Databases of homologous gene families for comparative genomics

xBASE, a collection of online databases for bacterial comparative genomics

The schema of the previously described Escherischia coli database coliBASE has been applied to a number of other bacterial taxa, under the collective name xBASE. The new databases include CampyDB for Campylobacter, Helicobacter and Wolinella; PseudoDB for pseudomonads; ClostriDB for clostridia; RhizoDB for Rhizobium and Sinorhizobium; and MycoDB, for Mycobacterium, Streptomyces and related orga...

Structural genomics of conserved gene families

Comparative genomics provides evidence for close evolutionary relationships between the urotensin II and somatostatin gene families.

Although urotensin II (UII) and somatostatin 1 (SS1) exhibit some structural similarities, their precursors do not show any appreciable sequence identity and, thus, it is widely accepted that the UII and SS1 genes do not derive from a common ancestral gene. The recent characterization of novel isoforms of these two peptides, namely urotensin II-related peptide (URP) and somatostatin 2 (SS2)/cor...

Ancient signals: comparative genomics of plant MAPK and MAPKK gene families.

MAPK signal transduction modules play crucial roles in regulating many biological processes in plants, and their components are encoded by highly conserved genes. The recent availability of genome sequences for rice and poplar now makes it possible to examine how well the previously described Arabidopsis MAPK and MAPKK gene family structures represent the broader evolutionary situation in plant...

A Transcriptomics and Comparative Genomics Analysis Reveals Gene Families with a Role in Body Plan Complexity

We analyzed tissue-specific transcriptomes of Arabidopsis thaliana and identified 66 gene families with a high frequency of "gradient genes" - genes showing a significant expression gradient between tissues. Gradient gene families include many with roles in hormone and peptide signaling, cell wall synthesis and remodeling, secondary metabolism, transcriptional regulation, and transport between ...