IMEG

Institute of Molecular
Evolutionary Genetics

 
 
 
          
 

IMEG SEMINARS
SPRING  2003
 
Previous IMEG Seminars and Abstracts:
Fall 2009

Spring 2009

Fall 2008

Spring 2008

Fall 2007

Spring 2007
Fall 2006
 

Spring 2006
Fall 2005
Spring 2005

Fall 2004
Spring 2004

Fall 2003

Spring 2003
Fall 2002

Spring 2002

Fall 2001
Spring 2001

Fall 2000

Fall 1999
Spring 1998

Fall 1997

 Date Speaker and title of seminar
 
 01/15/03

Speaker: Kerstin Kauffman, Dept. of Biology, Penn State Univ. Cancelled

 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


 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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