Nolan Coburn Kane

Nolan Coburn Kane
University of Colorado Boulder | CUB · Department of Ecology and Evolutionary Biology (EBIO)

Ph.D. Indiana University 2007

About

178
Publications
33,485
Reads
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5,682
Citations
Additional affiliations
January 2012 - present
November 2007 - present
University of British Columbia - Vancouver
Position
  • Genome of Sunflower
Description
  • Sequencing, assembly and annotation of the sunflower genome
January 2007 - December 2012
Education
September 2001 - November 2007
Indiana University Bloomington
Field of study
  • Evolution, Ecology and Behavior

Publications

Publications (178)
Article
Full-text available
Premise of study: To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA-barcoding using next-generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions of the traditional DNA-barcoding loci in the...
Article
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The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genom...
Article
While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric rela...
Article
Restoring native plant populations is an essential component of conserving biodiversity, ecological function, and ecosystem services. Restoration using local, ecotypic source materials is largely acknowledged as best practice, however local populations are not always available or adapted to current or future site conditions. A major challenge in re...
Article
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The Asteraceae are the largest plant family but among the least studied at the genome level. Our work investigated practical methods to reduce the influence of secondary metabolites – specifically, phenolic compounds – on the extraction of DNA from Silphium spp. This genus is in the Heliantheae tribe of Asteraceae that also includes sunflower ( Hel...
Article
Full-text available
Background Pathogens are key components in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa popu...
Article
Full-text available
Currently, the amount of genetic data for Cannabis is lacking due to the illegal nature of the plant. Our study used 73 Cannabis sativa whole genome shotgun libraries to reveal eight different mtDNA haplotypes. The most common haplotype contained 60 of the 73 samples studied and was composed of only dioecious individuals. However, other haplotypes...
Article
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The National Institute on Drug Abuse (NIDA) is the sole producer of Cannabis for research purposes in the United States, including medical investigation. Previous research established that cannabinoid profiles in the NIDA varieties lacked diversity and potency relative to the Cannabis produced commercially. Additionally, microsatellite marker analy...
Article
Genome-scale studies have revealed divergent mRNA splicing patterns between closely related species or populations. However, it is unclear whether splicing differentiation is a simple byproduct of population divergence, or whether it also acts as a mechanism for reproductive isolation. We examined mRNA splicing in wild domesticated sunflower hybrid...
Article
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As the effects of climate change continue to alter crop-growing conditions year-to-year on both prime and marginal agricultural landscapes, we must consider the effects not only on yield but also on quality. This is particularly true for oilseed crops. In this review, we explore the importance of oilseeds in general and the specific uses of major o...
Article
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The flowering plant Cannabis sativa , cultivated for centuries for multiple purposes, displays extensive variation in phenotypic traits in addition to its wide array of secondary metabolite production. Notably, Cannabis produces two well-known secondary-metabolite cannabinoids: cannabidiolic acid (CBDA) and delta-9-tetrahydrocannabinolic acid (THCA...
Preprint
Full-text available
The National Institute on Drug Abuse (NIDA) is the sole producer of Cannabis for research purposes in the United States, including medical investigation. Previous research established that cannabinoid profiles in the NIDA varieties lacked diversity and potency relative to the Cannabis produced commercially. Additionally, microsatellite marker analy...
Article
Full-text available
Key message We provide results rooted in quantitative genetics, which combined with knowledge of candidate gene function, helps us to better understand the resistance to two major necrotrophic pathogens of sunflower. Abstract Necrotrophic pathogens can avoid or even benefit from plant defenses used against biotrophic pathogens, and thus represent...
Preprint
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Cannabis is one example in angiosperms that appears to have a recent origin of dioecy and X/Y sex chromosomes. Several evolutionary explanations for this transition have been proposed, with the most parsimonious beginning with a mitochondrial mutation leading to cytoplasmic male sterility (CMS). Our study utilized 73 Cannabis sativa whole genome sh...
Preprint
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Alternative spicing is an integral part of gene expression in multicellular organisms that allows for diverse mRNA transcripts and proteins to be produced from a single gene. However, most existing analyses have focused on macro-evolution, with only limited research on splice site evolution over shorter term, micro-evolutionary time scales. Here we...
Preprint
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Conspecific populations living in adjacent, but contrasting, microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow maintains genetic homogeneity except at loci experiencing strong, divergent selection. A history of reciprocal transplant and common garden studies in such systems, a...
Article
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De novo domestication has received recent attention because of the potential to produce new crop species with additional agroecosystem functions and useful products for climate-resilient agricultural systems of the future. However, there are often traits in wild species that make them difficult to domesticate. One key domestication trait selected b...
Article
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There is now abundant evidence of rapid evolution in natural populations, but the genetic mechanisms of these changes remain unclear. One possible route to rapid evolution is through changes in the expression of genes that influence traits under selection. We examined contemporary evolutionary gene expression changes in plant populations responding...
Preprint
Host-microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity, and community-scale ecological processes. However, less is known about how genetic variation affects hosts' associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbors substantial, herit...
Article
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Hirundo is the most species-rich genus of the passerine swallow family (Hirundinidae) and has a cosmopolitan distribution. Here we report the complete, annotated mitochondrial genomes for 25 individuals from 10 of the 14 extant Hirundo species; these include representatives from four subspecies of the barn swallow, H. rustica. Mitogenomes were cons...
Article
Full-text available
Gene copy number (CN) variation is known to be important in nearly every species where it has been examined. Alterations in gene CN may provide a fast way of acquiring diversity, allowing rapid adaptation under strong selective pressures, and may also be a key component of standing genetic variation within species. Cannabis sativa plants produce a...
Preprint
Pathogens have dramatic effects in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa population,...
Preprint
Full-text available
BACKGROUND Pathogens are key components in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa popu...
Preprint
Full-text available
BACKGROUND: Pathogens are key components in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa pop...
Article
Silphium spp. have garnered interest in Europe as a bioenergy crop and in North America as a perennial oilseed crop. However, very little has been done at this early stage of domestication to characterize wild collections for many key characteristics, including important oilseed traits. The objective of this work was to develop a basic understandin...
Preprint
Full-text available
Gene copy number variation is known to be important in nearly every species where it has been examined. Alterations in gene copy number may provide a fast way of acquiring diversity, allowing rapid adaptation under strong selective pressures, and may also be a key component of standing genetic variation within species. Cannabis sativa plants produc...
Article
Premise Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and import...
Article
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Diatoms are the most diverse lineage of algae, but the diversity of their chloroplast genomes, particularly within a genus, has not been well documented. Herein, we present three chloroplast genomes from the genus Halamphora (H. americana, H. calidilacuna, and H. coffeaeformis), the first pennate diatom genus to be represented by more than one spec...
Article
Range expansions are crucibles for rapid evolution, acting via both selective and neutral mechanisms. While selection on traits such as dispersal and fecundity may increase expansion speed, neutral mechanisms arising from repeated bottlenecks and genetic drift in edge populations (i.e. gene surfing) could slow spread or make it less predictable. Th...
Article
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Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondri...
Article
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The mitochondrial genome of the Gunnison’s prairie dog, Cynomys gunnisoni gunnisoni, is described and incorporated into a phylogenetic inference of the genus Cynomys based on seven new mitochondrial genomes and published genomes from Cynomys leucurus and Cynomys ludovicianus. The mitochondrial genome from Ictidomys tridecemlineatus, the sister genu...
Article
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Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characteri...
Article
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Climate change is occurring in the central US and is interacting with agroecological factors to increase biotic stress in sunflower. Certain species of Diaporthe cause Phomopsis stem canker in sunflower and other dicotyledonous weeds and crops. The increase in precipitation already observed in the states of North Dakota, South Dakota, and Minnesota...
Article
Lecanora markjohnstonii is described as new to science from the southeastern United States, with a primary center of distribution in the southern Appalachian Mountain region. This sterile, sorediate crust is saxicolous on both sandstone and granite and occurs commonly in mixed hardwood-conifer forests with rock outcrops. It is characterized by a gr...
Article
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Organic dormancy, the inability to germinate under favorable conditions, is a common problem in many crop species and their wild relatives, leading to more variable emergence, plant density, and growth rates, thus increasing costs, and lowering yield. To overcome these problems, several different methods have been developed for various crop and mod...
Article
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Cladonia is among the most species-rich genera of lichens globally. Species in this lineage, commonly referred to as reindeer lichens, are ecologically important in numerous regions worldwide. In some locations, species of Cladonia can comprise the dominant groundcover, and are a major food source for caribou and other mammals. Additionally, many s...
Article
Alternative splicing enables organisms to produce the diversity of proteins necessary for multicellular life by using relatively few protein-coding genes. Although differences in splicing have been identified among divergent taxa, the shorter-term evolution of splicing is understudied. The origins of novel splice forms, and the contributions of alt...
Article
Diatoms are the most diverse lineage of algae and at the base of most aquatic food webs, but only 11 of their mitochondrial genomes have been described. Herein, we present the mitochondrial genomes of six diatom species, including: Melosira undulata, Nitzschia alba, Surirella sp., Entomoneis sp., Halamphora coffeaeformis, and Halamphora calidilacun...
Article
Human modification of the environment can result in the fragmentation and isolation of natural populations. If isolated populations are small, they may experience higher probabilities of extirpation from genetic, demographic, and environmental effects. One approach for managing fragmented and isolated populations is facilitated migration in which i...
Article
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Background The repetitive content of the genome, once considered to be “junk DNA”, is in fact an essential component of genomic architecture and evolution. In this study, we used the genomes of three varieties of Cannabis sativa, three varieties of Humulus lupulus and one genotype of Morus notabilis to explore their repetitive content using a graph...
Article
Symbioses among co-evolving taxa are often marked by genome reductions such as a loss of protein-coding genes in at least one of the partners as a means of reducing redundancy or intergenomic conflict. To explore this phenomenon in an iconic yet under-studied group of obligate symbiotic organisms, mitochondrial genomes of 22 newly sequenced and ann...
Article
Full-text available
Capitate glandular trichomes (CGT), one type of glandular trichomes, are most common in Asteraceae species. CGT can produce various secondary metabolites such as sesquiterpene lactones (STLs) and provide durable resistance to insect pests. In sunflower, CGT-based host resistance is effective to combat the specialist pest, sunflower moth. However, t...
Article
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Known colloquially as ‘Old Man’s Beard’, Usnea is a genus of lichenized Ascomycete fungi characterized by having a fruticose growth form and cartilaginous central axis. The complete mitochondrial genomes of Usnea halei, U. mutabilis, U. subfusca, U. subgracilis, and U. subscabrosa were sequenced using Illumina data and then assembled de novo. These...
Article
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Phenotypic differentiation plays an important role in the formation and maintenance of reproductive barriers. In some cases, variation in a few key aspects of phenotype can promote and maintain divergence; hence the identification of these traits and their associations with patterns of genomic divergence are crucial for understanding the patterns a...
Patent
Full-text available
Compositions and methods for providing desired cannabinoid content in Cannabis plants. More particularly, the invention relates to compositions and methods for using cannabinoid synthase paralogs as guidance for breeding Cannabis plants with a desired cannabinoid content, including but not limited to cultivars, varieties, lines, and methods of bree...
Article
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Hybrid zones are geographic regions where isolating barriers between divergent populations are challenged by admixture. Identifying factors that facilitate or inhibit hybridization in sympatry can illuminate the processes that maintain those reproductive barriers. We analyzed patterns of hybridization and phenotypic variation across two newly-disco...