Jarkko Salojarvi

Jarkko Salojarvi
Nanyang Technological University | ntu · School of Biological Sciences

DSc (Tech)

About

193
Publications
39,824
Reads
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9,709
Citations
Citations since 2016
87 Research Items
7159 Citations
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201620172018201920202021202202004006008001,0001,200
201620172018201920202021202202004006008001,0001,200
201620172018201920202021202202004006008001,0001,200
Additional affiliations
October 2010 - present
University of Helsinki
Position
  • Researcher

Publications

Publications (193)
Article
Full-text available
Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly underst...
Article
Full-text available
SignificanceInterspecific hybridization is a widespread phenomenon, but measuring its extent, directionality, and adaptive importance remains challenging. Ancient genomes, however, can help illuminate the history of modern organisms. Here, we present a genome retrieved from a 130,000- to 115,000-y-old polar bear and perform genome analyses of moder...
Article
Full-text available
Sapindus is an important forest tree genus with utilization in biodiesel, biomedicine, and it harbors great potential for biochemical engineering applications. For advanced breeding of Sapindus, it is necessary to evaluate the genetic diversity and construct a rationally designed core germplasm collection. In this study, the genetic diversity and p...
Article
Full-text available
Vaccinium darrowii is a subtropical wild blueberry species, which was used to breed economically important southern highbush cultivars. The adaptation traits of V. darrowii to subtropical climates would provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembl...
Article
Full-text available
Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar ‘Feizixiao’ was assembled into 15 pseudochromosomes, totaling ~470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. Analyses of 72 resequenced lych...
Preprint
The polar bear ( Ursus maritimus ) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population...
Preprint
Full-text available
Inonotus obliquus, Chaga mushroom, is a fungal species from Hymenochaetaceae family (Basidiomycota) which has been widely used for traditional medicine in Europe and Asia. Here, chaga genome was sequenced using Pacbio sequencing into a 50.7Mbp assembly consisting of 301 primary contigs with an N50 value of 375 kbp. Genome evolution analyses reveale...
Preprint
Full-text available
Species radiations have long fascinated biologists, but the contribution of adaptation to observed diversity and speciation is still an open question. Here, we explore this question using the clove genus, Syzygium, the world’s largest genus of tree species comprising approximately 1200 species. We dissect Syzygium diversity through shotgun sequenci...
Preprint
Full-text available
Yeasts are important plant-associated organisms that can modulate host immunity to either promote or prevent disease. Mechanisms of plant-yeast interactions, specifically of yeast perception by the plant innate immune system, remain unknown. Progress has been hindered by the scarcity of yeast species associated with the model plant Arabidopsis thal...
Preprint
Polyploidization is a common event in plant evolution, and it plays an important role in plant speciation and adaptation. To address the role of polyploidization in grass diversification, we studied Phragmites australis, a species with intraspecific variation of chromosome numbers ranging from 2n=36 to 144. A combined analysis of genome structure,...
Preprint
Full-text available
Vaccinium darrowii is a subtropical wild blueberry species, which was used to breed economically important southern highbush cultivars. The adaptation traits of V. darrowii to subtropical climate would provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assemble...
Article
Full-text available
High levels of phenotypic variation in resistance appears to be nearly ubiquitous across natural host populations. Molecular processes contributing to this variation in nature are still poorly known, although theory predicts resistance to evolve at specific loci driven by pathogen-imposed selection. Nucleotide-binding leucine-rich repeat (NLR) gene...
Article
Full-text available
Inflammatory bowel diseases (IBD), ulcerative colitis (UC) and Crohn’s disease (CD), are chronic debilitating disorders of unknown etiology. Over 200 genetic risk loci are associated with IBD, highlighting a key role for immunological and epithelial barrier functions. Environmental factors account for the growing incidence of IBD, and microbiota ar...
Preprint
Full-text available
Guard cells regulate plant gas exchange by controlling the aperture of stomatal pores. Stomatal closure involves a multi-input signaling network that governs the activity of ion channels, which in turn regulate guard cell turgor pressure and volume. We describe a forward genetic screen to identify novel components involved in stomatal movements. Th...
Preprint
Full-text available
The photoreceptors UV RESISTANCE LOCUS 8 (UVR8) and CRYPTOCHROMES 1 and 2 (CRYs) play major roles in the perception of UV-B (280–315 nm) and UV-A/blue radiation (315–500 nm), respectively. However, it is poorly understood how they function in sunlight. The roles of UVR8 and CRYs were assessed in a factorial experiment with Arabidopsis thaliana wild...
Article
Tree architecture has evolved to support a top-heavy above-ground biomass, but this integral feature poses a weight-induced challenge to trunk stability. Maintaining an upright stem is expected to require vertical proprioception through feedback between sensing stem weight and responding with radial growth. Despite its apparent importance, the prin...
Article
Due to its ubiquity across northern latitudes, silver birch (Betula pendula Roth) is an attractive model species for studying geographical trait variation and acclimation capacity. Six birch provenances from 60 to 67°N across Finland were grown in a common garden and studied for provenance and genotype variation. We looked for differences in height...
Article
Full-text available
Plants optimize their growth and survival through highly integrated regulatory networks that coordinate defensive measures and developmental transitions in response to environmental cues. Protein phosphatase 2A (PP2A) is a key signaling component that controls stress reactions and growth at different stages of plant development, and the PP2A regula...
Article
Full-text available
The avocado, Persea americana , is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. a...
Article
Full-text available
In the version of this article initially published, there was a mistake in the calculation of the nucleotide mutation rate per site per generation: 1 × 10⁻⁹ mutations per site per generation was used, whereas 9.5 × 10⁻⁹ was correct. This error affects the interpretation of population-size changes over time and their possible correspondence with kno...
Preprint
Full-text available
The avocado, Persea americana , is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently-diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. a...
Preprint
Full-text available
The remarkable vertical and radial growth observed in tree species, encompasses a major physical challenge for wood forming tissues. To compensate with increasing size and weight, cambium-derived radial growth increases the stem width, thereby supporting the aerial body of trees. This feedback appears to be part of a so-called 'proprioception' (1,...
Preprint
Full-text available
We describe the genome contents of six Protomyces species that are pathogenic within the typical host range of the genus and a novel Protomyces strain (SC29) that was previously isolated from the phylloplane of wild Arabidopsis thaliana (Arabidopsis), an atypical host. Genome-wide phylogenetic analysis defined SC29 as a distinct Protomyces species....
Article
Full-text available
Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III....
Article
Full-text available
Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation. However, gene and genome duplications pose difficulties for functional characterization and translational research. Here we infer the evolutionary history of the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26...
Article
Full-text available
•Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem–environment barrier called periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in ter...
Article
The use of draft genomes of different species and re-sequencing of accessions and populations are now a common tool for plant biology research. The de novo assembled draft genomes make it possible to identify pivotal divergence points in the plant lineage and provide an opportunity to investigate the genomic basis and timing of biological innovatio...
Article
Full-text available
Reactive oxygen species (ROS) are key signalling intermediates in plant metabolism, defence, and stress adaptation. In plants, both the chloroplast and mitochondria are centres of metabolic control and ROS production, which coordinate stress responses in other cell compartments. The herbicide and experimental tool, methyl viologen (MV) induces ROS...
Preprint
Full-text available
Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation in plants. Here we infer the evolutionary history of a representative protein family, the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 first appeared in secreted proteins. Domain duplications and rearrangeme...
Article
Full-text available
Guard cells control the aperture of stomatal pores to balance photosynthetic carbon dioxide uptake with evaporative water loss. Stomatal closure is triggered by several stimuli that initiate complex signaling networks to govern the activity of ion channels. Activation of SLOW ANION CHANNEL1 (SLAC1) is central to the process of stomatal closure and...
Article
Guard cells control the aperture of stomatal pores to balance photosynthetic carbon dioxide uptake with evaporative water loss. Stomatal closure is triggered by several stimuli that initiate complex signaling networks to govern the activity of ion channels. Activation of SLOW ANION CHANNEL1 (SLAC1) is central to the process of stomatal closure and...
Preprint
Full-text available
Reactive oxygen species (ROS) are key signalling intermediates in plant metabolism, defence, and stress adaptation. The chloroplast and mitochondria are centres of metabolic control and ROS production, which coordinate stress responses in other cell compartments. The herbicide and experimental tool, methyl viologen (MV) induces ROS generation in th...
Article
Full-text available
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Article
Full-text available
Dogs are excellent animal models for human disease. They have extensive veterinary histories, pedigrees, and a unique genetic system due to breeding practices. Despite these advantages, one factor limiting their usefulness is the canine genome reference (CGR) which was assembled using a single purebred Boxer. Although a common practice, this result...
Preprint
Full-text available
Signaling from chloroplasts and mitochondria, both dependent on reactive oxygen species (ROS), merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). ROS produced in the chloroplasts affect the abundance, thiol redox state and oligomerization of RCD1. RCD1 directly interacts in vivo with ANAC013 and ANAC017 transcription factors, which ar...
Article
The cuticular wax layer on silver birch (Betula pendula Roth) leaves is rich in cyclic secondary metabolites that provide defense against various environmental factors. Micropropagated trees from the southern (60°N), central (62°N), and northern (66°N) latitudes of Finland were grown in a common garden setup and quantified for variation in leaf sur...
Article
The atmospheric pollutant ozone (O3) is a strong oxidant that causes extracellular reactive oxygen species (ROS) formation, has significant ecological relevance, and is used here as a non-invasive ROS inducer to study plant signalling. Previous genetic screens identified several mutants exhibiting enhanced O3-sensitivity, but few with enhanced tole...
Chapter
With the rapidly dropping costs of sequencing, it is now possible to study the genomes and populations of any species to obtain precise evidence about their evolution and adaptation. Here, we will give an overview of software tools for processing raw sequencing reads into population-level data, and then go through the common population genomics ana...
Article
The intestinal microbiota has been implicated in insulin resistance, although evidence regarding causality in humans is scarce. We therefore studied the effect of lean donor (allogenic) versus own (autologous) fecal microbiota transplantation (FMT) to male recipients with the metabolic syndrome. Whereas we did not observe metabolic changes at 18 we...
Chapter
Analysis of gene families and identification of homologous genes are important for phylogenetic analysis and for translating results from model to crop species. While numerous plant genomes have been sequenced and made available, the identification of gene models can be difficult, in particular for large gene families arranged in tandem repeats or...
Article
Full-text available
Plants adapt to the environment by either long-term genome evolution or by acclimatization processes where the cellular processes and metabolism of the plant are adjusted within the existing potential in the genome. Here we studied the adaptation strategies in date palm, Phoenix dactylifera, under mild heat, drought and combined heat and drought by...
Data
Significantly enriched GOs in different treatments. (XLSX)
Data
Enrichment analysis of the regulatory motifs among the differentially expressed genes in drought, heat, and combined heat and drought treatments. (XLSX)
Data
Differentially expressed genes encoding ROS and redox-related enzymes in heat, drought, or combined heat and drought treatments. (XLSX)
Data
Treemap of significantly enriched (Log2FC > 0) Gene Ontology terms in drought. (PDF)
Data
Treemap of significantly enriched (Log2FC > 0) Gene Ontology terms in heat. (PDF)
Data
Samples and their sequencing statistics. (XLSX)
Data
GO enrichment analysis of genes containing CCA1, light responsive, ABA, drought and sugar motifs in their promoter regions. (XLSX)
Data
Expressed genes (24504 genes) and their differential expression values. (XLSX)
Data
Differentially abundant metabolites in the heat, drought, and combined heat and drought treatments, and their annotations. (XLSX)
Data
Genes putatively associated with cell wall biogenesis and their differential expression. (XLSX)
Data
Putative orthologs genes from A. thaliana mapped to P. dactylifera, and tested for enrichment among the differentially expressed genes (abs(log2FC) ≥ 1) using Fisher exact test. (XLSX)
Data
Differentially expressed heat shock protein genes in drought, heat, and combined heat and drought experiments. (XLSX)
Data
Treemap of significantly enriched (Log2FC > 0) Gene Ontology terms in combined heat and drought. (PDF)
Article
Full-text available
Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from...