Nathaniel R Street

Nathaniel R Street
Umeå University | UMU · Department of Plant Physiology

PhD

About

108
Publications
19,976
Reads
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4,733
Citations
Citations since 2016
18 Research Items
2806 Citations
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
20162017201820192020202120220100200300400
Additional affiliations
January 2008 - present
Umeå University
Position
  • Professor (Assistant)
January 2006 - December 2010
University of Southampton
Position
  • PostDoc Position

Publications

Publications (108)
Article
With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on th...
Article
Full-text available
In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-produc...
Preprint
Full-text available
Wood represents the majority of the biomass on lands, and it constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, meaning that feedstocks must be improved. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior biore...
Preprint
Full-text available
Understanding local adaptation in plants from a genomic perspective has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating s...
Article
Full-text available
Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Erica...
Preprint
Full-text available
There are an ever-increasing number of genomes being sequenced, many of which have associated RNA sequencing and other genomics data. The availability of user-friendly web-accessible mining tools ensures that these data repositories provide maximum benefit to the community. However, there are relatively few options available for setting up such sta...
Preprint
Full-text available
The genome assembly of the European aspen Populus tremula proved difficult for a short-read based strategy due to high genomic variation. As a consequence, the fragmented sequence is impeding studies that benefit from highly contiguous data, particularly genome-wide association studies (GWAS) and comparative genomics. Here we present an updated ass...
Chapter
Visualization - the process of interpreting data into visual forms - is increasingly important in science as data grows rapidly in volume and complexity. A common challenge faced by many biologists is how to benefit from this data deluge without being overwhelmed by it. Here, our main interest is in the visualization of genomes, sequence alignments...
Preprint
Full-text available
Gene network analysis is a powerful tool to identify and prioritize candidate genes, especially from data sets where experimental design renders other approaches, such as differential expression analysis, limiting or infeasible. Numerous gene network inference algorithms have been published and are commonly individually applied in transcriptomics s...
Conference Paper
Visualization - the process of interpreting data into visual forms - is increasingly important in science as data grows rapidly in volume and complexity. A common challenge faced by many biologists is how to benefit from this data deluge without being overwhelmed by it. Here, our main interest is in the visualization of genomes, sequence alignments...
Article
Full-text available
Significance We performed de novo, full-genome sequence analysis of two Populus species, North American quaking and Eurasian trembling aspen, that contain striking levels of genetic variation. Our results showed that positive and negative selection broadly affects patterns of genomic variation, but to varying degrees across coding and noncoding reg...
Article
Full-text available
Apoplastic events such as monolignol oxidation and lignin polymerization are difficult to study in intact trees. To investigate the role of apoplastic H2O2 in gymnosperm phenolic metabolism, an extracellular lignin-forming cell culture of Norway spruce (Picea abies) was used as a research model. Scavenging of apoplastic H2O2 by KI repressed lignin...
Article
Full-text available
Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and d...
Article
Full-text available
A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome re-sequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum and population-sc...
Article
Full-text available
After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts,...
Research
Full-text available
A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome re-sequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum and population-sc...
Article
Full-text available
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard feature...
Chapter
Full-text available
Analysis of next-generation sequencing (NGS) data is rapidly becoming an important source of information for genetics and genomics studies. The utility of such data does, however, rely crucially on the accuracy and quality of SNP and genotype calling. Identification of genetic variants (SNPs and short indels) from NGS data is an area of active rese...
Article
Full-text available
Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both P. tremula L. and Populus balsamifera...
Article
Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expre...
Article
Full-text available
Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despi...
Article
Full-text available
Background Evolutionary theory suggests that males and females may evolve sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximise reproductive success and fitness. Such sexual dimorphism would result in sex biased gene expression patterns in non-floral orga...
Article
Full-text available
Divergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regulation of genes. We inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual...
Article
Full-text available
Information about relatedness between individuals in wild populations is advantageous when studying evolutionary, behavioural and ecological processes. Genomic data can be used to determine relatedness between individuals either when no prior knowledge exists or to confirm suspected relatedness. Here we present a set of 96 SNPs suitable for inferri...
Article
Full-text available
Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsi...
Article
Full-text available
DNA methylation is involved in the control of plant development and adaptation to the environment through modifications of chromatin compaction and gene expression. In poplar (Populus trichocarpa), a perennial plant, variations in DNA methylation have been reported between genotypes and tissues or in response to drought. Nevertheless, the relations...
Article
Full-text available
In paramutation, epigenetic information is transferred from one allele to another to create a gene expression state which is stably inherited over generations. Typically, paramutation describes a phenomenon where one allele of a gene down-regulates the expression of another allele. Paramutation has been described in several eukaryotes and is best u...
Data
Location of the premature stop codon in srf6-4 and the T-DNA insertions in COBRA and SRF6 . (TIFF)
Data
Complementation of cob-6 with a genomic COBRA construct. (TIF)
Data
Truncated co-expression network from Cluster 86 in [23]. Brief annotations of genes are indicated in black text. Different coloured edges indicate strength of transcriptional coordination. Green; mutual rank ≤10, Orange; mutual rank ≤20, Red; mutual rank ≤30. Low mutual rank indicates stronger co-expression relationships. Coloured nodes indicate em...
Data
Amplification of full length COBRA cDNA from cob-6 and Col-0. (TIF)
Data
Phenotype comparison of the srf6-4cob-6 and cob-6 etiolated seedlings. Picture is representative of multiple seedlings. (TIF)
Data
Phenotype of six-week-old Col-0, srf6-1, cob-6 and srf6-1cob-6 plants grown in 16-h light, 8-h dark. Scale bar 5 cm. (TIF)
Data
Cellulose content in four-day-old dark grown seedlings. Genotypes, mean and SE are indicated. A, B, and C indicate significant difference of the genotypes ranked by Duncan’s test at P<0.01, a, b, c indicate ranking by Duncan test at P≤0.05. (TIFF)
Data
The phenotype of etiolated F1 seedlings derived from the cross between srf6-1cob-6 and cob-6. Picture is representative of multiple seedlings. (TIF)
Data
Hypocotyl length of Col-0, srf6-1, srf6-1cob-6, epicob-6 and cob-6. (PPTX)
Data
Hypocotyl length of three-day-old etiolated ros1-4 mutant combinations. (PPTX)
Data
The effect of DNA demethylase ros1-4 mutation on COBRA transcript levels. Also shown is the effect of DNA methylation inhibitor 5-azacytidine (5-Aza) on COBRA expression in ros1-4 and ros1-4cob-6. Genotypes, mean and SE are indicated. RNA was extracted from etiolated seedlings, n = 3 pools of seedlings. (TIF)
Data
Hypocotyl length of the epicob-6 and the F2 plants derived from epicob-6 crossed with cob-6. And the cob-6 and F2 cob-6 plants derived from epicob-6 crossed with Col-0 (PPTX)
Data
List of Arabidopsis mutants and primers used in the study. (DOC)
Data
Hypocotyl length of the different epicob-6 generations. (PPTX)
Article
Full-text available
One of the important steps of genome assembly is scaffolding, in which contigs are linked using information from read-pairs. Scaffolding provides estimates about the order, relative orientation and distance between contigs. We have found that contig distance estimates are generally strongly biased and based on false assumptions. Since erroneous dis...
Article
Full-text available
Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in Populus is genetically controlled, the precise gender-determining systems remain unclear. The recently released second draft assembly and annotated gene set of the Populus genome provided an opportunity to revisit th...
Article
Full-text available
The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes Arabidopsis thaliana an ideal platform for genetic mapping. PCR markers based on INsertions/DELetions (INDELs) are currently the most frequently used polymorphisms. For the mo...
Chapter
As a model species, Populus offers opportunities to study processes unique to woody, perennial species, such as seasonal senescence, dormancy and wood production. As a long-lived species, it is also possible that different adaptive survival strategies have been selected for in comparison to annual species. To date, a number of miRNAs have been show...
Article
Association mapping is rapidly becoming the main method for dissecting the genetic architecture of complex traits in plants. Currently most association mapping studies in plants are preformed using sets of genes selected to be putative candidates for the trait of interest, but rapid developments in genomics will allow for genome-wide mapping in vir...
Data
Transcriptional modules. All transcriptional modules in the library with over-represented function information.
Data
Predicted regulatory mechanisms. The regulatory mechanisms predicted for each transcriptional module.
Data
Gene expression data. The gene expression matrix used in this study.
Data
Transcriptional network. The inferred transcriptional network in text format (ready to be viewed in Cytoscape).
Data
Co-expression network. The inferred co-expression network based on pair-wise similarity (ready to be viewed in Cytoscape).
Data
Conserved transcriptional modules. Transcriptional modules that have conserved regulation in the Arabidopsis developmental data.
Article
Full-text available
Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene int...
Chapter
Full-text available
As a model system, Populus offers the opportunity to study biological questions pertinent to perennial growth habits such as lignocellulosic cell wall biogenesis and dormancy cycles. In the past years, much has been learnt about the transcriptional control of such processes and there is an ever-growing resource of publicly available transcriptomics...
Article
Relatively little is known about the transcriptional response or genetic control of response and adaptation of trees to tropospheric ozone exposure. Such understanding is needed as up to 50% of forests, globally, may be subjected to phytotoxic concentrations of ozone. The physiological, transcriptional and genetic response to ozone was examined in...
Article
The delay in autumnal senescence that has occurred in recent decades has been linked to rising temperatures. Here, we suggest that increasing atmospheric CO2 may partly account for delayed autumnal senescence and for the first time, through transcriptome analysis, identify gene expression changes associated with this delay. Using a plantation of Po...
Article
*The delay in autumnal senescence that has occurred in recent decades has been linked to rising temperatures. Here, we suggest that increasing atmospheric CO2 may partly account for delayed autumnal senescence and for the first time, through transcriptome analysis, identify gene expression changes associated with this delay. *Using a plantation of...
Data
Significant loci of short RNAs. Loci identified across all short RNA size classes using the siLoCo tool from the UEA sRNA toolkit.
Data
Significant loci of short 21 nt short RNAs. Loci identified for 21 nt short RNAs using the siLoCo tool from the UEA sRNA toolkit.
Data
Chromosome distribution plot for 1st 1 Mb of chromosome 19. short RNA, gene and repeat density plot for the 1st 1 Mb of chromosome 19 (LG_XIX). Coloured bars, above the axis for plus strand and below the axis for minus strand, show expression counts in 0.1 Mb windows for 18 (grey), 19 (yellow), 20 (purple), 21 (cyan), 22 (dark blue), 23 (green) and...
Data
Predicted miRNA loci with no match the miRBase. All loci predicted as miRNA using the miRCat tool from the UEA sRNA toolkit that do not match existing miRBase entries and are therefore candidate non-conserved miRNAs.
Data
Phylogenetic tree of predicted ARF gene family members. Phylogenetic tree of predicted members of the ARF gene family. Family members were identified using an HMM model search for the presence of the ARF domain within the Jamboree gene model set. Phylogenetic tree was used using [57].
Data
Predicted phased loci. Phased loci with a p values <0.001 using the UEA sRNA toolkit.
Data
Hairpin structure of miR475. Diagrammatic representation of the predicted stem-loop hairpin structure of miR475. The read count of sequences along the sequence is indicated using coloured shading.
Data
Hairpin structure of miR476. Diagrammatic representation of the predicted stem-loop hairpin structure of miR475. The read count of sequences along the sequence is indicated using coloured shading.
Data
Genes with >100 Over-lapping siRNAs. short RNA distribution within genes having >100 over-lapping sequences. The frequency within the gene is shown on the plus strand (above) and the minus strand (below) the gene structure. Exons are shown as solid bars and introns as connecting lines. The size class (18-24 nt) frequency distribution is also shown.
Data
Frequency of starting base pairs for different classes of predicted miRNAs. The frequency of predicted miRNAs starting with an A, U, C or G for miRNA loci matching existing miRBase entries, not-matching and with predicted targets and not-matching with no predicted targets.