IMEG Seminars and Abstracts:
Speaker and title of seminar
Dr. Stephen Schaeffer
Department of Biology
Genomics of Drosophila: Insights on chromosomal and repetitive DNA
levels of nucleotide diversity in a chromosomal region can be due to
selective constraint, directional selection, or chromosomal
context. Breakpoints for chromosomal rearrangements will tend to
have low levels of variation due to reduced genetic flux that
homogenizes variation among gene arrangements.
I will talk about
recent advances in our knowledge of chromosomal evolution that has
comparative genomic sequencing in Drosophila and
examine how chromosomal context influences levels of nucleotide
Navarro, A., E. Betrán, A. Barbadilla and A. Ruiz, 1997
Recombination and gene flux caused by gene
conversion and crossing
over in inversion heterokaryotypes. Genetics 146: 695-709.
Schaeffer, S. W., P. Goetting-Minesky, M. Kovacevic, J. Peoples, J.
L. Graybill, J. M. Miller, K. Kim, J. G. Nelson
and W. W. Anderson,
2003 Evolutionary genomics of inversions in Drosophila
pseudoobscura: Evidence for epistasis. Proceedings of the
National Academy of Sciences USA 100: 8319-8324.
Richards, S., Y. Liu, B. R. Bettencourt, P. Hradecky, S. Letovsky,
R. Nielsen, K. Thornton, M. A. Todd, R. Chen,
R. P. Meisel, O.
Couronne, S. Hua, M. A. Smith, H. J. Bussemaker, M. F. V. Batenburg,
S. L. Howells, S. E.
Scherer, E. Sodergren, B. B. Matthews, M. A.
Crosby, A. J. Schroeder, D. Ortiz-Barrientos, C. M. Rives, M. L.
Metzker, D. M. Muzny, G. Scott, D. Steffen, D. A. Wheeler, K. C.
Worley, P. Havlak, K. J. Durbin, A. Eagan, R. Gill,
J. Hume, M. B.
Morgan, Y. Huang, L. Waldron, D. Verduzco, K. P. Blankenburg, H.
Robertson, I. Dubchak,
M. A. F. Noor, W. W. Anderson, K. White, A.
G. Clark, S. W. Schaeffer, W. M. Gelbart, G. Weinstock and R. A.
Gibbs, 2005 Comparative genome sequencing of Drosophila
pseudoobscura: Chromosomal, gene and
evolution. Genome Research 15: 1-18.
Shashikant - Department of Molecular and Developmental Biology
of a Mouse Homeobox Gene."
There is a considerable
interest in understanding how cis-regulatory modifications drive
morphological changes across species. Because developmental
regulatory genes, including Hox genes, are remarkably conserved,
their noncoding regulatory regions are likely sources for
variations. Modifications of
Hox cis-regulatory elements have
potential to alter Hox gene expression, and, hence axial
morphologies. In vertebrates, differences in the axial levels of
Hox gene expression correlate with differences in the number
relative position of thoracic vertebrae. Variation in cis-regulatory
elements of Hox genes can be identified
by comparative sequence
and reporter gene analysis in transgenic mouse embryos. Using
these approaches,we show a remarkable divergence of the Hoxc8
early enhancers between mammals and fishes representing diverse
axial morphologies. Extensive restructuring of the Hoxc8 early
enhancer including nucleotide
substitutions, inversion and
divergence result in distinct patterns of reporter gene expression
embryonic axis. Our results provide an evolutionary
perspective on how the enhancer elements are
support the hypothesis that remodeling Hox regulatory elements in
different species has
played a significant role in generating
Shashikant C., S.A. Bolanowski, J. Danke,
and C.T. Amemiya. Hoxc8 early enhancer of the Indonesian
coelacanth, Latimeria menadoensis. J.Exp.Zool. Mol.Dev.Evol. 302,
Wang, C.H.W., S. Anand, D.R. Powell, A.B. Pawashe, C.T. Amimiya,
and C.S. Shashikant. Comparative cis-regulatory analyses identify
new elements of the mouse Hoxc8 early enhancer. J.Exp.Zool.
Anand, S., W.C.H. Wang, D.R Powell, S.A. Bolanowski, J. Zhang, C.
Ledje, A.B. Pawashe, C.T. Amemiya, and C.S. Shashikant. Divergence
of Hoxc8 early enhancer parallels diverged axial morphologies
and fishes. Proc. Natl. Acad. Sci. (USA) 100,
Dr. Reka Albert -
Department of Physics
modeling Drosophila segmentation: robustness of gene regulatory
The segmentation of the fruit fly Drosophila melanogaster is
controlled by about 40 genes organized in a hierarchical cascade
of gene families. These genes are expressed in consecutive stages
of embryonic development in a spatial pattern that is successively
more precisely-defined, the genes at one step initiating or
modulating the expression of those involved in the next step of
the cascade. While most of these genes act only transiently, the
segment polarity genes have a stable expression pattern that
defines and maintains the borders between different parasegments
and contributes to subsequent developmental processes.
The segment polarity genes refine and maintain their expression
through a network of intra- and intercellular regulatory
interactions between gene products. This seminar will present a
model of these interactions and of how they lead to stable gene
expression patterns. The model is deeply rooted in the topology of
the segment polarity gene network, while it disregards the
biochemical details of the interactions. This simple model is able
to reproduce the wild type expression pattern of the segment
polarity genes, as well as the ectopic expressions obtained for
gene mutation experiments, and suggests a remarkable robustness in
the function of the gene network. We will discuss how interaction
patterns such as feedback loops and switches contribute to this
robustness. The strong evolutionary conservation of the segment
polarity genes suggests that these interaction patterns should be
relevant to a host of other organisms as well.
Reka Albert and Hans G. Othmer. The topology of the regulatory
interactions predicts the expression pattern of the Drosophila
segment polarity genes. Journal of Theoretical Biology 223, 1-18
Reka Albert. Boolean modeling of genetic regulatory networks. In:
Complex Networks editors: E. Ben-Naim, H. Frauenfelder and Z.
Toroczkai), (Springer Verlag 2004).
Ross Hardison -
Department of Biochemistry and Molecular Biology
"Gene regulatory elements
discovered by vertebrate genome comparisons."
Four way comparisons of the human, rat, mouse and chicken genomes
present an unprecedented opportunity to explore critical issues in
genome evolution, structure and function. We find that about
of DNA align in all three mammals. This conserved mammalian core
contains not only about 95% of known functional sequences (coding
exons and gene regulatory elements), but also a considerable
apparently neutral DNA. In contrast, only about 70Mb align
reliably between human and chicken. Almost all of
this is under purifying selection, but it does not include some
functional mammalian sequences. Thus
comparison of human to chicken will find functional elements with
high specificity but at a considerable cost
in sensitivity. To find candidates for cis-regulatory modules (CRMs)
within these human-mouse-rat alignments,
we compute (i) likelihood that a DNA sequence is subject to
purifying selection (and hence is likely to be functional), (ii)
the extent to which patterns in the alignments match those that
are distinctive for known
regulatory regions, and (iii) conserved matches to transcription
factor binding sites. The scores are recorded in
a public database of Genome ALignments and Annotation (GALA,
http://www.bx.psu.edu/) and the UCSC
Genome Browser (http://genome.ucsc.edu/),
and we are developing a new metaserver, Galaxy, to integrate
data from multiple sources and analyze it more completely. We
applied these predictions to erythroid genes,
in particular those revealed by microarray expression analysis to
be co-expressed in two different mouse cell culture models of late
erythroid differentiation (MEL cells and the Gata1-null G1E
cells). Predicted CRMs
around the co-expressed genes are tested for the ability to affect
expression of the reporter after transient transfection of
unintegrated plasmids into erythroid cells and after site-directed
integration of the reporter cassettes into a chromosome, as well
as by chromatin immunoprecipitations. Current results show that
70% of the predicted CRMs have significant effects in these
assays. The combination of bioinformatic
predictions and experimental tests in somatic cell developmental
models serves as a paradigm for global
analysis of regulation in any tissue.
Waterston et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:
Elnitski et al. 2003. Distinguishing regulatory DNA from neutral sites. Genome Res. 13: 64-72.
Hardison et al. 2003. Global Predictions and Tests of Erythroid Regulatory Regions. In The Genome of Homo
sapiens, pp. 335-344. Cold Spring Harbor Press, Cold Spring Harbor, NY.
Gibbs, et al. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature 428: 493-521.
Hillier et al. 2004. Sequence and comparative analysis of the chicken genome provide unique
perspectives on vertebrate evolution. Nature 432: 695-716.
Miller et al. 2004. Comparative genomics. Annu Rev Genomics Hum Genet 5: 15-56.
Elnitski et al. 2005. Improvements to GALA and dbERGEII: Databases featuring genomic sequence
alignment, annotation and experimental results. Nucl. Acids Res. 33 Database Issue: D466-D447.
Dr. Chris House -
Department of Geosciences
"Linking Molecular Taxonomy with Environmental Geochemsitry: the
Anaerobic Oxidation of Methane in Cold Seeps & deeply Buried
The linking of molecular taxonomy (including 16s rRNA) to
environmental geochemistry is a powerful way to work out the
interactions, metabolic activities, and food webs of
microorganisms in their natural setting, whether it is sediment,
soil, or a water column. To this end, we developed a method for
coupling an extant microorganism’s genetic information with
geochemical data derived from the direct analysis of its cell.
FISH–SIMS combines fluorescent in-situ hybridization (FISH)
with secondary ion mass spectrometry (SIMS). FISH is a
culture-independent technique used to visually identify naturally
occurring microorganisms by staining their ribosomal RNA.
Secondary ion mass spectrometry (SIMS) is a method by which
geochemical information can be obtained from microsamples. Using
FISH-SIMS, a researcher can measure a target cell’s isotopic or
elemental composition in a mixed environment.
The identification and study of methane-consuming microorganisms
is an important step toward understanding the methane cycle and
microbial response to methane release. The recent identification
of two distinct Archaea capable of anaerobic methane oxidation was
in part accomplished using FISH-SIMS. Because natural methane is
highly depleted in 13C, FISH-SIMS is particularly powerful at
determining if a particular cell, collected from the environment,
consumed methane as a substrate for its cell carbon. This research
demonstrated that both the ANME-1 and ANME–2 Archaea from the Eel
River Methane Seep are highly depleted in 13C due to growth on
The deep marine biosphere is thought to contain abundant microbial
inhabitants, estimated to be a tenth of the Earth’s total biomass.
Sediments from this environment were recovered during Ocean
Drilling Program (ODP) Leg 201, and were analyzed by both
molecular biological and organic geochemical techniques. Of
particular interest in these sediments were four sulfate/methane
transition zones (SMTZ) seen at ODP Sites 1227, 1229 and 1230, two
of which coincided with strongly elevated cell counts. Archaeal
cells in these zones were analyzed for abundance and d13C
composition by whole cell analysis (FISH-SIMS) and intact membrane
lipids (HPLC-ESI-MSn). Fluorescent in-situ hybridization cell
counts showed greater archaeal abundance than bacterial, which was
reflected by intact membrane lipid abundance. Isotopic
compositions by both techniques (often around -20?) suggest that
methane is not an important carbon source for these cells.
Autotrophic carbon fixation appears to be an unlikely metabolism
given the relationship between the isotopic composition of DIC and
archaeal biomass. The isotopic evidence suggests that the bulk
archaeal community is heterotrophic, possibly mediating the
oxidation of methane without consuming it as a carbon source.
This novel information about the metabolism of uncultivated deeply
buried Archaea raises interesting new questions regarding
the significance of the elevated cell counts and archaeal activity
at SMTZs in deep marine sediments.
Orphan, V. J., Ussler III, W., Naehr, T., House, C.H., Hinrichs,
K. U. and Paull, C. K., 2004. Geological, Geochemical, and
Microbiological Heterogeneity of the Seafloor Around Methane Vents
in the Eel River Basin, offshore California. Chemical Geology,
D’Hondt, S., and 34 others., 2004. Distributions of Microbial
Activities in Deep Subseafloor Sediments. Science, 306:
Dr. Valeria Souza -
National Autonomous University of Mexico
is the unit of selection in E. coli?"
genomic analysis is a powerful tool for understanding the history
and organization of complete genomes. The mathematical tools of
population genetics combined with genomic analysis provide a
powerful approach to dissect heterogeneities in genome evolution.
This study presents a hierarchical analysis of the island LEE
(35kb), which is found in the pathogenic E. coli strains
EPEC and EHEC and in Citrobacter rodentium. The LEE locus
in E.coli is considered to be a clonal unit inside a clonal
organism and is expected to evolve as a single unit. This analysis
examines the clonal assumption by determining genetic diversity,
GC content and the substitution rates at the different functional
levels of (1) the complete pathogenic island, (2) the five operons
in which the island is organized, and (3) for each of the
individual 41 genes that comprise the locus. We find that there is
a conserved region that is composed of genes that belong to the
Type III Secretion System (TTSS) and that may be products of
horizontal transfer. A more diverse region is composed of genes
for secreted proteins and genes that we infer to be original
components of the E.coli genome. This genetic mosaic seems
to be differentially affected by selection and mutation. Our
results suggest that recombination and selection may be breaking
this structure so that different elements are at best weakly
coupled in their evolution. These observations suggest that the
units of selection are not the complete island, but rather much
smaller units within the island.
Castillo, A., L.E. Eguiarte, and V.
Souza. 2005. A genomic population genetics analysis of the
pathogenic locus of the enterocyte effacement island in
Escherichia coli: The search for the unit of selection. Proc.
Natl. Acad. Sci. USA in press.
Bjedov, I., O. Tenaillon, B. Gerard, V. Souza, E. Denamur, M.
Radman,F. Taddei, and I. Matic1. 2003. Stress-Induced
Mutagenesis in Bacteria. Science 300:1404-1409
Peek, A.S., V. Souza, L.E. Eguiarte, and B.S. Gaut. 2001. The
Interaction of Protein Structure, Selection, and Recombination on
the Evolution of the Type-1 Fimbrial Major Subunit (fimA) from
Escherichia coli. J Mol Evol 52:193–204
Dr. Alexander Bolshoy -
Institute of Evolution, University of Haifa and School of
Informatics, Indiana University
messages as a strategy for vulnerability reduction."
The phenomenon of overlapping of
various sequence messages in genomes is a puzzle for evolutionary
theoreticians, geneticists, and sequence researchers. The
overlapping is possible due to degeneracy of the messages, in
particular, degeneracy of codons. It is often observed in
organisms with a limited size of genome, possessing polymerases of
low fidelity. The most accepted view considers the overlapping as
a mechanism to increase the amount of information per unit length.
Here we present a model that suggests direct evolutionary
advantage of the message overlapping. Two opposing drives are
considered: (a) reduction in the amount of vulnerable points when
the overlapping of two messages involves common critical points
and (b) cumulative compromising cost of coexistence of messages at
the same site. Over a broad range of conditions the reduction of
the target size prevails, thus making the overlapping of messages
Peleg O, Kirzhner V, Trifonov E,
Bolshoy A. Overlapping messages and survivability. J Mol. Evol.
Dr. Eric Harvill -
Department of Veterinary Science
"Effects of host population
dynamics on evolution of the bordetellae."
diseases with high transmission rates and long lasting immunity
result in disease primarily in children and immune adults. Under
these conditions there is strong selection for the ability to
reinfect immune hosts. Although whooping cough is considered a
childhood disease, there is substantial evidence that children are
infected by asymptomatic adult carriers, and there are increasing
numbers of adult cases of Bordetella pertussis disease. In
order to improve the control of this and other such diseases it is
critical to understand how B. pertussis is able to remain
endemic even in highly vaccinated or immune populations. Acute,
highly contagious, immunizing pathogens face the significant
epidemiological challenge of long-term persistence within the host
population. Immunity results in depletion of susceptible hosts
through the course of each epidemic, thereafter host replenishment
requires births or loss of immunity -- which is why pathogens that
convey perfect immunity result in ‘childhood diseases’ (22).
Rapid contagion, in turn, results in fast transmission among
hosts, which is a short-term evolutionary benefit to the pathogen
However, it also results in large-amplitude epidemics with
intervening deep epidemic troughs; In small and medium host
populations the chain of transmission will be broken in the
troughs so that the pathogen will go extinct. The most relevant
theoretical models for childhood infections, the so-called
realistic age-structured (RAS) models (4, 18), predict an endemic
threshold of around 1/2 million hosts for transmission to be
sustained through the epidemic troughs of acute, immunizing
infections. This prediction is closely matched by epidemiological
surveillance data (3, 10). Previous theoretical studies have
highlighted two key adaptations that increase the height of the
epidemic troughs to allow long-term endemism within smaller host
communities. These are: (1) reinfection of previously immunized
hosts and adult carriers and (2) prolongation of the infectious
period (5). Our study is of wide epidemiological significance in
showing that B. pertussis, through expression of PTX, slows
migration of neutrophils and thereby extends the infection period
(relative to B. pertussisDptx
strains) and allow for transient reinfection of previously
immunized hosts. PTX expression may, therefore, be a key
adaptation by B. pertussis for interacting with the unique
population dynamics of its human host.
V.C., Pishko, E.J., Preston, A., Maskell, D.J. and Harvill, E.T.,
The Role of Bordetella O-antigen in Respiratory Tract
Infection (2003), Infection and Immunity,71(1):86-94.
G.S., Mann, P.B., Harvill, E.T., (2003) The Role of Antibodies in
Immunity to Bordetella Infections, Infection and
17. Preston, A., Maxim, E., Toland, E., Pishko, E.J., Harvill,
E.T., Caroff, M., and Maskell, D.J. (2003) Bordetella
bronchiseptica PagP is a Bvg-regulated lipid A palmitoyl
transferase that is required for persistent colonisation of the
mouse respiratory tract. Molecular Microbiology,
18. Pishko, E.J.,
Betting, D.J., Hutter, C.S. and Harvill, E.T., (2003) Bordetella
pertussis Acquires Resistance to Complement Mediated Killing in
vivo. Infection and Immunity,
19. Mann, P.B.,
Kennett, M.J., Harvill, E.T., (2004),Toll-Like
Receptor 4 Is Critical to Innate Host Defense in a Murine Model of
Bordetellosis. J Infect Dis. 2004 Mar 1;189(5):833-836.
20. Pishko, E.J.,
Kirimanjeswara, G.S, Gopinathan, L., Pilione, M.R., Kennett, M.J.
and Harvill, E.T., (2004) Antibody-mediated Bacterial Clearance
from the Lower Respiratory Tract of Mice Requires Complement
Eur J Immunol.
M., Liu, Y., Doulatov, S.R., Gingery, M., Eiserling, F.A., Baker,
S., Davis, P., Preston, A., Maskell, D.J., Harvill, E.T., Parkhill,
J. and Miller, J.F. (2004)
Genomic and genetic analysis of Bordetella bacteriophages
encoding reverse transcriptase-mediated tropism-switching
J Bacteriol. 186(5):1503-17.
22. Pilione MR, Pishko
EJ, Preston A, Maskell DJ, Harvill ET. (2004) pagP is required for
resistance to antibody-mediated complement lysis during Bordetella
bronchiseptica respiratory infection. Infection and Immunity.
23. Mann, P.B., Elder,
K.D., Kennett, M.J., and Harvill, E.T. (2004), TLR4 Dependent
Early Elicited TNFa Expression is Critical for Innate Host Defense
Against Bordetella bronchiseptica. Infection and Immunity.
24. Elder, K.D. and
Harvill, E.T. (2004). Strain-Dependent Role of BrkA during
Bordetella pertussis Infection of the Murine Respiratory
Tract. Infection and Immunity, 72(10):5919-24.
No Classes - SPRING
Dr. Webb Miller - Department of Biology
Genome Sequences of Ancient Mammals."
optimally organize genome sequence data from placental mammals,
the genome browser at Santa Cruz is adopting an evolutionary
perspective. The basic mammalian genome sequence, to which
sequenced genomes are related by identified evolutionary
operations, will be a computational reconstruction of the genome
of a mammalian ancestor, as perhaps existed 100 million years ago.
Moreover, we intend to provide reconstructions of genomes that
existed at time points intermediate between that ancestor and
modern mammals, together with an accounting of the evolutionary
operations that occurred on each branch of the phylogenetic tree.
We outline the reconstruction procedure, describe approaches for
validating its results, and present some of what it has taught us
about the evolution of mammalian genomes.
Blanchette, E. Green, W. Miller, and D. Haussler (2004)
Reconstructing large regions of an ancestral mammalian genome in
silico. Genome Research 14, 2412-2423.
Dr. Kateryna Makova -
Department of Biology
and weak male mutation bias at different sites in the primate
genomes: Insights from the human-chimpanzee comparison."
While several studies indicated male bias for nucleotide
substitutions in primates, they disagreed about the magnitude of
this bias. Furthermore, it is presently unknown whether all types
of nucleotide substitutions exhibit male bias and thus result from
errors in DNA replication. Here we investigate male mutation bias
using human-chimpanzee whole-genome alignments. When all
nucleotide substitutions are considered together, male mutation
bias is strong: the male-to-female mutation rate ratio (alpha) is
~4-6, similar to the male-to-female ratio in the number of
germline cell divisions. This suggests that most substitution
mutations that occurred in the human and chimpanzee lineages since
their common ancestor were caused by errors in DNA replication.
The observed bias is not explained by regional variation in
substitution rate. Remarkably, while male mutation bias is strong
at non-CpG sites (alpha is around 4-6), it is weak at CpG
dinucleotides (alpha is around 2), which are usually methylated.
This is consistent with the methylation-induced and
replication-independent origin of transitions leading to loss of
CpG sites. In contrast, unmethylated CpG sites located in CpG
islands exhibit strong male mutation bias, suggesting that
mutations at these sites are replication-dependent. Thus, the
strength of male mutation bias appears to be non-uniform in the
Dr. Anton Nekrutenko
- Department of Biochemistry and Molecular Biology
"Oscillating Evolution of a Mammalian Locus with Overlapping
Reading Frames: an XLas/ALEXrelay."
XLas and ALEX are
structurally unrelated mammalian proteins translated from
alternative overlapping reading frames of a single
transcript. Not only are they encoded by the same locus, but a
specific XLas/ALEX interaction is essential for G-protein
signaling in neuroendocrine cells. A disruption of this
interaction leads to abnormal human phenotypes including mental
retardation and growth deficiency. The region of overlap between
the two reading frames evolves at a remarkable speed: the
divergence between human and mouse ALEX polypeptides makes them
virtually unalignable! To trace the evolution of this puzzling
locus, we sequenced it in apes, Old World monkeys, and a New World
monkey. We show that the overlap between the two reading frames
and the physical interaction between the two proteins forces
the locus to evolve in an unprecedented way. Namely, to maintain
two overlapping protein-coding regions the locus is forced to have
high GC content, which significantly elevates its intrinsic
evolutionary rate. However, the two encoded proteins cannot afford
to change too quickly relative to each other as this may impair
their interaction and lead to severe physiological
consequences. As a result XLas and ALEX evolve in an oscillating
fashion constantly balancing the rates of amino acid replacements.
This is the first example of a rapidly evolving locus encoding
interacting proteins via overlapping reading frames with a
possible link to the origin of species-specific neurological
Valer Gotea - Department
contributed to proteomes: support from molecular evolution and
With an initial dataset
restricted to proteins likely to be functional, we showed that
about 2% of human proteins contain fragments encoded by TE-like
sequences. As most of the TE-cassettes found have low alignment
scores, we attempted to reconstruct the phylogeny of every
protein, to demonstrate when and how the exaptation of TE
cassettes occurred. As the presence of most protein TE cassettes
found can be reasonably explained in a phylogenetic context, TEs
should be regarded as an important factor that contributed to the
evolution of genomes.
and Makalowski W. (2003) Transposable Elements and Vertebrate
Protein Diversity. Genetica, 118: 183-191.
Dr. Laura Zahn - Department
of the SEPALLATA subfamily: A Pre-Angiosperm Origin of a Potentially
Floral Specific MADS-box gene."
of the SEPALLATA (SEP) MADS-box subfamily are required
for specifying the “floral state” by contributing to floral organ
and meristem identity. SEP genes have not been detected in
gymnosperms and have previously been hypothesized to have originated
since the lineage leading to extant angiosperms diverged from extant
gymnosperms. Therefore, both functional and evolutionary studies
suggest they may have been critical for the origin of the flower. To
gain insights into the evolution of SEP genes, we isolated
nine genes from plants that occupy phylogenetically important
positions. Phylogenetic analyses of SEP sequences show that
several gene duplications occurred during the evolution of this
subfamily providing potential opportunities for functional
divergence. The timing of the first SEP duplication
approximately coincides with duplications in the DEFICIENS/GLOBOSA
and AGAMOUS MADS-box subfamilies, which may have resulted
from either a proposed genome-wide duplication in the ancestor of
extant angiosperms or multiple independent duplication events.
Regardless of the mechanism of gene duplication, these pairs of
duplicate transcription factors provided new possibilities of
genetic interactions that may have been important in the origin of
G., A. PINYOPICH, P. ROBLES, S. PELAZ and M. F. YANOFSKY, 2004 The
SEP4 gene of Arabidopsis thaliana functions in floral
organ and meristem identity. Curr Biol 14: 1935-1940.
PELAZ, S., G. S. DITTA, E. BAUMANN, E. WISMAN and M. F. YANOFSKY,
2000 B and C floral organ identity functions require SEPALLATA
MADS-box genes. Nature 405: 200-203.
ZAHN, L. M., H. KONG, J. H.
LEEBENS-MACK, S. KIM, P. S. SOLTIS, L. L. LANDHERR, D. E. SOLTIS, C.
W. dePAMPHILIS, and H. MA,
Evolution of the SEPALLATA subfamily of MADS-box genes: A
pre-angiosperm origin with multiple duplications throughout
angiosperm history. Genetics. In press.
Jaime Blair -
Department of Biology
Sequence Analysis of Complete Eukaryote Genomes."
duplication and gene loss during the evolution of eukaryotes have
hindered attempts to estimate phylogenies and divergence times of
species. Although current methods that identify clusters of
orthologous genes in complete genomes have helped to investigate
gene function and gene content, they have not been optimized for
evolutionary sequence analyses requiring strict orthology and
complete gene matrices. Here we adopt a relatively simple and fast
genome comparison approach designed to assemble orthologs for
evolutionary analysis. Our approach identifies single-copy genes
representing only species divergences (panorthologs) in order to
minimize potential errors caused by gene duplication. We apply this
approach to complete sets of proteins from published eukaryote
genomes specifically for phylogeny and time estimation. Despite the
conservative criterion used, 753 panorthologs (proteins) were
identified for evolutionary analysis with four genomes, resulting in
a single alignment of 287,000 amino acids. With this data set, we
estimate that the divergence between deuterostomes and arthropods
took place in the Precambrian, approximately 400 million years
before the first appearance of animals in the fossil record.
Additional analyses were performed with seven, 12, and 15 eukaryote
genomes resulting in similar divergence time estimates and
phylogenies. Our results with available eukaryote genomes agree with
previous results using conventional methods of sequence data
assembly from genomes. They show that large sequence data sets can
be generated relatively quickly and efficiently for evolutionary
analyses of complete genomes.
JE Blair & SB Hedges (2005) BMC Bioinformatics 6:53.
Wei Hu - Department
and functional study of zinc finger homeodomain protein family."
finger homeodomain protein (ZF-HD) family was recently recognized in
plants. These proteins have a putative novel zinc finger domain at N
terminus that functions for homo- and hetero-dimer formation. The
C-terminal homeodomain is distantly related to the classic
homeodomains and was demonstrated to be able to bind to DNA.
However, the evolutionary history and in vivo function of
these ZF-HD proteins are largely unknown. Our studies show that the
origin of this family can be traced back to the earliest land plant
Physcomitrella, but not unicellular green algae
Chlamydomonas. The complete genome of Arabidopsis, rice
and poplar indicates the size of ZF-HD family is quite stable. Gene
duplication is studies in particular in Arabidopsis, along
with examination of gene expression pattern. The challenge of
functional study of this family using reversed genetics approach is
evaluated with our current experimental results and understanding of
their evolutionary aspect. We further identified a group of small
genes with only the N-terminal zinc finger domain, which we named
them as MINI ZINC FINGER (MIF). These MIF proteins are highly
conserved at least among seed plants, as indicated by analysis of
available sequences. The possibility that MIF proteins evolved from
the loss of HD domain of ZF-HD proteins, or ZF-HD proteins evolved
from the gain of HD domain of MIF proteins is addressed from
sequence analysis and phylogenetic perspective. Overexpression of
one of Arabidopsis MIF genes resulted in pleiotropic
growth defects. Phenotypic, physiological, and whole-genome
expression profiling analyses all suggest that multiple hormonal
signaling pathways were interfered in the transgenic plants. Our
long-term goal is to elucidate ZF-HD family, plus its MIF subfamily,
as important plant regulatory genes throughout evolution.
Windhovel A, Hein I,
Dabrowa R, Stockhaus J (2001) Characterization of a novel class of
plant homeodomain proteins that bind to the C4 phosphoenolpyruvate
carboxylase gene of Flaveria trinervia. Plant Mol Biol