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82 results for “monocot”
Fig. 4 in Specialized diterpenoid metabolism in monocot crops: Biosynthesis and chemical diversity
Fig. 4. Diterpenoid metabolism in wheat. Overview of the established modular diterpenoid-metabolic network in wheat (Triticum aestivum), involving the conversion of the central precursor geranylgeranyl diphosphate (GGDP) through the combined activity of class II diterpene synthases (green boxes) and class I diterpene synthases (blue boxes). Representative pathway intermediates are highlighted. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Specialized diterpenoid metabolism in monocot crops: Biosynthesis and chemical diversity
Fig. 2. Diterpenoid metabolism in rice. Overview of the established modular diterpenoid-metabolic network in rice (Oryza sativa), involving the conversion of the central precursor geranylgeranyl diphosphate (GGDP) through the combined activity of class II diterpene synthases (green boxes), class I diterpene synthases (blue boxes), cytochrome P450 monooxygenases (orange) and select other enzyme classes (pink). Representative pathway intermediates and end products are highlighted. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Specialized diterpenoid metabolism in monocot crops: Biosynthesis and chemical diversity
Fig. 1. Size and functional diversity of diterpene synthase families in Poaceous crops. (A) Genome size (grey) and number of demonstrated or predicted diterpene synthases (diTPSs; black) in selected Poaceous crop species. Genome sizes were retrieved from public repositories (https://phytozome.jgi.doe.gov/; https://www.maizegdb.org/; http://www.gramene.org/). (B) Presence of functionally characterized Poaceous class II diTPSs involved in general (black circles), specialized (white circles), and general and/or specialized (grey circles) metabolism. Triangles represent class I diTPSs shown to function in combination with individual class II diTPSs in in vitro or in vivo activity assays.
Fig. 3 in Specialized diterpenoid metabolism in monocot crops: Biosynthesis and chemical diversity
Fig. 3. Diterpenoid metabolism in maize. Overview of the established modular diterpenoid-metabolic network in maize (Zea mays), involving the conversion of the central precursor geranylgeranyl diphosphate (GGDP) through the combined activity of class II diterpene synthases (green boxes), class I diterpene synthases (blue boxes), cytochrome P450 monooxygenases (orange) and select other enzyme classes (pink). Representative pathway intermediates and end products are highlighted. KA, A-series kauralexins 1-4; KB, B-series kauralexins 1-4. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Data from: A pre-Miocene Irano-Turanian cradle: origin and diversification of the species-rich monocot genus Gagea (Liliaceae)
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Tunicate bulb size variation in monocots explained by temperature and phenology
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Data from: Geophytism in monocots leads to higher rates of diversification
● Geophytes, plants with buds on underground structures, are found throughout the plant tree of life. These below ground structures allow plants to inhabit highly seasonal and disturbance-prone environments across ecosystems. Past researchers have hypothesized the bulbous, cormous and tuberous habits promote diversification, but this had yet to be tested. ● Using a comprehensive monocot data set of almost 13,000 taxa, we investigated the effects of the geophytic habit on diversification using both state-dependent and state-independent models. ● We found that geophytes exhibit increased rates of diversification relative to non-geophytes. State-dependent analyses recovered higher yet similar rates of diversification for bulbous, cormous and tuberous taxa compared to rhizomatous and non-geophytic taxa. However, the state-independent model returned no difference in rates among the different traits. ● Geophytism shows higher rates of diversification relative to non-geophytes but we find little support for the hypothesis that the evolution of the bulb, corm or tuber appears to provide a diversification increase relative to rhizomatous and non-geophytic taxa. Our broad scale analysis highlights the overall evolutionary importance of the geophytic habit (i.e., belowground bud placement). However, our results also suggest that belowground morphological diversity alone cannot explain this rate increase. In order to further test the evolutionary significance of these underground structures, future studies should consider them in combination with other biotic and abiotic factors.
Data from: Exploitation of interspecific diversity for monocot crop improvement
In many cultivated crop species there is limited genetic variation available for the development of new higher yielding varieties adapted to climate change and sustainable farming practises. The distant relatives of crop species provide a vast and largely untapped reservoir of genetic variation for a wide range of agronomically important traits that can be exploited by breeders for crop improvement. In this paper, in what we believe to be the largest introgression programme undertaken in the monocots, we describe the transfer of the entire genome of Festuca pratensis into Lolium perenne in overlapping chromosome segments. The L. perenne/F. pratensis introgressions were identified and characterised via 131 simple sequence repeats and 1612 SNPs anchored to the rice genome. Comparative analyses were undertaken to determine the syntenic relationship between L. perenne/F. pratensis and rice, wheat, barley, sorghum and Brachypodium distachyon. Analyses comparing recombination frequency and gene distribution indicated that a large proportion of the genes within the genome are located in the proximal regions of chromosomes which undergo low/very low frequencies of recombination. Thus, it is proposed that past breeding efforts to produce improved varieties have centred on the subset of genes located in the distal regions of chromosomes where recombination is highest. The use of alien introgression for crop improvement is important for meeting the challenges of global food supply and the monocots such as the forage grasses and cereals, together with recent technological advances in molecular biology, can help meet these challenges.
A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae
<p>Premise</p> <p>Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated: (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) integration of plastome data from off-target reads with existing plastome datasets; and (4) how do the novel inferencescoincide with infra-familial classification </p> <p>Methods</p> <p>We generated two large datasets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid dataset was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees, and also usingmaximum likelihood analyzes from concatenated and partitioned data.</p> <p>Results</p> <p>The nuclear, plastome, and extended-plastid datasets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling made for the order to date, which includes seven never-before sequenced genera.</p> <p>Conclusions</p> <p>We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered a Pontederiaceae-Haemodoraceae and a Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes synonymization of <em>Tapheocarpa </em>in <em>Commelina.</em></p>
Data from: Exploitation of interspecific diversity for monocot crop improvement
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Data from: Geophytism in monocots leads to higher rates of diversification
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Ground tissue circuitry regulates organ complexity in monocot roots [root meristem scRNA-seq]
GEO Series GSE173087. Zea mays. 9 samples. Type: Expression profiling by high throughput sequencing.
Novel resources to investigate leaf plasmodesmata formation in C3 and C4 monocots
GEO Series GSE260855. Setaria viridis; Oryza sativa. 38 samples. Type: Expression profiling by high throughput sequencing.
Ground tissue circuitry regulates organ complexity in monocot roots [roottissues]
GEO Series GSE172280. Zea mays. 24 samples. Type: Expression profiling by high throughput sequencing.
Ground tissue circuitry regulates organ complexity in monocot roots [slices]
GEO Series GSE172277. Zea mays. 32 samples. Type: Expression profiling by high throughput sequencing.
Draft assemblies of the bacterium Orrella dioscoreae recovered from herbarium samples of the monocot Dioscorea sansibarensis
<p>Annotated <em>d</em><em>e novo</em> genome assemblies of the bacterium <em>Orrella dioscoreae</em> derived from metagenomic shotgun sequencing of leaf glands collected from herbarium samples of the monocot <em>Dioscorea sansibarensis</em>. </p>
Data from: Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica
We present the first phylogenomic analysis of relationships among all ten families of Liliales, based on 75 plastid genes from 35 species in 29 genera, and 97 additional plastomes stratified across angiosperm lineages. We used a supermatrix approach to extend our analysis to 58 of 64 genera of Liliales, and calibrated the resulting phylogeny against 17 fossil dates to produce a new timeline for monocot evolution. Liliales diverged from other monocots 124 Mya and began splitting into separate families 113 Mya. Our data support an Australian origin for Liliales, with close relationships between three pairs of lineages (Corsiaceae/Campynemataceae, Philesiaceae/Ripogonaceae, tribes Alstroemerieae/Luzuriageae) in South America and Australia or New Zealand reflecting teleconnections of these areas via Antarctica. Long-distance dispersal (LDD) across the Pacific and Tasman Sea led to re-invasion of New Zealand by two lineages (Luzuriaga, Ripogonum); LDD allowed Campynemanthe to colonize New Caledonia after its submergence until 37 Mya. LDD permitted Colchicaceae to invade East Asia and Africa from Australia, and re-invade Africa from Australia. Periodic desert greening permitted Gloriosa and Iphigenia to colonize Southeast Asia overland from Africa, and Androcymbium–Colchicum to invade the Mediterranean from South Africa. Melanthiaceae and Liliaceae crossed the Bering land-bridge several times from the Miocene to the Pleistocene.
Data from: Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica
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Ground tissue circuitry regulates organ complexity in monocot roots
GEO Series GSE172302. Zea mays. 65 samples. Type: Expression profiling by high throughput sequencing.
FIGURE. Monocots. A. Scaphyglottis crurigera, B. Scaphyglottis hondurensis, C. Scaphyglottis imbricata, D. Sobralia decora, E. Specklinia marginata, F. Stanhopea martiana, G. Stanhopea tigrina, H in Mexican Vascular Epiphytes: Richness and Distribution
FIGURE. Monocots. A. Scaphyglottis crurigera, B. Scaphyglottis hondurensis, C. Scaphyglottis imbricata, D. Sobralia decora, E. Specklinia marginata, F. Stanhopea martiana, G. Stanhopea tigrina, H. Trichocentrum andreanum. (Photographs by Adolfo Espejo- Serna).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.