Research Topics
Genomes and Genes | Jeffrey L BooreSummaryAffiliation: Lawrence Berkeley National Laboratory Country: USA Publications
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The mitochondrial genome of the Sipunculid Phascolopsis gouldii supports its association with Annelida rather than MolluscaJeffrey L Boore
Department of Biology, University of Michigan DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA
Mol Biol Evol 19:127-37. 2002..This requires reinterpretation of the homology of several embryological features and of patterns of animal body plan evolution...- Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum EchiuraJeffrey L Boore
Evolutionary Genomics Department, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA, USA
BMC Genomics 5:67. 2004..This is the first description of a complete mitochondrial genome sequence of a representative of the phylum Echiura, that of the fat innkeeper worm, Urechis caupo... - Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the bivalve Mytilus edulisJeffrey L Boore
Department of Biology, University of Michigan, Ann Arbor, MI, USA
Mol Biol Evol 21:1492-503. 2004.... - Sequencing and comparing whole mitochondrial genomes of animalsJeffrey L Boore
Evolutionary Genomics Department, Department of Energy Joint Genome Institute and Lawrence, Berkeley National Lab, Walnut Creek, California 94598, USA
Methods Enzymol 395:311-48. 2005..On several topics, we offer general observations based on our experiences with determining and comparing complete mitochondrial DNA sequences... - The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingiiJ Robert Macey
Department of Evolutionary Genomics, DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
Mol Phylogenet Evol 36:188-93. 2005 - Phylogenetic position of the Pentastomida and (pan)crustacean relationshipsDennis V Lavrov
Department of Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109 1048, USA
Proc Biol Sci 271:537-44. 2004..In addition, gene arrangement comparisons strongly support an unforeseen assemblage of pentastomids with maxillopod and cephalocarid crustaceans, to the exclusion of remipedes, branchiopods, malacostracans and hexapods... - The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNAJames F Parham
Department of Evolutionary Genomics, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA
BMC Evol Biol 6:11. 2006.... - Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomesSusan E Masta
Department of Biology, Portland State University, USA
Mol Biol Evol 25:949-59. 2008..Together, our data demonstrate variability in structural evolution among different tRNAs as well as evidence for parallel evolution of the loss of sequence coding for tRNA arms within an ancient and diverse group of animals... - The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAsSusan E Masta
Department of Energy Joint Genome Institute, Department of Evolutionary Genomics, Walnut Creek, California, USA
Mol Biol Evol 21:893-902. 2004..Such mechanisms may have allowed for the minimization of the spider mitochondrial genome... - A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) databaseParamvir S Dehal
Evolutionary Genomics Department, DOE Joint Genome Institute and Lawrence, Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
BMC Bioinformatics 7:201. 2006.... - Group II introns break new boundaries: presence in a bilaterian's genomeYvonne Vallès
Department of Energy DOE, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California, USA
PLoS ONE 3:e1488. 2008..Our findings hold implications for understanding mechanisms, constraints, and selective pressures that account for patterns of animal mitochondrial genome evolution... - Crawling through time: Transition of snails to slugs dating back to the Paleozoic, based on mitochondrial phylogenomicsMonica Medina
Evolutionary Genomics, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
Mar Genomics 4:51-9. 2011..Finally we use molecular clock dating that suggests an earlier opisthobranch divergence than previously reported. The implications of this evolutionary scenario are discussed... - Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae)Richard H Baker
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
BMC Genomics 10:361. 2009..We used this set of genes to construct microarray slides and compare patterns of gene expression between lines of flies with divergent eyespan... - Naked corals: skeleton loss in ScleractiniaMonica Medina
Department of Evolutionary Genomics, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
Proc Natl Acad Sci U S A 103:9096-100. 2006..Corallimorpharians escaped extinction from aragonite skeletal dissolution, but some modern stony corals may not have such fortunate fates under the pressure of increased anthropogenic CO(2) in the ocean... - The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda)Jeffrey L Boore
Evolutionary Genomics Program, DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598, USA
BMC Genomics 7:182. 2006..Although complete mitochondrial genome sequences have been reported for more than 600 animals, the taxonomic sampling is highly biased toward vertebrates and arthropods, leaving much of the diversity yet uncharacterized... - Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequencesJ Robert Macey
Department of Evolutionary Genomics, DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
Mol Phylogenet Evol 33:22-31. 2004..Relative to most vertebrates, the Rhineuridae has the block nad6, trnE switched in order with the block cob, trnT, trnP, as they are in birds... - The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomesKevin G Helfenbein
Department of Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109, USA
Proc Natl Acad Sci U S A 101:10639-43. 2004..From this analysis, one can more clearly interpret the patterns of evolution of various developmental features, especially regarding the embryological fate of the blastopore... - The mitochondrial genome of Phoronis architecta--comparisons demonstrate that phoronids are lophotrochozoan protostomesKevin G Helfenbein
Department of Biology, University of Michigan, USA
Mol Biol Evol 21:153-7. 2004..e., the Lophotrochozoa-and solidly refutes the alternative of their being deuterostomes... - Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analysesSusan E Masta
Department of Biology, Portland State University, P O Box 751, Portland, OR 97207, USA
Mol Phylogenet Evol 50:117-28. 2009..Further refinement of amino acid recoding methods may help us better delineate interordinal relationships among these diverse organisms... - Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zoneJim Leebens-Mack
Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of Life Sciences, The Pennsylvania State University, PA, USA
Mol Biol Evol 22:1948-63. 2005.... - Requirements and standards for organelle genome databasesJeffrey L Boore
Department of Energy DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94598, USA
OMICS 10:119-26. 2006..Further, the descriptors necessary to make full use of these data are generally lacking. Here, I outline what is currently wrong and what must be done to make this data useful to the scientific community... - Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom lossDennis V Lavrov
Department of Biology, University of Michigan, Ann Arbor, USA
Mol Biol Evol 19:163-9. 2002..The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons... - The use of genome-level characters for phylogenetic reconstructionJeffrey L Boore
DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
Trends Ecol Evol 21:439-46. 2006..Here, I discuss the advancements, advantages, methods, and problems of the use of genome-level characters for reconstructing evolutionary relationships... - Two rounds of whole genome duplication in the ancestral vertebrateParamvir Dehal
Evolutionary Genomics Department, Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California, USA
PLoS Biol 3:e314. 2005..Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage... - The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)Paul G Wolf
Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322 5305, USA
Gene 350:117-28. 2005.... - Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishesKelly E O'Quin
Department of Biology, University of Maryland, College Park, MD 20742, USA
BMC Evol Biol 11:120. 2011.... - Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae)Debra R Hansen
Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404, University of Texas, Austin, TX 78712, USA
Mol Phylogenet Evol 45:547-63. 2007.... - Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoniSimone Hoegg
Lehrstuhl für Evolutionsbiologie und Zoologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
BMC Genomics 8:317. 2007..Since this diversity could be based on regulatory changes, we chose to study the coding as well as putative regulatory regions of their Hox clusters within a comparative genomic framework... - Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae)Matthew K Fujita
Department of Integrative Biology, University of California, Berkeley, USA
Mol Biol Evol 24:2775-86. 2007..These results demonstrate that, despite their long-term stasis in gene content and arrangement in some lineages, vertebrate mitochondrial genomes can be evolutionary dynamic even at short timescales... - The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence ratesSkip R McCoy
Biological Sciences, Central Washington University, Ellensburg, WA 98926 7537, USA
BMC Evol Biol 8:130. 2008.... - The Physcomitrella genome reveals evolutionary insights into the conquest of land by plantsStefan A Rensing
Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D 79104 Freiburg, Germany
Science 319:64-9. 2008..The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics... - Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genesRosemarie C Haberle
Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
J Mol Evol 66:350-61. 2008..Genes for tRNAs occur at many but not all inversion endpoints, so some combination of repeats and tRNA genes may have mediated these rearrangements... - Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstructionJeffrey L Boore
Genome Project Solutions, Hercules, CA 94547, USA
Philos Trans R Soc Lond B Biol Sci 363:1445-51. 2008.... - Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamandersRachel Lockridge Mueller
Museum of Vertebrate Zoology, 3101 Valley Life Sciences Bldg, University of California, Berkeley, CA 94720 3160, USA
Zoology (Jena) 111:218-30. 2008.... - Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthusLinda A Raubeson
Biological Sciences, Central Washington University, Ellensburg, WA 98926 7537, USA
BMC Genomics 8:174. 2007.... - Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamandersRachel Lockridge Mueller
Museum of Vertebrate Zoology, University of California, Berkeley, USA
Mol Biol Evol 22:2104-12. 2005.... - Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomesRachel Lockridge Mueller
Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA 94720 3160, USA
Proc Natl Acad Sci U S A 101:13820-5. 2004..In addition, they suggest surprising evolutionary lability in traits previously interpreted to be conservative... - Methods for obtaining and analyzing whole chloroplast genome sequencesRobert K Jansen
Section of Integrative Biology, The University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, Texas 78712-0253, USA
Methods Enzymol 395:348-84. 2005.... - Automatic annotation of organellar genomes with DOGMAStacia K Wyman
Department of Computer Sciences, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
Bioinformatics 20:3252-5. 2004..Annotations are stored on our password-protected server to enable repeated sessions of working on the same genome. Finished annotations can be extracted for direct submission to GenBank... - The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera)Antonio Carapelli
Department of Evolutionary Biology, University of Siena, Italy
Gene 376:248-59. 2006..The hypothetical secondary structure of the LSU rRNA has also been reconstructed, obtaining a structural model similar to that of other insects... - Using partial genomic fosmid libraries for sequencing complete organellar genomesJoel R McNeal
The Pennsylvania State University, University Park, PA, USA
Biotechniques 41:69-73. 2006..This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available... - Molecular evolution and recombination in gender-associated mitochondrial DNAs of the Manila clam Tapes philippinarumMarco Passamonti
Dipartimento di Biologia Evoluzionistica Sperimentale, Universita degli Studi di Bologna, Italy
Genetics 164:603-11. 2003..quot; Moreover, our data suggest that recombinants, although occurring in soma, may seldom be transmitted to progeny in T. philippinarum... - The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plantsTimothy W Chumley
The University of Texas at Austin, TX, USA
Mol Biol Evol 23:2175-90. 2006..We propose simple models that account for the major rearrangements with a minimum of 8 IR boundary changes and 12 inversions in addition to several insertions of duplicated sequence... - Evolutionary conservation of regulatory elements in vertebrate Hox gene clustersSimona Santini
Department of Biology, University of Konstanz, 78457 Konstanz, Germany
Genome Res 13:1111-22. 2003..This suggests that the conserved elements are involved in different gene regulatory networks and supports the duplication-deletion-complementation model of functional divergence of duplicated genes... - Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesisBrett M Tyler
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
Science 313:1261-6. 2006.... - Hexapod origins: monophyletic or paraphyletic?Francesco Nardi
Department of Evolutionary Biology, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
Science 299:1887-9. 2003..Therefore, the taxon Hexapoda, as commonly defined to include all six-legged arthropods, is not monophyletic... - Extensive variation in nuclear mitochondrial DNA content between the genomes of Phytophthora sojae and Phytophthora ramorumKonstantinos Krampis
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 0477, USA
Mol Plant Microbe Interact 19:1329-36. 2006..No clear examples were found of NUMTs forming functional nuclear genes or of NUMTs inserted into exons or introns of any nuclear gene... - Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojaeFrank N Martin
U S Department of Agriculture ARS, Salinas, CA 93905, USA
Curr Genet 51:285-96. 2007.... - Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae)Joel R McNeal
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
BMC Biol 5:55. 2007..A strong phylogenetic framework for this large genus is essential to understand the interesting ecological, morphological and molecular phenomena that occur within these parasites in an evolutionary context... - Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus CuscutaJoel R McNeal
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
BMC Plant Biol 7:57. 2007..We sequenced plastid genomes of two species in the parasitic genus Cuscuta along with a non-parasitic relative, Ipomoea purpurea, to investigate changes in the plastid genome that may result from transition to the parasitic lifestyle... - Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliidsZhengqiu Cai
Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA
BMC Evol Biol 6:77. 2006.... - Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patternsRobert K Jansen
Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
Proc Natl Acad Sci U S A 104:19369-74. 2007..Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements...