A binary search approach to whole-genome data analysis

Brodsky, Leonid; Kogan, Simon; Ben‐Jacob, Eshel; Nevo, Eviatar

doi:10.1073/pnas.1011134107

Cited by 8 publications

(12 citation statements)

References 13 publications

(22 reference statements)

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“…The whole-genome interslope divergence showed up-regulation of drought resistance genes on the AS = SFS and shade resistance and up-regulation of photosynthetic genes on the ES = NFS (69). The method of whole-genome analysis (70) showed the following gene ontology results on the AS = SFS drought-stressful slope: the blue light signaling pathway, circadian rhythm, ethylene-mediated genes, leaf development, protein amino acid phosphorylation, RNA splicing, and transcribed transposon development. In addition, more heat-response genes are activated at the AS = SFS as well as a fivefold increase in flower development (69).…”

Section: Resultsmentioning

confidence: 99%

“Evolution Canyon,” a potential microscale monitor of global warming across life

Nevo

2012

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

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Climatic change and stress is a major driving force of evolution. The effects of climate change on living organisms have been shown primarily on regional and global scales. Here I propose the "Evolution Canyon" (EC) microscale model as a potential life monitor of global warming in Israel and the rest of the world. The EC model reveals evolution in action at a microscale involving biodiversity divergence, adaptation, and incipient sympatric speciation across life from viruses and bacteria through fungi, plants, and animals. The EC consists of two abutting slopes separated, on average, by 200 m. The tropical, xeric, savannoid, "African" south-facing slope (AS = SFS) abuts the forested "European" north-facing slope (ES = NFS). The AS receives 200-800% higher solar radiation than the ES. The ES represents the south European forested maquis. The AS and ES exhibit drought and shade stress, respectively. Major adaptations on the AS are because of solar radiation, heat, and drought, whereas those on the ES relate to light stress and photosynthesis. Preliminary evidence suggests the extinction of some European species on the ES and AS. In Drosophila, a 10-fold higher migration was recorded in 2003 from the AS to ES. I advance some predictions that could be followed in diverse species in EC. The EC microclimatic model is optimal to track global warming at a microscale across life from viruses and bacteria to mammals in Israel, and in additional ECs across the planet.climate and evolution | species extinction | climate impact | adaptive response | natural selection C limate variation and change are major abiotic stresses driving life's evolution (1-22). Parmesan and Yohe (9), analyzing results for 1,700 species, showed that recent biological trends match climate-change predictions. Global meta-analyses documented significant range shifts averaging 6.1 km per decade northward (or 6.1 m per decade upward) and significant mean advancement of spring events by 2.3 d per decade. A significant globally coherent fingerprint of climate change across natural systems was identified for 289 species (9). Parmesan (7) reviewed evidence of climate change indicating that climate change is already affecting living systems in diverse perspectives, including phenological changes, species interactions, range shifts, contractions and abundance, elevation shifts, marine communities' shifts, pest and disease shifts, tree-line patterns, extinctions, and evolutionary genetic and plasticity changes. New concerns have been raised about the ability of the earth's biodiversity of plants and animals to maintain a viable foothold on the planet if temperatures continue to rise. (See ref. 21 for an alternative point of view). In a recent review on global warming, during the last three decades in wild cereals, the progenitors of cultivated wheat and barley showed earliness in flowering time and in genetic changes (22) and global decline in cultivars' crops (19). Rapid range shifts of species are associated with high levels of climate warming, shifting to ...

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Section: Resultsmentioning

confidence: 99%

“Evolution Canyon,” a potential microscale monitor of global warming across life

Nevo

2012

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

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“…A similar approach should be useful in many crop systems. Future studies of this type can with current and emerging technologies include consideration of the whole genome by complete analysis of whole‐genome sequences (Brodsky et al ., ).…”

Section: Study Of Adaptation To Climate Under Natural Selection As a mentioning

confidence: 97%

“…Recent advances in DNA sequencing technology (Brodsky et al ., ; Loman et al ., ) make whole‐genome analysis (Bilsborough, ) of plant populations more feasible. This technology is being applied to the study of genetic variation within the gene pools of cultivated crop species (Xu et al ., ).…”

Section: Advances In Tools Suitable For Analysis Of Genome‐wide Adaptmentioning

confidence: 98%

Exploring natural selection to guide breeding for agriculture

Henry

Nevo

2014

Plant Biotechnology Journal

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Summary Climate change threatens reduced crop production and poses major challenges to food security. The breeding of climate‐resilient crop varieties is increasingly urgent. Wild plant populations evolve to cope with changes in their environment due to the forces of natural selection. This adaptation may be followed over time in populations at the same site or explored by examining differences between populations growing in different environments or across an environmental gradient. Survival in the wild has important differences to the objective of agriculture to maximize crop yields. However, understanding the nature of adaptation in wild populations at the whole genome level may suggest strategies for crop breeding to deliver agricultural production with more resilience to climate variability.

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“…Detection of new putative transcripts (the analysis was performed only for samples of the GEO accession number data set) was based on the BS segmentation algorithm (Brodsky, Kogan, Benjacob, & Nevo, ), which detects genomic fragments significantly enriched by the read mapping counts. New putative transcripts were annotated using Blast2Go (with BLASTx as a search engine) (Conesa & Götz, ; Conesa et al., ; Götz et al., ).…”

Section: Methodsmentioning

confidence: 99%

Adaptation of the pine fungal pathogen Grosmannia clavigera to monoterpenes: Biochemical mechanisms revealed by RNA‐seq analysis

et al. 2017

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SummaryThe blue stain fungus Grosmannia clavigera (G. clavigera) is a pathogen of pines that can tolerate monoterpenes in oleoresin. Grosmannia clavigera has developed several mechanisms to cope with the host's monoterpene defence: a monoterpene efflux system mediated by an ABC transporter and enzymes that utilize or modify monoterpenes. In this study, we integrated two expression data sets based on a match between their multidimensional distributions. The data sets are raw RNA-seq and already processed transcriptome expression data with partially matching biological conditions. As a result, several new regulatory mechanisms, including the upregulation of the stress response and the developmental process at early-time-point terpene treatment, were involved in the adaptation of G. clavigera to monoterpenes and were supported by both data sets. In addition, several genes related to terpenoid modification were upregulated within 36 h (in rich media) and 7 days (in poor media) of terpene treatment. These results led us to the assumption that G. clavigera used terpenes as an energy source within 7 days when no other energy source was available, while within 36 h of terpene treatment on rich media these genes took part in terpene detoxification. As the G. clavigera genome is not well annotated, we performed detection of new putative transcripts as genome fragments enriched by read mapping. Several newly detected transcripts annotated as putative retrotransposons were upregulated mostly under early-time-point terpene treatment, while others annotated as putative ribonuclease and protease were downregulated mostly during early-time-point terpene treatment. Based on these results, it can be hypothesized that these new transcripts could play a role in previously unidentified G. clavigera terpene response regulatory mechanisms. Overall, this study identified gene expression regulations supported by two data sets as well as new putative transcripts related to new processes that might be important for G. clavigera tolerance to terpenes.

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A binary search approach to whole-genome data analysis

Cited by 8 publications

References 13 publications

“Evolution Canyon,” a potential microscale monitor of global warming across life

“Evolution Canyon,” a potential microscale monitor of global warming across life

Exploring natural selection to guide breeding for agriculture

Adaptation of the pine fungal pathogen Grosmannia clavigera to monoterpenes: Biochemical mechanisms revealed by RNA‐seq analysis

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