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1. Prospects of pan-genomics in barley

Author:
Monat, Cécile; Schreiber, Mona; Stein, Nils; Mascher, Martin
Source:
Theoretical and applied genetics 2019 v.132 no.3 pp. 785-796
ISSN:
0040-5752
Subject:
Brachypodium distachyon,   etc   ; Hordeum vulgare; barley; bioinformatics; corn; evolution; gene banks; genes; genomics; genotype; grain crops; grasses; models; quantitative genetics; rice;     Show all 15 Subjects
Abstract:
... The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants. The large size and complex structure of Triticeae genomes were for a long time an obstacle for genomic research i ...
DOI:
10.1007/s00122-018-3234-z

2. Phylogenetic and expression analysis of histone acetyltransferases in Brachypodium distachyon

Author:
Tan, Shenglong; Gao, Lifen; Li, Tiantian; Chen, Lihong
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
Brachypodium distachyon,   etc   ; Magnoliopsida; abiotic stress; acetylation; eukaryotic cells; genes; histone acetyltransferase; histone deacetylase; histones; models; phylogeny; post-translational modification;     Show all 12 Subjects
Abstract:
... Histone acetylation is an important post-translational modification in eukaryotes and is regulated by two antagonistic enzymes, namely histone acetyltransferase (HAT) and histone deacetylase (HDAC). However, little has been done on the HAT superfamily in Brachypodium distachyon (B. distachyon), a new model plant of Poaceae. In this study, eight HATs were identified from B. distachyon and classifie ...
DOI:
10.1016/j.ygeno.2019.01.008

3. Brachypodium histone deacetylase BdHD1 positively regulates ABA and drought stress responses

Author:
Song, Jingpu; Henry, Hugh A.L.; Tian, Lining
Source:
Plant science 2019 v.283 pp. 355-365
ISSN:
0168-9452
Subject:
Brachypodium distachyon,   etc   ; RNA interference; abscisic acid; acetylation; drought; drought tolerance; gene overexpression; genes; histone deacetylase; phenotype; stress response; transcription factors; water stress;     Show all 13 Subjects
Abstract:
... Despite recent evidence that HDACs are involved in the environmental stress responses of plants, their roles in the abiotic stress responses of monocot plants remain largely unexplored. We investigated a HDAC gene, Bradi3g08060 (BdHD1), in Brachypodium distachyon. The Brachypodium BdHD1-overexpression plants displayed a hypersensitive phenotype to ABA and exhibited better survival under drought co ...
DOI:
10.1016/j.plantsci.2019.03.009

4. Genome-wide identification of Lysin-Motif Receptor-Like Kinase (LysM-RLK) gene family in Brachypodium distachyon and docking analysis of chitin/LYK binding

Author:
Tombuloglu, Guzin; Tombuloglu, Huseyin; Cevik, Emre; Sabit, Hussein
Source:
Physiological and molecular plant pathology 2019 v.106 pp. 217-225
ISSN:
0885-5765
Subject:
Brachypodium distachyon,   etc   ; Fusarium graminearum; chitin; enzymes; fungi; gene expression; genes; grains; host-pathogen relationships; immune response; models; pathogens; peptides; plasma membrane; proteins;     Show all 15 Subjects
Abstract:
... Lysin-Motif Receptor-Like Kinase (LysM-RLK) family proteins have critical function in plant-microbe interaction. During infection, common peptide domain of these proteins, namely LysM, interacts with bacterial gylcans or fungal chitins which triggers; (1) plant immune responses, (2) plant defense responses, or (3) plant-microorganism symbiotic interactions. Since pathogenic diseases cause severe a ...
DOI:
10.1016/j.pmpp.2019.03.002

5. Identification and molecular characterization of the Brachypodium distachyon NRT2 family, with a major role of BdNRT2.1

Author:
Wang, Jiang; Hüner, Norman; Tian, Lining
Source:
Physiologia plantarum 2019 v.165 no.3 pp. 498-510
ISSN:
0031-9317
Subject:
Brachypodium distachyon,   etc   ; Arabidopsis; ammonium; crops; gene expression; gene expression regulation; genes; genetically modified organisms; models; mutants; nitrates; nitrogen; transcription (genetics); transfer DNA; transporters;     Show all 15 Subjects
Abstract:
... The small monocot plant Brachypodium distachyon is rapidly emerging as a powerful model system to study questions unique to the monocot crops. An extensive BLAST search was carried to identify putative orthologues of the Arabidopsis NRT2 genes in the fully sequenced Brachypodium genome. Seven genes encoding putative high‐affinity nitrate transporters (BdNRT2) were identified. Transcriptional analy ...
DOI:
10.1111/ppl.12716

6. Lipo‐chitooligosaccharides promote lateral root formation and modify auxin homeostasis in Brachypodium distachyon

Author:
Buendia, Luis; Maillet, Fabienne; O'Connor, Devin; van de‐Kerkhove, Quitterie; Danoun, Saida; Gough, Clare; Lefebvre, Benoit; Bensmihen, Sandra
Source:
Thenew phytologist 2019 v.221 no.4 pp. 2190-2202
ISSN:
0028-646X
Subject:
Brachypodium distachyon,   etc   ; Medicago truncatula; genes; homeostasis; indole acetic acid; indole butyric acid; legumes; models; phenotype; root growth; roots; vesicular arbuscular mycorrhizae;     Show all 12 Subjects
Abstract:
... Lipo‐chitooligosaccharides (LCOs) are microbial symbiotic signals that also influence root growth. In Medicago truncatula, LCOs stimulate lateral root formation (LRF) synergistically with auxin. However, the molecular mechanisms of this phenomenon and whether it is restricted to legume plants are not known. We have addressed the capacity of the model monocot Brachypodium distachyon (Brachypodium) ...
DOI:
10.1111/nph.15551

7. Spatial and temporal distribution of cell wall polysaccharides during grain development of Brachypodium distachyon

Author:
Francin-Allami, Mathilde; Alvarado, Camille; Daniel, Sylviane; Geairon, Audrey; Saulnier, Luc; Guillon, Fabienne
Source:
Plant science 2019 v.280 pp. 367-382
ISSN:
0168-9452
Subject:
Brachypodium distachyon,   etc   ; arabinans; arabinoxylan; beta-glucans; cell walls; cellulose; chemical structure; developmental stages; endosperm; epitopes; grain crops; methylation; models; phylogeny; polygalacturonic acid; rice; seed development; testa; tissues; xyloglucans;     Show all 20 Subjects
Abstract:
... Brachypodium distachyon (Brachypodium) is now well considered as being a suitable plant model for studying temperate cereal crops. Its cell walls are phylogenetically intermediate between rice and poaceae, with a greater proximity to these latter. By microscopic and biochemical approaches, this work gives an overview of the temporal and spatial distribution of cell wall polysaccharides in the grai ...
DOI:
10.1016/j.plantsci.2018.12.018

8. Regulation of cell wall development in Brachypodium distachyon in vitro as affected by cytokinin and gas exchange

Author:
Mamedes-Rodrigues, T. C.; Batista, D. S.; Napoleão, T. A.; Fortini, E. A.; Cruz, A. C. F.; Costa, M. G. C.; Otoni, W. C.
Source:
Plant cell, tissue, and organ culture 2019 v.136 no.2 pp. 207-219
ISSN:
0167-6857
Subject:
Brachypodium distachyon,   etc   ; CCR1 receptor; antioxidants; benzyladenine; biosynthesis; cell walls; cellulose; cytokinins; enzyme activity; gas exchange; gene expression; genes; grasses; hyperhydricity; lignin; lignin content; models; peroxidases; transcription (genetics);     Show all 19 Subjects
Abstract:
... Brachypodium distachyon is successfully used as a model grass species. The present study used molecular and chemical approaches to investigate the effects of the addition of the cytokinin 6-benzyladenine (BA) and two levels of gas exchange on the transcriptional regulation of lignin biosynthesis in B. distachyon. It was observed that the control of lignin biosynthesis is affected by both BA and th ...
DOI:
10.1007/s11240-018-1506-6

9. The Brachypodium distachyon UGT Bradi5gUGT03300 confers type II fusarium head blight resistance in wheat

Author:
Gatti, M.; Cambon, F.; Tassy, C.; Macadre, C.; Guerard, F.; Langin, T.; Dufresne, M.
Source:
Plant pathology 2019 v.68 no.2 pp. 334-343
ISSN:
0032-0862
Subject:
Brachypodium distachyon,   etc   ; Fusarium graminearum; Fusarium head blight; Triticum aestivum; deoxynivalenol; fungi; genes; glucosylation; grain crops; host specificity; models; pathogens; transferases; transgenic plants; wheat;     Show all 15 Subjects
Abstract:
... Fusarium head blight (FHB), caused by fungi belonging to the Fusarium genus, is a widespread disease of wheat (Triticum aestivum) and other small‐grain cereal crops. The main causal agent of FHB, Fusarium graminearum, produces mycotoxins mainly belonging to type B trichothecenes, such as deoxynivalenol (DON), that can negatively affect humans, animals and plants. DON detoxification, mainly through ...
DOI:
10.1111/ppa.12941

10. Highly efficient generation of T-DNA insertion lines and isolation of flanking sequence tags (FSTs) of Brachypodium distachyon

Author:
Han, Hongjiang; Shen, Guoan; An, Tianyue; Song, Bo; Zhao, Suzhen; Qi, Xiaoquan
Source:
Plant biotechnology reports 2018 v.12 no.4 pp. 237-248
ISSN:
1863-5466
Subject:
Brachypodium distachyon,   etc   ; computer software; genomics; grasses; models; mutants; polymerase chain reaction; transfer DNA;     Show all 8 Subjects
Abstract:
... Brachypodium distachyon (Brachypodium) has been developed as a model system for the temperate grasses. Hence, establishing a large insertion mutant population and identifying T-DNA insertion sites are imperative for functional genomics studies. Currently, Brachypodium has an established T-DNA collection resource, but it is far less than needed. In addition, the conventional methods for the isolati ...
DOI:
10.1007/s11816-018-0489-4

11. Host status of Brachypodium distachyon to the cereal cyst nematode

Author:
CHEN, Chang-long; LIU, Shu-sen; LIU, Qian; NIU, Jun-hai; LIU, Pei; ZHAO, Jian-long; LIU, Zhi-yong; LI, Hong-jie; JIAN, Heng
Source:
Journal of integrative agriculture 2018 v.17 no.2 pp. 381-388
ISSN:
2095-3119
Subject:
Brachypodium distachyon,   etc   ; Heterodera avenae; cyst nematodes; fibrous roots; grain crops; inbred lines; juveniles; models; pathotypes; China;     Show all 10 Subjects
Abstract:
... Cereal cyst nematode (Heterodera avenae, CCN) distributes worldwide and has caused severe damage to cereal crops, and a model host will greatly aid in the study of this nematode. In this research, we assessed the sensitivity of 25 inbred lines of Brachypodium distachyon to H. avenae from Beijing, China. All lines of B. distachyon were infested by second-stage juveniles (J2s) of H. avenae from Daxi ...
DOI:
10.1016/S2095-3119(17)61745-3

12. BdACT2a encodes an agmatine coumaroyl transferase required for pathogen defence in Brachypodium distachyon

Author:
Carere, Jason; Powell, Jonathan; Fitzgerald, Timothy; Kazan, Kemal; Gardiner, Donald M.
Source:
Physiological and molecular plant pathology 2018 v.104 pp. 69-76
ISSN:
0885-5765
Subject:
Brachypodium distachyon,   etc   ; Fusarium pseudograminearum; agmatine; amides; anti-infective agents; coumaric acids; genes; mycelium; pathogens; spore germination; substrate specificity; transferases;     Show all 12 Subjects
Abstract:
... Plants have a variety of enzymes which help defend from pathogen attack by producing antimicrobial compounds. One of these enzymes, agmatine coumaroyl transferase (ACT) is responsible for producing hydroxycinnamic acid amides (HCAAs). In this study, we identified a tightly clustered group of ACT genes in Brachypodium distachyon responsive to Fusarium infection and functionally characterised one of ...
DOI:
10.1016/j.pmpp.2018.09.003

13. Global analysis of H3K4me3/H3K27me3 in Brachypodium distachyon reveals VRN3 as critical epigenetic regulation point in vernalization and provides insights into epigenetic memory

Author:
Huan, Qing; Mao, Zhiwei; Chong, Kang; Zhang, Jingyu
Source:
Thenew phytologist 2018 v.219 no.4 pp. 1373-1387
ISSN:
0028-646X
Subject:
Brachypodium distachyon,   etc   ; ambient temperature; chromatin; chronic exposure; dose response; epigenetics; flowering; genes; genome-wide association study; histones; photoperiod; vernalization;     Show all 12 Subjects
Abstract:
... Vernalization, the requirement of plants for long‐term exposure to low environmental temperature for flowering, is an epigenetic phenomenon. Histone modification regulation has been revealed in vernalization, but is limited to key genes. Now, we know that VRN1 is epigenetically critical for monocots. Genome‐wide analysis is still unavailable, however. We performed chromatin immunoprecipitation‐seq ...
DOI:
10.1111/nph.15288

14. Silicon affects seed development and leaf macrohair formation in Brachypodium distachyon

Author:
Głazowska, Sylwia; Murozuka, Emiko; Persson, Daniel P.; Castro, Pedro Humberto; Schjoerring, Jan K.
Source:
Physiologia plantarum 2018 v.163 no.2 pp. 231-246
ISSN:
0031-9317
Subject:
Brachypodium distachyon,   etc   ; abiotic stress; awns; bioenergy; biomass; grasses; leaves; lignocellulose; mutants; seed development; seed weight; shoots; silicon; spectroscopy; tissues;     Show all 15 Subjects
Abstract:
... Silicon (Si) has many beneficial effects in plants, especially for the survival from biotic and abiotic stresses. However, Si may negatively affect the quality of lignocellulosic biomass for bioenergy purposes. Despite many studies, the regulation of Si distribution and deposition in plants remains to be fully understood. Here, we have identified the Brachypodium distachyon mutant low‐silicon 1 (B ...
DOI:
10.1111/ppl.12675

15. Downy Brome (Bromus tectorum) Vernalization: Variation and Genetic Controls

Author:
Lawrence, Nevin C.; Hauvermale, Amber L.; Burke, Ian C.
Source:
Weed science 2018 v.66 no.3 pp. 310-316
ISSN:
0043-1745
Subject:
Brachypodium distachyon,   etc   ; Bromus tectorum; annuals; flowering; genes; grasses; greenhouse experimentation; phenology; temporal variation; vernalization; weed science; winter; North America;     Show all 13 Subjects
Abstract:
... Downy brome (Bromus tectorum L.) is a widely distributed invasive winter annual grass across western North America. Bromus tectorum phenology can vary considerably among populations, and those differences are considered adaptively significant. A consensus hypothesis in the literature attributes the majority of observed differences in B. tectorum phenology to differing vernalization requirements am ...

16. Intact leaf gas exchange provides a robust method for measuring the kinetics of stomatal conductance responses to abscisic acid and other small molecules in Arabidopsis and grasses

Author:
Ceciliato, Paulo H. O.; Zhang, Jingbo; Liu, Qing; Shen, Xin; Hu, Honghong; Liu, Chen; Schäffner, Anton R.; Schroeder, Julian I.
Source:
Plant methods 2019 v.15 no.1 pp. 38
ISSN:
1746-4811
Subject:
Brachypodium distachyon,   etc   ; Arabidopsis; abscisic acid; aquaporins; carbon dioxide; dose response; flagellin; gas exchange; grasses; guard cells; leaves; light intensity; mesophyll; mutants; peptides; phenotype; plasma membrane; relative humidity; stomata; stomatal conductance; stomatal movement;     Show all 21 Subjects
Abstract:
... BACKGROUND: Guard cells perceive external and internal stimuli and regulate stomatal conductance in plants. With the use of gas exchange analyzers, time-resolved stomatal conductance responses to light intensity, [CO₂] concentration and relative humidity changes can be measured. This is more difficult to achieve when measuring stomatal responses to small soluble molecules such as the plant hormone ...
DOI:
10.1186/s13007-019-0423-y

17. Genomic dissection and transcriptional profiling of Cysteine-rich receptor-like kinases in five cereals and functional characterization of TaCRK68-A

Author:
Shumayla,; Tyagi, Shivi; Sharma, Alok; Singh, Kashmir; Upadhyay, Santosh Kumar
Source:
International journal of biological macromolecules 2019 v.134 pp. 316-329
ISSN:
0141-8130
Subject:
Brachypodium distachyon,   etc   ; Escherichia coli; Hordeum vulgare; Oryza sativa; Saccharomyces cerevisiae; Sorghum bicolor; Triticum aestivum; cold; drought; exons; gene duplication; genomics; grains; heat; hybridization; introns; phosphotransferases (kinases); phylogeny; plant development; plasma membrane; proteins; salt stress; stress response; transcription (genetics);     Show all 24 Subjects
Abstract:
... Cysteine-rich receptor-like kinases (CRK) constitute one of the largest subfamily of receptor-like kinases, which play crucial roles in plant development and stress response. In total, 43, 37, 36, 38 and 170 CRK genes including duplicated genes were identified in the genome of Brachypodium distachyon, Hordeum vulgare, Oryza sativa, Sorghum bicolor and Triticum aestivum, respectively. These CRK pro ...
DOI:
10.1016/j.ijbiomac.2019.05.016

18. Genome-wide identification, phylogeny and expression profiling of class III peroxidases gene family in Brachypodium distachyon

Author:
Zhu, Ting; Xin, Fang; Wei, ShuWei; Liu, Yue; Han, YuCui; Xie, Jiao; Ding, Qin; Ma, LingJian
Source:
Gene 2019 v.700 pp. 149-162
ISSN:
0378-1119
Subject:
Brachypodium distachyon,   etc   ; abiotic stress; amino acid sequences; biotic stress; chromosomes; gene expression; gibberellins; hydrogen peroxide; multigene family; peroxidases; phylogeny; plant hormones; protein-protein interactions; quantitative polymerase chain reaction; roots; transcriptome;     Show all 16 Subjects
Abstract:
... Class III peroxidases are classical secretory plant peroxidases belonging to a large multi-gene family. Class III peroxidases are involved in various physical processes and the response to biotic and abiotic stress to protect plants from environmental adversities. In this study, 151 BdPrx genes were identified using HMM and Blastp program. According to their physical location, the 151 BdPrx genes ...
DOI:
10.1016/j.gene.2019.02.103

19. One-Pot Multienzymatic Transformation of NH₃, CO₂, and Ornithine into the Organic Nitrogen Plant Fertilizer Citrulline Using a Single Recombinant Lysate of E. coli

Author:
Alissandratos, Apostolos; Hartley, Carol J.; French, Nigel G.; Kim, Hye-Kyung; Allen, Susan; Estavillo, Gonzalo M.; Scott, Colin; Easton, Christopher J.
Source:
ACS sustainable chemistry & engineering 2019 v.7 no.9 pp. 8522-8529
ISSN:
2168-0485
Subject:
Brachypodium distachyon,   etc   ; Escherichia coli; acetate kinase; adenosine triphosphate; ammonia; aqueous solutions; bacterial culture; biocatalysis; biocatalysts; carbon dioxide; citrulline; cost effectiveness; feedstocks; grasses; nitrogen fertilizers; ornithine; phosphates; pollutants; pollution control; protein synthesis; wheat;     Show all 21 Subjects
Abstract:
... Biocatalytic transformation of carbamate formed readily from CO₂ and NH₃ provides attractive green routes for mitigation of these important environmental pollutants. Accordingly, a coupled-enzyme system was developed for the one-pot production of citrulline through carbamoylation of ornithine in aqueous solutions of CO₂ and NH₃. Hyperthermophilic ornithine carbamoyltransferases are produced recomb ...
DOI:
10.1021/acssuschemeng.9b00301

20. Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

Author:
Mandadi, Kranthi K.; Scholthof, Karen-Beth G.
Source:
The plant cell 2015 v.27 no.1 pp. 71-85
ISSN:
1040-4651
Subject:
Brachypodium distachyon,   etc   ; alternative splicing; genes; landscapes; viruses;     Show all 5 Subjects
Abstract:
... Virus infection altered alternative splicing in >100 Brachypodium distachyon defense-related genes, with little effect on the genome-wide ratios of different splicing types. ...
DOI:
10.1105/tpc.114.133991
PubMed:
25634987
PubMed Central:
PMC4330581