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IMEG
SEMINARS
SPRING 2003
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Previous
IMEG Seminars and Abstracts: |
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Date |
Speaker and title of seminar |
01/15/03 |
Speaker:
Kerstin
Kauffman, Dept. of Biology, Penn State Univ.
Cancelled |
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01/22/03 |
Speaker:
Jongmin Nam, Dept. of
Biology, Penn State Univ.
Title: "Antiquity and
evolution of the MADS-box gene family controlling flower development
in plants."
Abstract: MADS-box genes in plants
control various aspects of development and reproductive processes
including flower formation. To obtain some insight into the roles
of these genes in morphological evolution, we investigated the
origin and diversification of floral MADS-box genes by conducting
phylogenetic and associated molecular evolutionary analyses. Our
results suggest that the most recent common ancestor of today's
floral MADS-box genes evolved about 637 million years ago (Ma),
about 100 million years earlier than the Cambrian explosion. They
also suggest that the functional classes R, B (and Bs), C, F (AGL20
or TM3), A, and G (AGL6) of MADS-box genes diverged sequentially in
this order from the class E gene lineage. The divergence between
the class G and E genes occurred around the time of the
angiosperm/gymnosperm split. Furthermore, the ancestors of three
classes of genes (class R genes, class B/Bs genes, and the common
ancestor of the other classes of genes) might have existed at the
time of the Cambrian explosion. It is likely that these ancestral
genes were involved in reproduction by spore formation. We also
conducted a phylogenetic analysis of MADS-domain sequences from
various species of plants and animals and presented a hypothetical
scenario of the evolution of MADS-box genes in plants and animals,
taking into account paleontological information. Our study supports
the idea that there are two main evolutionary lineages (type I and
type II) of MADS-box genes in plants and animals.
References:
Theissen, G. 2001.
Development of floral organ identity, stories from the MADS
house. Curr. Opin. Plant Biol. 4: 75-85.
Purugganan, M.
D. 1998. The molecular evolution of development. Bioessays 20:
700-711.
Nam, J., C.
dePamphilis, H. Ma, and M. Nei. Antiquity and evolution of the MADS-box
gene family controlling flower development in plants. (In
preparation).
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01/29/03 |
Speaker:
Dr. Blair Hedges, Dept. of
Biology, Penn State Univ.
Title:
Temporal Constraints on the Origin of Complex Multicellular
Life.
Abstract: It is of great interest to know how and when complex life
evolved on Earth to better understand the evolution of complex life
elsewhere. We have used all available nucleotide and protein data,
and collected some new sequence data, to address phylogenetic and
chronological questions concerning the origin of complex
multicellular life. As with previous molecular clock studies,
ancient divergences were found, implying large gaps in the fossil
record. In addition, the use of different global and local clock
methods gave concordant time estimates. A synthesis of information
from diverse areas leads to a new perspective on the rise of complex
life and insights into possible mechanisms.
References:
Wang, D. Y.-C., S. Kumar, and S. B. Hedges. 1999. Divergence
time estimates for the early history of animal phyla and the origin
of plants, animals, and fungi. Proc. Roy. Soc. London B
266:163-171.
Heckman, D. S., D. M. Geiser, B. R. Eidell, R.
L. Stauffer, N. L. Kardos, and S. B. Hedges. 2001. Molecular
evidence for the early colonization of land by fungi and plants.
Science 293:1129-1133.
Hedges, S. B. 2002. The origin and evolution of model organisms.
Nature Reviews Genetics 3:838-849.
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02/05/03 |
Speaker:
Helen Piontkivska,
Dept. of
Biology, Penn State Univ.
Title: Molecular evolution of the histones gene family in two sibling
nematode species, Caenorhabditis elegans and C. briggsae.
Abstract: Histones are small basic proteins responsible for the nucleosomal
organization of chromatin in eukaryotes. Using complete genomic
sequence of nematode C.elegans and preliminary draft assembly of
genomic sequences of closely related C. briggsae, the complete set
of histone genes present in both species was identified.
Phylogenetic analysis showed that although protein sequences are
highly conserved both within and between species, there was a
significant amount of synonymous substitutions accumulated in both
species. In the cases where the level of divergence at synonymous
site was relatively low, recent gene duplication appeared to be a
better explanation than gene conversion. Thus, purifying selection
rather than concerted evolution is the main force for maintaining
protein similarity among member genes. These results suggest that
histone genes in these Caenorhabditis species are subject to
birth-and-death evolution, and that in both species the histone gene
family continues to undergo the process of gene duplications and
losses.
References:
Nei M., X. Gu, and T. Sitnikova. Evolution by the birth-and-death process
in multigene families of the vertebrate immune system. Proc. Natl.
Acad. Sci. U S A. 1997 Jul 22;94(15):7799-806.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
cmd=Retrieve&db=PubMed&list_uids=9223266&dopt=Abstract
Nei, M., I. B. Rogozin, and H. Piontkivska. Purifying selection and
birth-and-death evolution in the ubiquitin gene family. Proc. Natl.
Acad. Sci. U S A. 2000 Sep 26;97(20):10866-71.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
cmd=Retrieve&db=PubMed&list_uids=11005860&dopt=Abstract
Piontkivska, H., A. P. Rooney, and M. Nei. Purifying selection and
birth-and-death evolution in the histone H4 gene family. Mol. Biol.
Evol. 2002 May;19(5):689-97.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
cmd=Retrieve&db=PubMed&list_uids=11961102&dopt=Abstract
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02/12/03 |
Speaker:
Dr. Hong Ma, Dept. of
Biology, Penn State Univ.
Title:
Functional and evolutionary analyses of Arabidopsis SKP1
homologs.
Abstract: SKP1 is a subunit of the SCF ubiquitin ligases that mediate
protein degradation and regulate many cellular processes. Whereas
the single SKP1 gene is essential in yeast, multiple SKP1 homologs exist
in plants and animals. In Arabidopsis, 19 genes have been revealed
by genomic sequences, called ASK genes. Among these, ASK1 is known
to be widely expressed and involved in regulating flower
development, meiosis, and hormonal signaling. ASK2 is very similar
to ASK1 in both sequence and expression, and can partially replace
ASK1 when expressed from a strong promoter. These results suggest
that ASK1 and ASK2 have related broad functions. Other ASK
genes are expressed at lower levels or with more specific spatial
patterns, suggesting that they have more specialized functions. For
organisms with whole-genome sequences available, rice, C. elegans,
and Drosophila have multiple copies, like Arabidopsis. In contrast,
human, fugu fish, and fungal species have only one functional copy
each. In addition, cDNA cloning and EST sequencing have uncovered
one or few copies per species from many other plants and animals,
representing the more highly expressed members of the gene family.
Molecular phylogenetic studies of the ASK genes and SKP1 homologs
from other plants, animals and fungi indicate that members of this
ancient gene family exhibit greatly variable rates of evolution.
Further analysis support the hypothesis that the most slowly
evolving members of each species have retained the original
non-specific functions, whereas the more rapidly evolving members
are highly divergent and probably have acquired new functions.
Furthermore, the lack of clear orthologous relationship between many
SKP1 homologs of major lineages of animals and plants suggest that
birth-and-death mechanisms may have played a significant role in the
evolution of the SKP1 gene family.
Contributors to this work include: Dazhong Zhao, Hongzhi Kong,
Weimin Ni, Ming Yang, Yi Hu, Jim Leebens-Mack, Claude dePamphilis,
and Hong Ma
This work is supported by grants from the National Science
Foundation and funds from the Biology Department and the Huck
Institute for Life Sciences at the Pennsylvania State University.
References:
Jackson, P. K. and A. G. Eldridge. 2002. The SCF ubiquitin ligase: an extended look. Mol Cell. 9:923-925.
Yang, M., Y. Hu, M. Lodhi, W. R. McCombie,
and H. Ma. 1999. The Arabidopsis SKP1-LIKE1 gene is
essential for male meiosis and may control homologue separation.
Proc. Natl. Acad. Sci. USA. 96: 11416-11421.
Zhao, D., Q. Yu, M. Chen, and H. Ma. 2001. The ASK1 gene regulates B function gene expression
in cooperation with UFO and LEAFY in Arabidopsis.
Development. 128: 2735-2746.
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02/19/03 |
Speaker:
Dr. Galina
Glazko, Dept. of Biology, Penn State Univ.
Title: Functional and evolutionary analyses of Arabidopsis SKP1
homologs.
Abstract: Although the times of divergence
of major lineages of primates species have been studied by a number
of authors, the time estimates are still controversial. This
controversy has been generated partly because different authors have
used different types of molecular data, different statistical
methods, and different calibration points. We have therefore
examined the effects of these factors on the estimates of divergence
times. We also studied the range of the divergence time estimates
obtainable from different functional categories of proteins from
major eukaryotic groups (i.e. humans, rodents, Drosophila, nematode,
Arabidopsis, and yeast). It was shown that for large data set (181
proteins) the inclusion of proteins, which evolved significantly
faster or slower than the average proteome rate did not seriously
affect the estimates. However, when the data set is small, the
estimates can be systematically biased. For small data set it would
be better to use several suitable functional categories of proteins.
In addition, a computer program TIMER was developed to estimate
divergence time from single and concatenated sequences. New features
of this program will be discussed.
References:
Glazko, G. V. and M. Nei. Estimation of divergence times for major
lineages of primate species. (2003). Mol. Biol. Evol. 20 (3).
Glazko, G. TIMER: Estimation of divergence times from individual and
concatenated sequences (http://mep.bio.psu.edu/).
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02/26/03 |
Speaker:
Erin McMullin, Dept. of
Biology, Penn State Univ.
Title: Migration and
genetic structure of two deep sea vestimentiferans from the Gulf of
Mexico revealed using variable microsatellite loci.
Abstract: Microsatellite markers were used to
study dispersal patterns within two species of deep sea hydrocarbon
seep vestimentiferans tube worms, Seepiophila jonesi and
Lamellibrachia luymesi, in the Gulf of Mexico (GoM).
Vestimentiferans are a dominant organism within the GoM hydrocarbon
seep communities, forming large aggregations, or ‘bushes’, composed
of both tubeworms species, which can be more than 2 meters in
height. The hydrocarbon seep communities of the Gulf of Mexico
are a significant source of organic matter in the deep sea, and may
be a resource for non-seep deep sea fauna. Oil companies often
drill near seep communities, damaging them in the process.
Genetically diverse and interbreeding populations that span wider
geographical ranges are theoretically more able to withstand damage
and loss of individuals within a single site than highly fragmented
and isolated communities. Five variable microsatellite markers were
isolated from L.luymesi, and 8 variable microsatellite
markers were isolated form S. jonesi. The variable products
of these thirteen primer pairs were scored according to size were
scored with Fragment Analysis using a Beckman CEQ2000 capillary
sequencer. Variable loci were scored for 165 S. jonesi and
235 L. luymesi collected from eight sites spanning 500km
apart and 100m depth. One site in particular, “Bush Hill”, was
heavily sampled. Collections as this site included aggregations
composed of smaller, medium sized, and larger worms. Worm length
has been shown to be correlated with the age of an individual,
therefore these aggregations represent “young,” “adult,” and “old”
tube worm aggregations. Shared allele frequencies within and between
sites are being used to estimate Wright’s F ST and other measures of
inbreeding and population mixing for L. luymesi and S.
jonesi within and between the eight GOM sample sites.
References:
Armour, J. A.,
R. Neumann, S. Gobert, and A. J. Jeffreys. 1994. Isolation of human
simple repeat loci by hybridization selection. Human Molecular
Genetics 3(4), 599-565.
Bergquist, D. C., F. M. Williams, and C. R. Fisher. 2000. Longevity
record for deep-sea invertebrate. Nature 403(6769),
499-500.
Bergquist, D. C., I. A. Urcuyo, and C. R. Fisher. 2002.
Establishment and persistence of seep vestimentiferan aggregations
from the upper Louisiana slope of the Gulf of Mexico. Marine
Ecology Progress Series. 241:89-98.
Black, M. B., A. Trivedi, P. A. Y. Maas, R. A. Lutz, and R. C. Vrijenhoek. 1998). Population genetics and biogeography of vestimentiferan tube worms. Deep-Sea Research Part Ii-Topical
Studies in Oceanography 45(1-3), 365-382.
Brooks, J. M., M. C. I. Kennicutt, I. R. MacDonald, D. L. Wilkinson,
N. L. J. Guinasso, and R. R. Bidigare. 1989. Gulf of Mexico
hydrocarbon seep communities: Part IV-Descriptions of known
chemosynthetic communities. OTC 5954, 663-667.
Childress, J. J., H. Felbeck, and G. N. Somero. 1987. Symbiosis in
the deep sea. Scient. Amer. 255, 114-120.
Corliss, J. B. and R. D. Ballard. 1977. Oases of life in the cold
abyss. Natl. Geogr. 152(4), 441-454.
Fisher, C. R. 1996. Ecophysiology of primary production at
deep-sea vents and seeps. In Deep-sea and extreme shallow-water
habitats: affinities and adaptations. (Uiblein, F., Ott, J. &
Stachowtisch, M., eds.), Vol. 11, pp. 313-336. Austrian Academy of
Sciences Press, Vienna.
Freytag, J. K., P. Girguis, D. C. Berkquist, J. P. Andras, J. J.
Childress, and C. R. Fisher. 2001. Sulfide acquisition by
roots of seep tubeworms sustains net chemoautotrophy. Proceedings
of the National Academy of Sciences USA 98, 13408-13413.
Gardiner, S. L., E. McMullin, and C. R. Fisher. 2001. Seepiophila
jonesi, a new genus and species of vestimentiferan tube worm (Annelida:
Pognophora) from hydrocarbon seep communities in the Gulf of Mexico.
Proceedings of the Biological Society of Washington 114,
694-707.
McMullin, E. R., S. Hourdez, S. W. Schaeffer, and
C. R. Fisher. 2003. Phylogeny and biogeography of deep sea vestimentiferan tubeworms and their bacterial symbionts.
Symbiosis 34(1): 1-41.
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03/05/03 |
Speaker:
Chiao-Feng
(Joanne) Lin, Dept. of Biology, Penn State Univ.
Title: Migration and
genetic structure of two deep sea vestimentiferans from the Gulf of
Mexico revealed using variable microsatellite loci.
Abstract:
21,698 out of 27,112 (80%) annotated Arabidopsis open reading
frames are interrupted by intronic sequences. Two distinct types of
introns, named U2- and U12-dependent, are found in most higher
organisms. Although they coexist in the same gene, they are excised
by different splicesomes during pre-mRNA processing. In most
eukaryotic genomes U12-dependent introns comprise only a minute
fraction of all introns, e.g. in the human genome only 0.1% of
introns are spliced by U12 spliceosome.
To understand the difference between both types of introns and the
mechanisms of their recognition we have scanned the Arabidopsis
genome for U12-dependent introns. We used Hidden Markov Modeling
technique to discriminate two classes of introns. 59 out of 115,388
analyzed introns were classified as U12-dependent. 57 genes
contained one U12-dependent intron and two have two U12-dependent
introns each. We call these genes U12-type genes, while U12
independent genes are called U2-type. Except the hallmarks of
U12-dependent introns - highly conserved 5’-, 3’- splice sites and
branch point site - sequence properties of the two types of introns
such as GC content and intron size are not significantly different.
However, the distributions of the number of intron within the two
types of genes show different patterns. All U12-type genes contain
at least 3 introns whereas single-intron genes occupy the biggest
proportion of U2-type genes.
U12 and U6atac snRNAs play key roles in the minor type of pre-mRNA
splicing as opposed to U2 and U6 in the major type. By using blast
search with these two snRNA genes from Arabidopsis we
identified the putative homologs in rice genome. This suggests that
U12-dependent splicing machinery might also exist in rice.
Phylogenetic analysis of these snRNA genes will be presented along
with results about U12-dependent introns in rice.
References:
Reference: Burge CB, Padgett RA, Sharp
PA (1998). Evolutionary fates and origins of U12-type introns. Mol
Cell 1998 Dec; 2(6):773-85
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03/12/03 |
SPRING
BREAK |
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03/19/03 |
Speaker:
Dr. Xun Gu, Dept. of
Zoology/Genetics, Iowa State Univ.
Title: Age distribution of human gene
families and the hypothesis of vertebrate genome duplication(s)
Abstract:
The classical (two-round) hypothesis1 of vertebrate genome
duplication proposes two successive whole-genome duplication(s) (polyploidizations)
predating the origin of fishes, a view now being seriously
challenged. As the debate largely concerns the relative merits of
the ‘big-bang mode’ theory (large-scale duplication) and the
‘continuous mode’ theory (constant creation by small-scale
duplications), we tested whether a significant proportion of
paralogous genes in the contemporary human genome was indeed
generated in the early stage of vertebrate evolution. After an
extensive search of major databases, we dated 1,739 gene duplication
events from the phylogenetic analysis of 749 vertebrate gene
families. We found a pattern characterized by two waves (I, II) and
an ancient component. Wave I represents a recent gene family
expansion by tandem or segmental duplications15, whereas wave II, a
rapid paralogous gene increase in the early stage of vertebrate
evolution, supports the idea of genome duplication(s) (the big-bang
mode). Further analysis indicated that large- and small-scale gene
duplications both make a significant contribution during the early
stage of vertebrate evolution to build the current hierarchy of the
human proteome, as illustrated by the human protein kinase super
gene family.
References:
Gu, J, Gu, X* (2003) Induced gene expression in human brain
after the split from chimpanzee. Trend in Genetics 19:63-65.
Gu, X*, Wang Y, Gu, J (2002) Age-distribution of human gene
families showing equal roles of large and small-scale duplications
in vertebrate evolution. Nature Genetics 31:205-209
Gu X* (1999) Statistical methods for testing functional
divergence after gene duplication. Molecular Biology and Evolution
16:1664-1674.
Wang Y, Gu X* (2001) Predicting functional divergence of
caspase gene family. Genetics. 158:1311-1320.
Gu, X*, Vander Velden K (2002) DIVERGE: Phylogeny-based
Analysis for Functional-Structural Divergence of a Protein Family.
Bioinformatics 18:500-501
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03/26/03 |
Speaker:
Dr. Mark
Shriver, Dept. of Anthropology, Penn State Univ.
Title: The genomic
distribution of human population substructure
Abstract:
Understanding the nature of evolutionary relationships among persons
and populations is important for the efficient application of genome
science to biomedical research. We have analyzed 8,525 autosomal
SNPs in 84 individuals from four populations: African-American,
European-American, Chinese, and Japanese. Individual phylogenetic
relationships were reconstructed using ape data to root the tree.
Trees show clear clustering according to population with the root
branching from the African-American clade. The African-American
cluster is much less star-like than European and East Asian
clusters, primarily because of admixture. Furthermore, on the East
Asian branch, all 10 Chinese individuals cluster together and all 10
Japanese individuals cluster together. Using positional information
we demonstrate strong correlations between intermarker distance and
both locus-specific FST levels and branch lengths.
Chromosomal maps of the distribution of locus-specific branch
lengths were constructed by combining these data with other
published SNP markers (total of 33,704 SNPs). These maps clearly
illustrate a nonrandom distribution of human genetic variation, an
instructional and useful paradigm for education and research.
References:
Akey, J. M., G. Zhang, K. Zhang, L. Jin, and M. D. Shriver (2002)
Interrogating a high-density SNP map for signatures of natural
selection. Genome Research, 12:1805-1814
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04/02/03 |
Dr. Nikolas
Nikolaidis, Dept. of
Biology, Penn State Univ.
Title:
Evolutionary relationships of hsp70 genes from two sibling
species of nematodes
Abstract:
The hsp70 gene sequences
of Caenorhabditis elegans were utilized in order to identify
their orthologues in the C. briggsae genome. Phylogenetic
analysis of the C. elegans and C. briggsae hsp70
sequences classified them according to their sub-cellular
localization (cytoplasm, endoplasmic reticulum, and mitochondrion).
Most nematode hsp70s had orthologs in both the budding yeast
(Saccharomyces cerevisiae) and the fruit fly (Drosophila
melanogaster). Both nematodes contained four hsp70 genes
that their proteins localize in the endoplasmic reticulum (two in
the HSP70 and two in the HSP110 subfamily), differently from
drosophila and yeast. The genomic organization and the phylogenetic
output revealed that the major differences between the two nematode
species were due to the hsp70 sequences of the cytoplasmic
group. C. briggsae contained 13 open reading frames belonging
to the cytoplasmic group, five of which encode a complete Hsp70
polypeptide, while C. elegans contained five frames, one of
which was a pseudogene. These data suggested that the hsp70s
of the cytoplasmic group followed different evolutionary pathways in
the two nematode species. Furthermore, the effect of several amino
acid changes in the functional differentiation among the major Hsp70
groups was investigated. This analysis showed that amino acid
residues with different biochemical properties composed almost 30%
of the observed changes, affecting the polarity and the charge
distribution in the Hsp70 polypeptides. These differentiating
properties although did not seem to affect the secondary structure
of the Hsp70s could result in functional specification by either
having a direct role in the target protein interactions or by
affecting the tertiary structure of the Hsp70 polypeptides.
References:
Boorstein, W. R. T.
Ziegelhoffer, and E. A. Craig. 1994. Molecular evolution of
the HSP70 multigene family. J. Mol. Evol. 38:1-17.
Davis, J. E., C. Voisine, and
E. A. Craig. 1999. Intragenic suppressors of Hsp70 mutants:
interplay between the ATPase- and peptide-binding domains. Proc.
Natl. Acad. Sci. U. S. A. 96:9269-76.
Easton, D. P., Y.
Kaneko, and J. R. Subjeck. 2000. The hsp110 and Grp1 70
stress proteins: newly recognized relatives of the Hsp70s. Cell
Stress Chaperones 5:276-90.
Heschl, M. F., and D. L. Baillie.
1990a. The HSP70
multigene family of Caenorhabditis elegans. Comp.
Biochem. Physiol. B. 96:633-7.
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04/7-8/03 |
Speaker:
Dr. Jan Klein,
Max-Planck-Institue fϋr Biologie, Germany
SEMINARS:
Monday, April 7, 2003 at 7:30 p.m.
Location: Room 207, The
Penn Stater
Title: “The Place of Our
Species in Nature”
Reception to follow.
Tuesday, April 8, 2003 at 11:30
a.m.
Location: 101 Althouse Laboratory
Title: “The Origin of Species:
Lessons Learned from East African Cichlid Fishes”
Tuesday,
April 8, 2003 at 4:00 p.m.
Location: 101 Althouse
Laboratory
Title: “The Emergence of Novel Organ Systems in Evolution: The Origin of
the Adaptive Immune System”
Refreshments served at 3:45 p.m.
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04/16/03 |
Speaker:
Liying Cui, Dept. of
Biology, Penn State Univ.
Title:
Unusual gene clustering in a highly rearranged chloroplast genome
Abstract:
Plant cells have three genomic
compartments with different evolutionary origins and dynamics.
Plastid genomes are compact and highly conserved in most
photosynthetic land plants, and have been important targets of
phylogenetic and functional studies. The typical plastid genome
encodes 100-200 proteins, tRNAs and rRNAs, with genes arranged in
two single copy regions and flanking inverted repeat regions,
totaling 120-200 kb in length. With few exceptions, the
quadrapartite structure is ubiquitous, and the gene order is similar
in most organisms. However, in green algae, chloroplast genomes show
a high degree of variation in gene order. We found in an earlier
study that protein coding regions of the Chlamydomonas
reinhardtii chloroplast genome have evolved at a higher rate
than in other chloroplast genomes, and that numerous short repeat
elements populate non-coding regions. The gene order differs greatly
from its closest relative Chlorella vulgaris, and from the
gene order inferred for their common ancestor. We observed that
adjacent genes are strikingly concentrated on one single coding
strand of Chlamydomonas, a phenomenon we term “sidedness”. To
investigate the possible selective forces that could have shaped the
dramatic changes to the Chlamydomonas cp genome, we performed
simulations of structural evolution using a conservative model of
genome rearrangement. We defined the single strand coding block
count Sb as a measure of the observed sidedness in the
genomic sequence, where smaller values of Sb correspond to
higher degree of sidedness. We examined sequenced chloroplast
genomes, and found that Chlamydomonas shows a higher degree
of sidedness than all other sequenced cpDNAs (except for Euglena),
and it is significantly more sided than randomly generated genomes
derived from the inferred green algal ancestral gene order. The
results suggest that the chloroplast genome of Chlamydomonas
has evolved to form highly organized and novel gene clusters in
which genes from the same functional category are more likely to be
adjacent. We hypothesize that the pattern may lead to a higher
efficiency of transcription, and co-regulation of gene expression.
References:
Jason W.
Lilly, Jude E. Maul, Liying Cui, Claude W. dePamphilis, Webb Miller,
Elizabeth Harris and David B. Stern. The Chlamydomonas reinhardtii
plastid chromosome: islands of genes in a sea of repeats. Plant
Cell. 2002 ;14(11):2659-79.
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04/23/03 |
Speaker:
Dr.
Stephen Schaeffer, Dept. of Biology, Penn State Univ.
Title:
Evolutionary genomics of paracentric inversions in Drosophila
pseudoobscura
Abstract:
Drosophila pseudoobscura
harbors a rich polymorphism for paracentric inversions on the third
chromosome, and the clines in the inversion frequencies across the
southwestern United States indicate that strong natural selection
operates on them. Isogenic inversion strains were made from
isofemale lines collected from four localities and eight molecular
markers were mapped on the third chromosome. Nucleotide diversity
was measured for these loci and formed the basis of an evolutionary
genomic analysis. The loci were differentiated among inversions. The
inversions did not show significant differences among populations,
however, likely the result of extensive gene flow among populations.
Some loci had significant reductions in nucleotide diversity within
inversions compared to interspecies divergence suggesting that these
loci are near inversion breakpoints or are near targets of
directional selection. Linkage disequilibrium (LD) levels tended to
decrease with distance between loci, indicating that some genetic
exchange occurs among gene arrangements despite the presence of
inversions. In some cases, however, adjacent genes had low levels of
interlocus LD and loosely linked genes had high levels of interlocus
LD suggesting strong epistatic selection. We propose that the
inversions of D. pseudoobscura have emerged as suppressors of
recombination because they maintain positive epistatic relationships
among loci within gene arrangements that developed as the species
adapted to a heterogeneous environment. Analysis of synteny between
D. pseudoobscura and D. melanogaster will be discussed
in the context of genomic rearrangement.
References:
Aquadro CF, Weaver AL, Schaeffer SW and Anderson WW, 1991.
Molecular evolution of inversions in Drosophila pseudoobscura
: The amylase gene region. Proc. Natl. Acad. Sci. USA 88:
305-309.
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04/30/03 |
Speaker:
Dr. Yoshihito Niimura, Dept. of
Biology, Penn State Univ.
Title:
Evolution of Olfactory Receptor Gene Clusters in the Human Genome
Abstract:
Olfactory receptor (OR) genes form the largest known multigene
family in the human genome. It was reported that the gene family
contains over 900 functional genes and pseudogenes, and more than
60% of them are pseudogenes. To obtain some insight into their
evolutionary history, we have identified a full set of OR genes and
their chromosomal locations from the latest version of the human
genome sequences, and conducted a large-scale phylogenetic analysis
of these genes. We detected 372 potentially functional genes that
have intact open reading frames, and this number is considerably
larger than previously reported. Our phylogenetic analysis has
shown that the OR genes in humans are clearly classified into Class
I and Class II genes, and the Class II OR genes can be further
grouped into 19 phylogenetic clades of which the bootstrap values
are significantly high. We found that there are many tandem arrays
of OR genes that are phylogenetically closely related to one
another, indicating that these genes have been generated by tandem
duplications. However, there are substantial cases in which the
genes in the same clade are located on several different chromosomal
regions. Moreover, we also found that OR genes that are belonging
to phylogenetically distant clades are often located very close to
one another and form a tight genomic cluster. These observations
are well explained by assuming that several chromosomal
rearrangements have occurred at the regions of OR gene clusters, and
eventually the OR genes contained in different genomic clusters have
been shuffled.
References:
Glusman, G., I. Yanai, I. Rubin, and D. Lancet. 2001. The
complete human olfactory subgenome. Genome Res. 11: 685-702.
Zozulya, S., F. Echeverri, and T. Nguyen. 2001.
The human olfactory receptor repertoire. Genome Biol. 2:
research0018.1-0018.12.
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