Jeffrey Boore

• Ph.D., University of Michigan
• Chief Technology Officer at Phenome Health

We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species Po...

Modern health care faces several serious challenges, including an ageing population and its inherent burden of chronic diseases, rising costs and marginal quality metrics. By assessing and optimizing the health trajectory of each individual using a data-driven personalized approach that reflects their genetics, behaviour and environment, we can sta...

We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa , two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species P...

Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of mitochondrial genome architecture and recombination. We used PacBio sequencing to re-assemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrg...

Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of mitochondrial genome architecture and landscapes of recombination. We used PacBio sequencing to re-assemble mitochondrial genomes from two species of New Zealand freshwater snai...

Why sexual reproduction is so common when asexual reproduction should be much more efficient and less costly remains an open question in evolutionary biology. Comparisons between otherwise similar sexual and asexual taxa allow us to characterize the genetic architecture underlying asexuality, which can, in turn, illuminate how this reproductive mod...

Vertebrate mitochondrial genomes have been extensively studied for genetic and evolutionary purposes, these are normally believed to be extremely conserved, however, different cases of gene rearrangements have been reported. To verify the level of rearrangement and the mitogenome evolution, we performed a comparative genomic analysis of the 2831 ve...

The evolution of the vertebrate mitochondrial genome has been the focus of numerous genetic and evolutionary studies over the last several decades. Initially, sampling was heavily biased toward taxonomic orders of greatest economic or health importance, but recent advances in DNA sequencing technology have facilitated a much broader phylogenetic sa...

How does asexual reproduction influence genome evolution? While is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits - mode of genomic inheritance - influences genome structure. We address this question with the New Zealand freshw...

The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a ‘textbook description’. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusc...

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 a...

Background Brown algae are key members of coastal marine ecosystems and the most recent eukaryotic lineage to transition to multicellularity. Browns are members of a heterogeneous assemblage of organisms, heterokonts, that include photosynthetic plankton, (e.g. diatoms) and non-photosynthetic taxa like the pseudofungi or labyrinthulas. We hypothesi...

Background Although animal mitochondrial DNA sequences are known to evolve rapidly, their gene arrangements often remain unchanged over long periods of evolutionary time. Therefore, comparisons of mitochondrial genomes may result in significant insights into the evolution both of organisms and of genomes. Mammalian mitochondrial genomes recently pu...

Potamopyrgus antipodarum , a New Zealand freshwater snail, is a powerful system to study the maintenance of sexual reproduction. Obligate asexual P. antipodarum (herein, Pa ) lineages include both triploids and tetraploids that are products of multiple separate transitions from diploid sexual ancestors. Distinct diploid sexual and polyploid asexual...

Potamopyrgus antipodarum , a New Zealand freshwater snail, is a powerful system to study the maintenance of sexual reproduction. Obligate asexual P. antipodarum (herein, Pa ) lineages include both triploids and tetraploids that are products of multiple separate transitions from diploid sexual ancestors. Distinct diploid sexual and polyploid asexual...

Reciprocal coevolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population- or genotype-specific evolutionary change. These host-parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of coevolving host-...

Reciprocal coevolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population- or genotype-specific evolutionary change. These host-parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of coevolving host-...

Transposable elements (TEs) constitute a large portion of eukaryotic genomes, and their insertion and accumulation can have major effects on genome evolution. Accordingly, understanding how and why TEs evolve within genomes is a major component of characterizing the evolutionary and genetic forces underlying the diversity of eukaryotic genome archi...

Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease such as cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, X. maculatus, offers a...

Harmful mutations are ubiquitous and inevitable, and the rate at which these mutations are removed from populations is a critical determinant of evolutionary fate. Closely related and otherwise similar sexual and asexual taxa provide a particularly powerful setting in which to study deleterious mutation elimination because sex should facilitate mut...

Background Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systema...

We report the complete mitochondrial genome sequence of the flowering plant Amborella trichopoda. This enormous, 3.9-megabase genome contains six genome equivalents of foreign mitochondrial DNA, acquired from green algae, mosses, and other angiosperms. Many of these horizontal transfers were large, including acquisition of entire mitochondrial geno...

Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease such as cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, X. maculatus, offers a...

Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychae...

The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favour...

The StramenopilePhotoCut genes

Transcriptional regulation of metabolic pathways

Supplementary Figures S1-S10, Supplementary Tables S1-S14, Supplementary Notes 1-5, Supplementary Methods and Supplementary References

Plastid Origins The glaucophytes, represented by the alga Cyanophora paradoxa , are the putative sister group of red and green algae and plants, which together comprise the founding group of photosynthetic eukaryotes, the Plantae. In their analysis of the genome of C. paradoxa , Price et al. (p. 843 ; see the Perspective by Spiegel ) demonstrate a...

The primary endosymbiotic origin of the plastid in eukaryotes more than 1 billion years ago led to the evolution of algae and plants. We analyzed draft genome and transcriptome data from the basally diverging alga Cyanophora paradoxa and provide evidence for a single origin of the primary plastid in the eukaryote supergroup Plantae. C. paradoxa ret...

We report here the isolation and sequencing of 10 Y-specific tammar wallaby (Macropus eugenii) BAC clones, revealing five hitherto undescribed tammar wallaby Y genes (in addition to the five genes already described) and several pseudogenes. Some genes on the wallaby Y display testis-specific expression, but most have low widespread expression. All...

We present the draft 273 Mb genome of the migratory monarch butterfly (Danaus plexippus) and a set of 16,866 protein-coding genes. Orthology properties suggest that the Lepidoptera are the fastest evolving insect order yet examined. Compared to the silkmoth Bombyx mori, the monarch genome shares prominent similarity in orthology content, microsynte...

Divergence within cis-regulatory sequences may contribute to the adaptive evolution of gene expression, but functional alleles in these regions are difficult to identify without abundant genomic resources. Among African cichlid fishes, the differential expression of seven opsin genes has produced adaptive differences in visual sensitivity. Quantita...

Synteny (Pip plots) of O. niloticus opsin-containing BACs against the genome assemblies of five teleost species.

Complete transcription factor binding site profiles for 20 CNEs in O. niloticus and M. zebra.

GenBank accession numbers for all sequences generated in this study.

Synteny (Pip plots) of O. niloticus and M. zebra opsin-containing BAC sequences.

Opsin gene content of five teleost genomes. Phylogeny of the teleost taxa is recreated from [118].

Orthology of RH2 and SWS2 opsin paralogs from five teleost fish genomes. A) RH2 phylogeny. B) SWS2 phylogeny. In both cases, broken lines indicate branches leading from the outgroup that were shortened to fit each tree into the figure; these do not represent missing or incomplete branch length information.

Complete list of miRNA target sites identified within the 3'-UTR of each opsin in O. niloticus and M. zebra.

Names, opsin expression values, and polymorphisms found within the proximal promoters of 18 Lake Malawi cichlid species.

Length and Dxy scores between O. niloticus and M. zebra for each coding and non-coding region examined.

Identification of opsin-containing BACs from Finger Printed Contigs. A-C) BACs fingerprinted contig containing the SWS2A-SWS2B-LWS (A) RH2 (B) and SWS1 (C) genes. Arrows indicate PCR products successfully amplified using primers designed to BAC end sequences for clones whose names are shown in the corresponding color. Colored circles are the approx...

Primers used to amplify and sequence the proximal promoter regions and 3'-UTR of several opsins from 18 Lake Malawi cichlid species.

FASTA file of 20 conserved non-coding elements (CNEs), promoter sequences, 3-UTRs, and seven non-opsin promoters from O. niloticus and M. zebra (80 sequences total).

Geraniaceae plastid genomes (plastomes) have experienced a remarkable number of genomic changes. The plastomes of Erodium texanum, Geranium palmatum, and Monsonia speciosa were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome. Geraniaceae plastomes were found to be highly variable in size, gene con...

Sea slugs (Gastropoda: Opisthobranchia) are characterized by extensive morphological homoplasy. In particular, reduced or absent shells are predominant throughout the group. This trend towards shell loss has resulted in a poor fossil record. DNA-based phylogenies have been helpful in improving our understanding of the evolution of this group and ma...

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia’s genes have no detectable homologs in any other available proteome, and the m...

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia’s genes have no detectable homologs in any other available proteome, and the m...

Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyalo...

Phylogenetic results using inferred amino acid data. A) Cladogram based on ML analysis using RAxML of 49 inferred amino acid sequences from all 43 plastomes sampled (-ln = 181034.78356; Table 1). RAxML and BI analyses including all taxa as well as those excluding both Selaginella spp. and gnetophytes (-ln = 149105.09124) also converged on this topo...

Insertion/deletion (indel) matrix Insertion/deletion events (indels) scored across the 49 aligned protein-coding genes used in this study. Characters were scored as 1 for presence or 0 for absence of a sequence stretch. Character state labels (CHARSTATELABELS) indicate in which gene the indel was identified and the position within that gene using t...

Nucleotide alignment Alignment of 49 genes from 43 plastomes used for phylogenetic analysis described in the text. Data are interleaved by gene and exclusion blocks are provided at the end of the file.

Angiosperm phylogenetic results using nucleotide data. The identical angiosperm topology was recovered using nucleotide data regardless of taxon set or analytical method. Nodes with bootstrap proportions (BP) = 100 or posterior probabilities (PP) = 1.0 are not shown (most nodes). Support was generally strong within the angiosperms with a few except...

Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexam...

Figure S3. Inferred tRNA secondary structures based on the nucleotide sequences of 22 mitochondrial tRNA genes identified from the complete mt genome of Eualetes tulipa. tRNA genes are labeled according to their amino acid specificity and are arranged alphabetically.

Figure S5. Inferred tRNA secondary structures based on the nucleotide sequences of eight mitochondrial tRNA genes identified from the partial mt genome of Thylaeodus sp. tRNA genes are labeled according to their amino acid specificity and are arranged alphabetically.

Figure S1. Inferred tRNA secondary structures based on the nucleotide sequences of 22 mitochondrial tRNA genes identified from the complete mt genome of Dendropoma maximum. tRNA genes are labeled according to their amino acid specificity and are arranged alphabetically.

Figure S2. Inferred tRNA secondary structures based on the nucleotide sequences of 23 mitochondrial tRNA genes identified from the complete mt genome of Dendropoma gregarium. tRNA genes are labeled according to their amino acid specificity and are arranged alphabetically.

Figure S6. Inferred tRNA secondary structures based on the nucleotide sequences of five mitochondrial tRNA genes identified from the partial mt genome of Vermetus erectus. tRNA genes are labeled according to their amino acid specificity and are arranged alphabetically.

Table S2. The conservation of amino acid identity in select codons from cox1, cox2, and cox3 genes from the mt genomes of Dendropoma maximum, D. gregarium, Eualetes tulipa, and Thylacodes squamigerus.

Figure S4. Inferred tRNA secondary structures based on the nucleotide sequences of 24 mitochondrial tRNA genes identified from the complete mt genome of Thylacodes squamigerus. tRNA genes are labeled according to the amino acid specificity and are arranged alphabetically.

Table S1. Base compositions and nucleotide skews for new vermetid mt genomes, existing caenogastropod mt genomes, and other select molluscs.

Table S3. Summary of codon usage across all protein-encoding genes in the mitochondrial genomes of Dendropoma maximum, D. gregarium, Eualetes tulipa, and Thylacodes squamigerus.

Widespread sampling of vertebrates, which comprise the majority of published animal mitochondrial genomes, has led to the view that mitochondrial gene rearrangements are relatively rare, and that gene orders are typically stable across major taxonomic groups. In contrast, more limited sampling within the Phylum Mollusca has revealed an unusually hi...

Supplemental methods and results. Additional details on sequencing methods and analysis results citing methods or data from [147-166].

Supplemental Tables S1 to S11 providing detailed lists and analyses.

Supplemental Figures S1 to S16, supporting data analyses.

Multiple sequence alignment of oomycete proteins with similarity to P. ultimum Family 3 proteins. Predicted secreted proteins (91) with similarity to Family 3 proteins from various oomycete species were aligned demonstrating the YxSL[KR] motif.

Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole tr...

The mitochondrial (mt) genomes of two soybean rust pathogens, Phakopsora pachyrhizi and P. meibomiae, have been sequenced. The mt genome of P. pachyrhizi is a circular 31 825-bp molecule with a mean GC content of 34.6%, while P. meibomiae possesses a 32 520-bp circular molecule with a mean GC content of 34.9%. Both mt genomes contain the genes enco...

Ecdysozoa is the recently recognized clade of molting animals that comprises the vast majority of extant animal species and the most important invertebrate model organisms—the fruit fly and the nematode worm. Evolutionary relationships within the ecdysozoans remain, however, unresolved, impairing the correct interpretation of comparative genomic st...

Table S1: Tortula ruralis chloroplast genome gene list. List of all genes annotated for the chloroplast genome of Tortula ruralis, indicating protein products position on genome and strand. Exons are listed separately for genes with introns.

Tortula ruralis, a widely distributed species in the moss family Pottiaceae, is increasingly used as a model organism for the study of desiccation tolerance and mechanisms of cellular repair. In this paper, we present the chloroplast genome sequence of T. ruralis, only the second published chloroplast genome for a moss, and the first for a vegetati...

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plasti...

Background - Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results -The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophtho...

Collembola are one of the few hexapod groups adapted to live in the harsh environmental conditions of Antarctic terrestrial ecosystems. Diversity is limited to a few species that can be very abundant in coastal deglaciated sites. A remarkable lack of overlap in Collembola species composition is evident between Western and Eastern Antarctica, and Fr...

Background Many species of stalk-eyed flies (Diopsidae) possess highly-exaggerated, sexually dimorphic eye-stalks that play an important role in the mating system of these flies. Eye-stalks are increasingly being used as a model system for studying sexual selection, but little is known about the genetic mechanisms producing variation in these ornam...

EST Assemblies. Nucleotide sequence, EST reads and Genbank accession numbers are provided for 11,545 consensus sequences (conseqs).

EST Annotation. Detailed annotation of 7,066 cluster sequences. Information is provided for the top hit for each cluster blasted against the protein databases of Drosophila melanogaster, Anopheles gambiae and the D. melanogaster Transposable Element database.