Genomic Signatures of Specialized Metabolism in Plants

Chae, Lee; Kim, Taehyong; Nilo-Poyanco, Ricardo; Rhee, Seung Y.

doi:10.1126/science.1252076

Cited by 263 publications

(265 citation statements)

References 51 publications

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“…Adaptations possibly related to the arborescent habit were visible in convergent tandem expansions shared by B. pendula and Populus trichocarpa, including genes associated with fungal pathogen defense, cell wall biogenesis, and cellulose synthase activity (Supplementary Tables 11 and 12). Through evolutionary information stored within single genomes, these results suggest that whereas polyploid duplicates tend to diversify core processes in developmental and physiological regulation, tandem duplicates enhance the diversity of a plant's environmental response capacity, which is in concurrence with previous studies 15,17,18 .…”

supporting

confidence: 88%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

246

253

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Forest ecosystems maintain a large share of Northern Hemisphere biodiversity. Boreal forests comprise roughly 30% of global forest area 1 and contain the highest tree density among climate zones 2 . Moreover, boreal regions are undergoing extensive climate change. Annual temperature increases exceeding 1.5 °C are projected to result in a warming of 4-11 °C by the end of this century, with little concomitant increase in precipitation 1 . At this pace, climate zones will shift northward at a greater speed than trees can migrate 3 . To understand how future populations of forest trees may respond to climate change, it is essential to uncover past and present signatures of molecular adaptation in their genomes. Silver birch, B. pendula, is a pioneer species in boreal forests of Eurasia. Flowering of the species can be artificially accelerated 4 , giving it an advantage over other tree species with published genome sequences (such as poplar 5 , spruce 6 , and pine 7 ) for the optimization of fiber and biomass production.Here we sequenced 150 birch individuals and assembled a B. pendula reference genome from a fourth-generation inbred line, resulting in a high-quality assembly of 435 Mb that was linked to chromosomes using a dense genetic map. We analyzed SNPs in the genomes of 80 birch individuals spanning most of the geographic range of B. pendula, as well as seven other members of Betulaceae. Population genomic analyses of these data provide insights into the deep-time evolution of the birch family and on recent natural selection acting on silver birch.Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch 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 the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightlylinked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.A full list of affiliations appears at the end of the paper.

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supporting

confidence: 88%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

246

253

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“…For example, Chae et al (39) compared the clustering of secondary metabolism among 16 unrelated plant genomes and recognized a significant presence of clustering among secondary metabolism pathways, especially of terpenoid, phenylpropanoid, and nitrogen-containing compounds, depending on the plant family member analyzed.…”

Section: Resultsmentioning

confidence: 99%

The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii

Itkin

Davidovich‐Rikanati

Cohen

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

152

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The consumption of sweeteners, natural as well as synthetic sugars, is implicated in an array of modern-day health problems. Therefore, natural nonsugar sweeteners are of increasing interest. We identify here the biosynthetic pathway of the sweet triterpenoid glycoside mogroside V, which has a sweetening strength of 250 times that of sucrose and is derived from mature fruit of luo-han-guo (Siraitia grosvenorii, monk fruit). A whole-genome sequencing of Siraitia, leading to a preliminary draft of the genome, was combined with an extensive transcriptomic analysis of developing fruit. A functional expression survey of nearly 200 candidate genes identified the members of the five enzyme families responsible for the synthesis of mogroside V: squalene epoxidases, triterpenoid synthases, epoxide hydrolases, cytochrome P450s, and UDP-glucosyltransferases. Protein modeling and docking studies corroborated the experimentally proven functional enzyme activities and indicated the order of the metabolic steps in the pathway. A comparison of the genomic organization and expression patterns of these Siraitia genes with the orthologs of other Cucurbitaceae implicates a strikingly coordinated expression of the pathway in the evolution of this species-specific and valuable metabolic pathway. The genomic organization of the pathway genes, syntenously preserved among the Cucurbitaceae, indicates, on the other hand, that gene clustering cannot account for this novel secondary metabolic pathway.

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“…Spatial relationships within the genome can sometimes indicate functional relationships (Chae et al, 2014;Wisecaver et al, 2017). This viewer can be used to quickly determine the physical location of coexpressed genes, for instance.…”

Section: Chromosome Viewermentioning

confidence: 99%

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

et al. 2017

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A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research

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Genomic Signatures of Specialized Metabolism in Plants

Cited by 263 publications

References 51 publications

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

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