Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Abstract Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

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Growth ofPseudotsuga menziesiiandTsuga heterophyllaseedlings along a light gradient: resource allocation and morphological acclimation

Canadian Journal of Botany ◽

10.1139/b97-857 ◽

1997 ◽

Vol 75 (9) ◽

pp. 1424-1435 ◽

Cited By ~ 32

Author(s):

D. Mailly ◽

J. P. Kimmins

Keyword(s):

Leaf Morphology ◽

Biomass Accumulation ◽

Tsuga Heterophylla ◽

Douglas Fir ◽

Western Hemlock ◽

Low Light ◽

Growing Seasons ◽

Light Levels ◽

Light Gradient ◽

Relative Light Intensity

Silvicultural alternatives that differ in the degree of overstory removal may create shady environments that will be problematic for the regeneration of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco). Gradients of light in the field were used to compare mortality, growth, and leaf morphological acclimation of two conifer species of contrasting shade tolerances: Douglas-fir and western hemlock (Tsuga heterophylla (Raf.) Sarg.). Results after two growing seasons indicated that Douglas-fir mortality occurred mainly at relative light intensity (RLI) below 20%, while western hemlock mortality was evenly distributed along the light gradient. Height, diameter, and biomass of the planted seedlings increased with increasing light for both species but at different rates, and maximum biomass accumulation always occurred in the open. Douglas-fir allocated more resources to stem biomass than western hemlock, which accumulated more foliage biomass. Increases in specific leaf area for Douglas-fir seedlings occurred at RLI ≤ 0.4 and red/far red (R/FR) ratio ≤ 0.6, which appear to be the minimal optimum light levels for growth. Conversely, western hemlock seedlings adjusted their leaf morphology in a more regular pattern, and changes were less pronounced at low light levels. These results, along with early mortality results for Douglas-fir, suggest that the most successful way to artificially regenerate this species may be by allowing at least 20% of RLI for ensuring survival and at least 40% RLI for optimum growth. Key words: light, light quality, leaf morphology, acclimation.

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Transcriptional Profiling of Rapidly Growing Cucumber Fruit by 454-Pyrosequencing Analysis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.135.4.291 ◽

2010 ◽

Vol 135 (4) ◽

pp. 291-302 ◽

Cited By ~ 34

Author(s):

Kaori Ando ◽

Rebecca Grumet

Keyword(s):

Gene Expression ◽

454 Pyrosequencing ◽

Transcriptional Profiling ◽

Transcript Abundance ◽

Yield And Quality ◽

Cucumber Fruit ◽

Polymerase Chain ◽

Expressed Sequence ◽

Development Proceeds ◽

Insight Into

Fruit development proceeds from cell division to expansion, maturation, and ripening. Expansion is critical for size, yield, and quality; however, this period of development has received little attention. We used 454-pyrosequencing to develop a cucumber (Cucumis sativus) fruit transcriptome, identify highly expressed transcripts, and characterize key functions during exponential fruit growth. The resulting 187,406 expressed sequence tags (ESTs) were assembled into 13,878 contigs. Quantitative real-time polymerase chain reaction (qRT-PCR) verification of differentially expressed genes from fruit of different ages, and high correlation in transcript frequency between replicates, indicated that number of reads/contig reflects transcript abundance. Putative homologs were identified in Arabidopsis thaliana for 89% of the contigs represented by at least 10 ESTs; another 4% had homologs in other species. The remainder had homologs only in cucurbit species. The most highly expressed contigs were strongly enriched for growth (aquaporins, vacuolar ATPase, phloem proteins, tubulins, actins, cell wall-associated, and hormone-related), lipid, latex, and defense-related homologs. These results provide a resource for gene expression analysis in cucumber, profile gene expression in rapidly growing fruit, and shed insight into an important, but poorly characterized, developmental stage influencing fruit yield and quality.

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Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

Frontiers in Microbiology ◽

10.3389/fmicb.2021.740610 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ola Alessa ◽

Yoshitoshi Ogura ◽

Yoshiko Fujitani ◽

Hideto Takami ◽

Tetsuya Hayashi ◽

...

Keyword(s):

Comparative Genomics ◽

Phylogenetic Relationship ◽

Distinct Species ◽

Genotypic Differences ◽

Clade C ◽

Single Genus ◽

Almost All ◽

Type Strains ◽

Dependent Pathway ◽

Insight Into

The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.

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Asymmetric responses to simulated global warming by populations of Colobanthus quitensis along a latitudinal gradient

PeerJ ◽

10.7717/peerj.3718 ◽

2017 ◽

Vol 5 ◽

pp. e3718 ◽

Cited By ~ 7

Author(s):

Ian S. Acuña-Rodríguez ◽

Cristian Torres-Díaz ◽

Rasme Hereme ◽

Marco A. Molina-Montenegro

Keyword(s):

Global Warming ◽

Latitudinal Gradient ◽

Biomass Accumulation ◽

South Shetland Islands ◽

Plant Populations ◽

Colobanthus Quitensis ◽

Growing Seasons ◽

Long Term Experiment ◽

Foliar Traits ◽

The Antarctic

The increase in temperature as consequence of the recent global warming has been reported to generate new ice-free areas in the Antarctic continent, facilitating the colonization and spread of plant populations. Consequently, Antarctic vascular plants have been observed extending their southern distribution. But as the environmental conditions toward southern localities become progressively more departed from the species’ physiological optimum, the ecophysiological responses and survival to the expected global warming could be reduced. However, if processes of local adaptation are the main cause of the observed southern expansion, those populations could appear constrained to respond positively to the expected global warming. Using individuals from the southern tip of South America, the South Shetland Islands and the Antarctic Peninsula, we assess with a long term experiment (three years) under controlled conditions if the responsiveness of Colobanthus quitensis populations to the expected global warming, is related with their different foliar traits and photoprotective mechanisms along the latitudinal gradient. In addition, we tested if the release of the stress condition by the global warming in these cold environments increases the ecophysiological performance. For this, we describe the latitudinal pattern of net photosynthetic capacity, biomass accumulation, and number of flowers under current and future temperatures respective to each site of origin after three growing seasons. Overall, was found a clinal trend was found in the foliar traits and photoprotective mechanisms in the evaluated C. quitensis populations. On the other hand, an asymmetric response to warming was observed for southern populations in all ecophysiological traits evaluated, suggesting that low temperature is limiting the performance of C. quitensis populations. Our results suggest that under a global warming scenario, plant populations that inhabiting cold zones at high latitudes could increase in their ecophysiological performance, enhancing the size of populations or their spread.

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Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months

International Journal of Microbiology ◽

10.1155/2017/9547063 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 5

Author(s):

Floor Hugenholtz ◽

Jarmo Ritari ◽

Lotta Nylund ◽

Mark Davids ◽

Reetta Satokari ◽

...

Keyword(s):

Gut Microbiota ◽

Transcriptional Profiling ◽

Lactobacillus Rhamnosus ◽

Rna Seq ◽

Faecal Samples ◽

Carbohydrate Fermentation ◽

Stool Samples ◽

The Impact ◽

Increased Activity ◽

Insight Into

Newborns are rapidly colonized by microbes and their intestinal tracts contain highly dynamic and rapidly developing microbial communities in the first months of life. In this study, we describe the feasibility of isolating mRNA from rapidly processed faecal samples and applying deep RNA-Seq analysis to provide insight into the active contributors of the microbial community in early life. Specific attention is given to the impact of removing rRNA from the mRNA on the phylogenetic and transcriptional profiling and its analysis depth. A breastfed baby was followed in the first six months of life during adaptation to solid food, dairy products, and formula. It was found that, in the weaning period, the total transcriptional activity of Actinobacteria, mainly represented by Bifidobacterium, decreased while that of Firmicutes increased over time. Moreover, Firmicutes and Actinobacteria, including the canonical Bifidobacteria as well as Collinsella, were found to be important contributors to carbohydrate fermentation and vitamin biosynthesis in the infant intestine. Finally, the expression of Lactobacillus rhamnosus-like genes was detected, likely following transfer from the mother who consumed L. rhamnosus GG. The study indicates that metatranscriptome analysis of the infant gut microbiota is feasible on infant stool samples and can be used to provide insight into the core activities of the developing community.

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Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts

mBio ◽

10.1128/mbio.01577-21 ◽

2021 ◽

Author(s):

Samantha C. Waterworth ◽

Shirley Parker-Nance ◽

Jason C. Kwan ◽

Rosemary A. Dorrington

Keyword(s):

Comparative Genomics ◽

Host Range ◽

Narrow Range ◽

Marine Sponges ◽

Broad Host Range ◽

Symbiotic Relationships ◽

Globally Distributed ◽

Insight Into ◽

Sponge Symbionts

Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa ( Entoporibacteria , SAUL , and Tethybacterales ) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two.

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Comparative genomics insight into phytopathogenic Xanthomonas arboricola pathovar corylina strains

Journal of Anatolian Environmental and Animal Sciences ◽

10.35229/jaes.832315 ◽

2021 ◽

Author(s):

Şafak KALINDAMAR

Keyword(s):

Comparative Genomics ◽

Xanthomonas Arboricola ◽

Insight Into

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Bargaining with Asymmetric Dispute Costs

Review of Law & Economics ◽

10.1515/rle-2013-0030 ◽

2014 ◽

Vol 10 (1) ◽

Cited By ~ 6

Author(s):

Paul Pecorino ◽

Mark Van Boening

Keyword(s):

Asymmetric Distribution ◽

Total Surplus ◽

Experimental Subjects ◽

Asymmetrically Distributed ◽

Insight Into

AbstractWe conduct a bargaining experiment in a stylized litigation setting. In the baseline, dispute costs are divided equally between the two parties. There are two treatments with an asymmetric distribution of dispute costs. The design allows us to gain insight into how a fair offer evolves with the distribution of dispute costs. The amount of surplus in the average offer depends on the total amount of surplus available and not on the distribution of dispute costs. About 28% of the total surplus is contained in the average offer, regardless of the distribution of dispute costs. Based on the empirical rejection frequencies, we calculate that the optimal offer contains 13% of the total surplus from settlement. We also find evidence that disputes are more likely when dispute costs are asymmetrically distributed. This suggests that the experimental subjects have more difficulty coordinating on a fair offer when dispute costs are not symmetric.

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