Plant evolutionary genomics.

Evolutionary genomics combines functional and evolutionary analyses of genome conservation and differentiation. Gene duplication and polyploidy have fundamentally shaped the genomes of Arabidopsis and all angiosperms. Recent comparative studies have focussed on gene regulation, the function of untranscribed genomic regions, and the effects of natural selection on protein function. A large fraction of interspecific protein divergence is probably adaptive, and may be useful for experimental studies of genes and proteins.

[1]  I. Bancroft,et al.  Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. , 2000, The Plant journal : for cell and molecular biology.

[2]  K. Okuno.  Geographical distribution of genes causing hybrid breakdown in varietal crosses of Asian cultivated rice , 1999, Genetic Resources and Crop Evolution.

[3]  M. Aguadé.  Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila. , 1999, Genetics.

[4]  H. A. Orr,et al.  THE EVOLUTION OF POSTZYGOTIC ISOLATION: ACCUMULATING DOBZHANSKY‐MULLER INCOMPATIBILITIES , 2001, Evolution; international journal of organic evolution.

[5]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[6]  Lee Hs,et al.  Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. , 2001 .

[7]  R. Guigó,et al.  SGP-1: prediction and validation of homologous genes based on sequence alignments. , 2001, Genome research.

[8]  T. Wróblewski,et al.  Arabidopsis and Brassica comparative genomics: sequence, structure and gene content in the ABI-Rps2-Ck1 chromosomal segment and related regions. , 2001, Genetics.

[9]  J. Bennetzen,et al.  Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. , 2001, Plant physiology.

[10]  Mathieu Blanchette,et al.  Algorithms for phylogenetic footprinting , 2001, RECOMB.

[11]  T Ohta.  Evolution of gene families. , 2000, Gene.

[12]  T. Mitchell-Olds,et al.  Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences. , 2001, American journal of botany.

[13]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[14]  A. Force,et al.  The probability of duplicate gene preservation by subfunctionalization. , 2000, Genetics.

[15]  S. Tanksley,et al.  Exploitation of Arabidopsis-tomato synteny to construct a high-resolution map of the ovatecontaining region in tomato chromosome 2. , 2001, Genome.

[16]  T. Mitchell-Olds.  Arabidopsis thaliana and its wild relatives: a model system for ecology and evolution , 2001 .

[17]  D. J. Howard.  Conspecific Sperm and Pollen Precedence and Speciation , 1999 .

[18]  M. Arnold,et al.  EFFECTS OF DIFFERENTIAL POLLEN‐TUBE GROWTH ON HYBRIDIZATION IN THE LOUISIANA IRISES , 1996, Evolution; international journal of organic evolution.

[19]  Michael Lynch,et al.  The Origin of Interspecific Genomic Incompatibility via Gene Duplication , 2000, The American Naturalist.

[20]  A. Clark,et al.  Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[21]  C. Lawrence,et al.  Human-mouse genome comparisons to locate regulatory sites , 2000, Nature Genetics.

[22]  B. Gaut,et al.  A Survey of the Molecular Evolutionary Dynamics of Twenty-Five Multigene Families from Four Grass Taxa , 2001, Journal of Molecular Evolution.

[23]  A. Ogurtsov,et al.  Selective constraint in intergenic regions of human and mouse genomes. , 2001, Trends in genetics : TIG.

[24]  W. Miller,et al.  Sequence conservation at human and mouse orthologous common fragile regions, FRA3B/FHIT and Fra14A2/Fhit , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[25]  D. G. Brown,et al.  The origins of genomic duplications in Arabidopsis. , 2000, Science.

[26]  N. Patel,et al.  Evidence for stabilizing selection in a eukaryotic enhancer element , 2000, Nature.

[27]  Ziheng Yang,et al.  Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[28]  J. McCarter,et al.  The population genetics of the origin and divergence of the Drosophila simulans complex species. , 2000, Genetics.

[29]  E. Radwanski,et al.  Comparative genetics of disease resistance within the solanaceae. , 2000, Genetics.

[30]  D. Preuss,et al.  Rapid initiation of Arabidopsis pollination requires the oleosin-domain protein GRP17 , 2000, Nature Cell Biology.

[31]  S. Goff,et al.  Sequence and analysis of the tomato JOINTLESS locus. , 2001, Plant physiology.

[32]  D. Schemske,et al.  Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[33]  A. Paterson,et al.  Genetics of Hybrid Sterility and Hybrid Breakdown in an Intersubspecific Rice ( O y a sativa L.) Population , 2022 .

[34]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[35]  Justin C. Fay,et al.  Positive and negative selection on the human genome. , 2001, Genetics.

[36]  H. Mewes,et al.  Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana. , 2001, Genome research.

[37]  Z. Yang,et al.  Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. , 2000, Molecular biology and evolution.

[38]  M. Feldman,et al.  Sequence Elimination and Cytosine Methylation Are Rapid and Reproducible Responses of the Genome to Wide Hybridization and Allopolyploidy in Wheat , 2001, The Plant Cell Online.

[39]  G. McVean,et al.  Genome sequences and evolutionary biology, a two-way interaction. , 2001, Trends in ecology & evolution.

[40]  E. Stahl,et al.  Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis , 1999, Nature.

[41]  R. Hardison.  Conserved noncoding sequences are reliable guides to regulatory elements. , 2000, Trends in genetics : TIG.

[42]  M A Koch,et al.  Comparative genomics and regulatory evolution: conservation and function of the Chs and Apetala3 promoters. , 2001, Molecular biology and evolution.

[43]  S. Tanksley,et al.  Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[44]  K. Theres,et al.  Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. , 2001, The Plant cell.

[45]  M. Feldman,et al.  Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops–Triticum) Group , 2001, The Plant Cell Online.

[46]  E. A. van der Biezen,et al.  Pronounced Intraspecific Haplotype Divergence at the RPP5 Complex Disease Resistance Locus of Arabidopsis , 1999, Plant Cell.

[47]  L. Rieseberg,et al.  The contribution of epistasis to species differences in annual sunflowers , 2001, Molecular ecology.

[48]  H. Kondoh,et al.  Identification of essential sequence motifs in the node/notochord enhancer of Foxa2 (Hnf3β) gene that are conserved across vertebrate species , 2001, Mechanisms of Development.

[49]  Sarah E. Johnstone,et al.  Gene Families from the Arabidopsis thaliana Pollen Coat Proteome , 2001, Science.

[50]  M. Clegg,et al.  Molecular evolution of the chalcone synthase multigene family in the morning glory genome , 2004, Plant Molecular Biology.

[51]  Jonathan F. Wendel,et al.  Genome evolution in polyploids , 2004, Plant Molecular Biology.

[52]  L. Rieseberg,et al.  INTERSPECIFIC POLLEN COMPETITION AS A REPRODUCTIVE BARRIER BETWEEN SYMPATRIC SPECIES OF HELIANTHUS (ASTERACEAE) , 1995 .

[53]  W. Miller,et al.  Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. , 2000, Science.

[54]  L. Rieseberg,et al.  Genetic architecture of species differences in annual sunflowers: implications for adaptive trait introgression. , 1999, Genetics.