Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 105

Genome-wideComparisoninPlants
The completion of a number of genome sequencing projects in plants has increased
information on genome-scale comparative analyses and data that facilitate identi-
fication of conserved and/or characteristic properties between plant species. Using
model and inferred proteome data deduced from sequenced genomes of plants has
enabled several efforts to completed and construct comprehensive gene families
in other species for comparison. The aim of establishing platforms to verify and
compare gene content and elucidating the process of gene duplication and func-
tional diversification among species is on the way (Sterck et al. 2007 ). Web-based
sites for genome-wide comparison in plants, their purpose and URL are detailed in
Table 2.11 .
Markov Clustering and Multi Dimensional Scaling
Comprehensive gene family data sets are usually produced by computational pro-
cedures including a step that conducts an all-against-all sequence similarity search
matrices, and then a step for building clusters of protein families by methods such
as Markov Clustering (MCL), multi dimensional scaling (MDS) (see Sects. 2.5, 3.4
and 5.1; programs and statistical URL sites are listed in Table 2.1 ).
PGDD
Correlated gene arrangements among taxa, along with chromosomal location, also
known as synteny and collinearity, have become valuable sites for inference of
shared ancestry amongst genes, and for transfer of knowledge from one species to
another related species (Tang et al. 2008a ). The plant genome duplication database
(PGDD) provides a data set of intra-genome or cross-genome syntenic relation-
ships identified throughout genome-sequenced plant species at present (Tang et al.
2008b ).
DatabasesforPlantGenomics
Databases housing sets of genomic information and annotations of cross-reference
species are now essential for a better understanding of the biology of plants, in
particular gene families and/or particular cellular processes. In plants, the genome-
wide identification of genes encoding transfer factors (TFs) in Arabidopsis have
been reported, and comparisons with other organisms revealed important informa-
tion (Riechmann et al. 2000 ; Guo et al. 2008 ). Further integration of such data must
be performed, establishing an integrative, knowledge-based resource across related
plant species in terms of comparative genomics of regulation processes. A number
of general and specific web-based crop plant databases, their purpose and URL are
detailed in Table 2.11 .