PMB290: Comparative Genomics Seminar

Meets Fridays, 2-3 pm in Koshland 338

This week's discussion will be led by Nhu and Kali and will cover the following papers regarding Speciation:

Konstantinidis KT, Ramette A, Tiedje JM.The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci. 2006
Carlos Canchaya et al. Diversity of the genus Lactobacillus revealed by comparative genomics of
five species microbiology (2006)

Comparing genomes enables us to better understand how the structures of genes and genomes have evolved and how genes are expressed, regulated and function. This seminar will survey the burgeoning field of comparative genomics. The class will meet once a week to review literature regarding this field. The focus will be on theory, methods and application, not on a particular organism. This seminar is open to anyone, but attendees are expected to have read the selected works and lead at least one discussion over the course of the semester.


 List of Topics to be Covered:
  • Genome Sequence and Annotation
  • Ortholog and Paralog Detection
  • Phylogenomics
  • Gene Evolution and Natural Selection
  • Gene Duplication and Deletion
  • Synteny and Gene Rearrangements
  • Chromosome Structure and Size
  • So called Junk DNA (repeats, transposons, function, uORFs, etc)
  • Cis-regulatory (promoter) sequence detection
  • Gene Structure Evolution
  • Population Genomics
  • Transcriptome evolution
  • Genomics of speciation
  • Genome evolution and co-evolution
  • Community genomics
  • Genome evolution and virulence
  • Genomics of artificial selection

Background and Review
Stone et al. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 6: 143-164 2005
Miller et al. Comparative genomics. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 5: 15-56 2004
Fay and Wu. Sequence divergence, functional constraint, and selection in protein evolution. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 4: 213-235 2003
Piskur, J; Langkjaer, RB. Yeast genome sequencing: the power of comparative genomics. MOLECULAR MICROBIOLOGY, 53 (2): 381-389 JUL 2004
Sidow, A. Sequence first. Ask questions later. CELL, 111 (1): 13-16 OCT 4 2002
Genome Sequencing and Annotation
Blattner et al. The Complete Genome Sequence of E.coli K-12. Science 1997
Venter et al. The Sequence of the Human Genome. Science 15 Feb 2001.
Batzoglou et al. ARACHNE: A whole-genome shotgun assembler. Genome Research 2002.
Galagan et al.The genome sequence of the filamentous fungus Neurospora crassa. Nature 422 2003.
Ortholog and Paralog Detection
Tatusov RL et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003 Sep 11;4:41. Epub 2003 Sep 11
Dufayard et al. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 2005.
Chen et al OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res. 2006
Storm CE, Sonnhammer EL. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics. 2002
Walter Fitch, Trends in Genetics 2000
Roy Jensen's comments, Genome Biology 2001
Eugene Koonin comments, Genome Biology 2001
Phylogenomics
Wu et al. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol. 2006
Eisen and Wu. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Popul Biol. 2002.
Fitzpatrick et al. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC EVOLUTIONARY BIOLOGY, 6: Art. No. 99 NOV 22 2006
Kuramae et al. Phylogenomics reveal a robust fungal tree of life. FEMS YEAST RESEARCH, 6 (8): 1213-1220 DEC 2006
Tekaia and Yeramian Genome trees from conservation profiles. PLOS COMPUTATIONAL BIOLOGY, 1 (7): 604-616 DEC 2005
Rokas et al. Genome-scale approaches to resolving incongruence in molecular phylogenies. NATURE, 425 (6960): 798-804 OCT 23 2003
Eisen and Wu. Phylogenetic analysis and gene functional predictions: Phylogenomics in action. THEORETICAL POPULATION BIOLOGY, 61 (4): 481-487 JUN 2002
Gene Evolution and Natural Selection
Nielsen et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLOS BIOLOGY, 3 (6): 976-985 JUN 2005
Clark et al. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. SCIENCE, 302 (5652): 1960-1963 DEC 12 2003
Gene Duplication and Deletion
Hahn MW et al. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 2005 Aug
Cotton JA, Page RD. Rates and patterns of gene duplication and loss in the human genome. Proc Biol Sci. 2005
VandePeer. Computational Approaches to Unveiling Ancient Genome Duplications. Nature Reviews Genetics. 2004
Kellis et al. Proof and Evolutionary Analysis of Ancient Genome Duplication in the yeast <i>Saccharomyces cerevisiae</i>. Nature 2004
Synteny and Gene Rearrangements
Fischer et al. Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages. PLOS GENETICS, 2 (3): 253-261 MAR 2006
Evan E. Eichler and David Sankoff. Structural Dynamics of Eukaryotic Chromosome Evolution. Science 301, 793 (2003)
Krithika Yogeeswaran et al. Comparative genome analyses of Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res. 2005 15: 505-515
Chromosome Structure and Size
van de Guchte et al. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103 (24): 9274-9279 JUN 13 2006
Kellis et al. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. NATURE, 428 (6983): 617-624 APR 8 2004.
Spirek et al. High-rate evolution of Saccharomyces sensu lato chromosomes FEMS YEAST RESEARCH, 3 (4): 363-373 JUN 2003
Dujon, et al. Genome evolution in yeasts. Nature 430, 35-44(1 July 2004)
So called Junk DNA
Chamary et al. Hearing silence: non-neutral evolution at synonymous sites in mammals. NATURE REVIEWS GENETICS, 7 (2): 98-108 FEB 2006
Cis-retulatory (promoter) sequence detection
Cliften et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. SCIENCE, 301 (5629): 71-76 JUL 4 2003
Kellis et al. Sequencing and comparison of yeast species to identify genes and regulatory elements. NATURE, 423 (6937): 241-254 MAY 15 2003
Gelfand. Recognition of regulatory sites by genomic comparison. Research in Microbiology 150:9 1999 (pdf currently unavailable)
Wels, Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxnomic groups. Nucleic Acids Research. V34 (7) 2006.
Haberer et. al. Large-Scale cis-Element Detection by Analysis of Correlated Expression and Sequence Conservation between Arabidopsis and Brassica oleracea. Plant Physiology. V 142: 2006.
Gene Structure Evolution
Population Genomics
Shanks et al. Competitive Metagenomic DNA Hybridization Identifies Host-Specific Microbial Genetic Markers in Cow Fecal Samples. AEM. 2006
Whitaker and Banfield. Population genomics in natural microbial communities. TRENDS IN ECOLOGY & EVOLUTION, 21 (9): 508-516 SEP 2006
Storz. Using genome scans of DNA polymorphism to infer adaptive population divergence. MOLECULAR ECOLOGY, 14 (3): 671-688 MAR 2005
Fay et al. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. GENOME BIOLOGY, 5 (4): Art. No. R26 2004.
DeLong, EF Microbial population genomics and ecology. CURRENT OPINION IN MICROBIOLOGY, 5 (5): 520-524 OCT 2002
Transcriptome Evolution
Stranger et al. Genome-wide associations of gene expression variation in humans. PLOS GENETICS, 1 (6): 695-704 DEC 2005
Rifkin et al. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. NATURE, 438 (7065): 220-223 NOV 10 2005
Brem and Kruglyak. The landscape of genetic complexity across 5,700 gene expression traits in yeast. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102 (5): 1572-1577 FEB 1 2005
Le Quere et al. Divergence in gene expression related to variation in host specificity of an ectomycorrhizal fungus. MOLECULAR ECOLOGY, 13 (12): 3809-3819 DEC 2004
Genomics of Speciation
Canchaya et al. Diversity of the genus Lactobacillus revealed by comparative genomics of five species. MICROBIOLOGY-SGM, 152: 3185-3196 NOV 2006
Genome Evolution and Co-evolution
Armbrust,et al. The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism. Science 306, 79 (2004)
G. McFadden. Primary and secondary endosymbiosis and the origin of plastids. J. Phycol. 37, 951-959 (2001)
Krause et al Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nature Biotechnology 2006.
Thieme et. Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the complete Genome Sequence. Journal of Bacteriology Nov. 2005
Community Genomics
DeLong and Karl. Genomic perspectives in microbial oceanography. NATURE, 437 (7057): 336-342 SEP 15 2005
Allen and Banfield, JF Community genomics in microbial ecology and evolution. NATURE REVIEWS MICROBIOLOGY, 3 (6): 489-498 JUN 2005
Genome Evolution and Virulence
Han et al. Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis. JOURNAL OF BACTERIOLOGY, 188 (9): 3382-3390 MAY 2006
Maione et al. Identification of a universal group B Streptococcus vaccine by multiple genome screen. SCIENCE, 309 (5731): 148-150 JUL 1 2005
Miller et al. Complete genome sequence of the broad-host-range vibriophage KVP40: Comparative genomics of a T4-related bacteriophage. JOURNAL OF BACTERIOLOGY, 185 (17): 5220-5233 SEP 2003
Ariel et al. Genome-based bioinformatic selection of chromosomal Bacillus anthracis putative vaccine candidates coupled with proteomic identification of surface-associated antigens. INFECTION AND IMMUNITY, 71 (8): 4563-4579 AUG 2003
Wolfgang et al. Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100 (14): 8484-8489 JUL 8 2003
Read et al The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. NATURE, 423 (6935): 81-86 MAY 1 2003
Hurst. The Ka/Ks ratio. Trends in Genetics 18:9 2002.
He et al. Molecular Evolution of the SARS Coronavirus During the Course of the SARS Epidemic in China. Science 2004
Tunlid and Talbot. Genomics of parasitic and symbiotic fungi. CURRENT OPINION IN MICROBIOLOGY, 5 (5): 513-519 OCT 2002
Genomics of Artificial Selection
Gu et al. Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae.: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102 (4): 1092-1097 JAN 25 2005


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