Jeffrey L. Boore

Institute for Systems Biology

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Jennifer V. Kuehl

Lawrence Berkeley National Laboratory

Robert K. Jansen

The University of Texas at Austin

Wesley M. Brown

Washington Center

Claude W. dePamphilis

Pennsylvania State University

Antonio Carapelli

University of Siena

Francesco Nardi

University of Palermo

Francesco Frati

University of Siena

Paramvir Dehal

Lawrence Berkeley National Laboratory

Romano Dallai

University of Siena

Mónica Medina

Pennsylvania State University

Cooperative Institutions

Joint Genome Institute

127

Lawrence Berkeley National Laboratory

University of California, Berkeley

Washington University in St. Louis

Lawrence Livermore National Laboratory

Kanazawa University

Indiana University Bloomington

Harvard University

Advanced Science Research Center

Kyoto University

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Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

Science (2006)

Brett M. Tyler Sucheta Tripathy Xuemin Zhang Paramvir Dehal Rays H. Y. Jiang

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

Phytophthora ramorum

Phytophthora sojae

Oomycete

10.1126/science.1128796

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The mitochondrial genomes of Campodea fragilis and C. lubbocki(Hexapoda: Diplura): high genetic divergence in a morphologically uniformtaxon

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (2005)

Lars Podsiadłowski Antonio Carapelli Francesco Nardi Romano Dallai Markus Koch

LBNL-59182 The mitochondrial genomes of Campodea fragilis and C. lubbocki (Hexapoda: Diplura): high genetic divergence in a morphologically uniform taxon L. Podsiadlowski, A. Carapelli, F. Nardi, R. Dallai, M. Koch, J.L.Boore, F. Frati

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Peer Review #3 of "Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae) (v0.1)"

Jeffrey L. Boore

Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia.We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family.We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms.Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence.The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π= 0.00025).Plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives plastid genomes.Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology.The N-fixing clade appears as sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.

10.7287/peerj.8392v0.1/reviews/3

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Why Evolutionary Biology and Genome Sciences Need Each Other

Lawrence Berkeley National Laboratory (2005)

Jeffrey L. Boore

LBNL-57628 LBNL-57628 Why Evolutionary Biology and Genome Sciences Need Each Other Jeffrey Boore Evolutionary Genomics Department Head PARC - May 5, 2005

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Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes

Proceedings of the National Academy of Sciences (2004)

Rachel Lockridge Mueller Jonathan R. Macey Martin Jaekel David B. Wake Jeffrey L. Boore

The evolutionary history of the largest salamander family (Plethodontidae) is characterized by extreme morphological homoplasy. Analysis of the mechanisms generating such homoplasy requires an independent molecular phylogeny. To this end, we sequenced 24 complete mitochondrial genomes (22 plethodontids and two outgroup taxa), added data for three species from GenBank, and performed partitioned and unpartitioned Bayesian, maximum likelihood, and maximum parsimony phylogenetic analyses. We explored four dataset partitioning strategies to account for evolutionary process heterogeneity among genes and codon positions, all of which yielded increased model likelihoods and decreased numbers of supported nodes in the topologies (Bayesian posterior probability >0.95) relative to the unpartitioned analysis. Our phylogenetic analyses yielded congruent trees that contrast with the traditional morphology-based taxonomy; the monophyly of three of four major groups is rejected. Reanalysis of current hypotheses in light of these evolutionary relationships suggests that (i) a larval life history stage reevolved from a direct-developing ancestor multiple times; (ii) there is no phylogenetic support for the "Out of Appalachia" hypothesis of plethodontid origins; and (iii) novel scenarios must be reconstructed for the convergent evolution of projectile tongues, reduction in toe number, and specialization for defensive tail loss. Some of these scenarios imply morphological transformation series that proceed in the opposite direction than was previously thought. In addition, they suggest surprising evolutionary lability in traits previously interpreted to be conservative.

Maximum parsimony

Monophyly

10.1073/pnas.0405785101

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Citations (258)

The Complete Sequence of the Mitochondrial Genome of the Chamberednautilus (Mollusca: Cephalopoda)

BMC Genomics (2005)

Jeffrey L. Boore

Nautilus

Polyplacophora

Heavy strand

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The phylogeny of Mediterranean tortoises and their close relativesbased on complete mitochondrial genome sequences from museumspecimens

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (2005)

James F. Parham J Robert Macey Theodore J. Papenfuss Chris R. Feldman Oğuz Türkozan

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Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule

Journal of Zoological Systematics & Evolutionary Research (2020)

Nikos Poulakakis Joshua M. Miller Evelyn L. Jensen Luciano B. Beheregaray Michael A. Russello

Galapagos giant tortoises (Chelonoidis spp.) are a group of large, long-lived reptiles that includes 14 species, 11 of which are extant and threatened by human activities and introductions of non-native species. Here, we evaluated the phylogenetic relationships of all extant and two extinct species (Chelonoidis abingdonii from the island of Pinta and Chelonoidis niger from the island of Floreana) using Bayesian and maximum likelihood analysis of complete or nearly complete mitochondrial genomes. We also provide an updated phylogeographic scenario of their colonization of the Galapagos Islands using chrono-phylogenetic and biogeographic approaches. The resulting phylogenetic trees show three major groups of species: one from the southern, central, and western Galapagos Islands; the second from the northwestern islands; and the third group from the northern, central, and eastern Galapagos Islands. The time-calibrated phylogenetic and ancestral area reconstructions generally align with the geologic ages of the islands. The divergence of the Galapagos giant tortoises from their South American ancestor likely occurred in the upper Miocene. Their diversification on the Galapagos adheres to the island progression rule, starting in the Pleistocene with the dispersal of the ancestral form from the two oldest islands (San Cristóbal and Española) to Santa Cruz, Santiago, and Pinta, followed by multiple colonizations from different sources within the archipelago. Our work provides an example of how to reconstruct the history of endangered taxa in spite of extinctions and human-mediated dispersal events and provides a framework for evaluating the contribution of colonization and in situ speciation to the diversity of other Galapagos lineages.

10.1111/jzs.12387

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The draft genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins

Paramvir Dehal Yutaka Satou R. Keith Campbell Jarrod Chapman Bernard M. Degnan

Chordate

Ciona

10.1126/science.1080049

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Citations (62)

Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction

Oxford University Press eBooks (2009)

Jeffrey L. Boore Susan I. Fuerstenberg

Abstract The first whole genomes to be compared for phylogenetic inference were those of mitochondria, which provided the first sets of genome-level characters for phylogenetic reconstruction. Most powerful among these characters has been comparisons of the relative arrangements of genes, which have convincingly resolved numerous branching points, including some that had remained recalcitrant even to very large molecular sequence comparisons. Now the world faces a tsunami of complete nuclear genome sequences. In addition to the tremendous amount of DNA sequence that is becoming available for comparison, there is also the potential for many more genome-level characters to be developed, including the relative positions of introns, the domain structures of proteins, gene family membership, presence of particular biochemical pathways, aspects of DNA replication or transcription, and many others. These characters can be especially convincing because of their low likelihood of reverting to a primitive condition or occurring independently in separate lineages, so reducing the occurrence of homoplasy. The comparisons of organelle genomes pioneered the way for using such features for phylogenetic reconstructions, and it is almost certainly true, as ever more genomic sequence becomes available, that further use of genome-level characters will play a big role in outlining the relationships among major animal groups.

Sequence (biology)

10.1093/acprof:oso/9780199549429.003.0013

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Citations (1)