relevance to agriculture and forestry. These clades include the gymosperms and the angiosperm clade that contains the rosids (eurosid I and eurosid II are highlighted), the asterids, the caryophyllids and the monocots. These 'rough' descriptive clades describe 80% of the species with more than 10,000 ESTs.

view of the plant kingdom. There is a wealth of comparative and functional data within the poorly sampled clades that will undoubtedly enlighten the research community as to the clusters of genes that are manifested throughout plant life and that account for the developmental, metabolic and ecological adaptations of the constituent plants (Pryer et al. 2002). This rather general criticism of the sequence content of the EST databases is however minor, and a number of research groups (ours included) is actively working towards filling in some of these taxonomic gaps (e.g. sequencing ESTs from untouched clades such as the hornworts) and in increasing the comparative genomic resolution within the poorly sampled plant lineages.

It is unclear as to whether EST collection can ever substitute a 'completed genome' quality genome assembly with associated annotation and analysis. EST sequencing has been adopted on such a large scale because ESTs are simple and cheap to produce when the genome sequence itself is impractical to sequence. ESTs are not actively sequenced as an alternative to the genome, but rather as an adequate interim solution. Substantial EST resources are an extremely valuable resource during the gene modelling and annotation of a complete genome sequence, so this 'interim sequence solution' has several valuable roles. It may therefore be concluded that ESTs are of interest in the broader studies of crop genomics. They may be sequenced to establish a glimpse of the sequence diversity reflected within the genome, or may be produced to facilitate the construction of cDNA microarrays (this will be discussed in more detail later in this chapter).

Was this article helpful?

0 0

Post a comment