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Plant genomics

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https://www.readbyqxmd.com/read/27924923/genome-wide-analysis-of-phosphoenolpyruvate-carboxylase-gene-family-and-their-response-to-abiotic-stresses-in-soybean
#1
Ning Wang, Xiujuan Zhong, Yahui Cong, Tingting Wang, Songnan Yang, Yan Li, Junyi Gai
Phosphoenolpyruvate carboxylase (PEPC) plays an important role in assimilating atmospheric CO2 during C4 and crassulacean acid metabolism photosynthesis, and also participates in various non-photosynthetic processes, including fruit ripening, stomatal opening, supporting carbon-nitrogen interactions, seed formation and germination, and regulation of plant tolerance to stresses. However, a comprehensive analysis of PEPC family in Glycine max has not been reported. Here, a total of ten PEPC genes were identified in soybean and denominated as GmPEPC1-GmPEPC10...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924540/targeting-fumonisin-biosynthetic-genes
#2
Robert H Proctor, Martha M Vaughan
The fungus Fusarium is an agricultural problem because it can cause disease on most crop plants and can contaminate crops with mycotoxins. There is considerable variation in the presence/absence and genomic location of gene clusters responsible for synthesis of mycotoxins and other secondary metabolites among species of Fusarium. Here, we describe a quantitative real-time PCR (qPCR) method for distinguishing between and estimating the biomass of two closely related species, F. proliferatum and F. verticillioides, that are pathogens of maize...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924130/stable-plastid-transformation-in-scoparia-dulcis-l
#3
Narra Muralikrishna, Kota Srinivas, Kalva Bharath Kumar, Abbagani Sadanandam
In the present investigation we report stable plastid transformation in Scoparia dulcis L., a versatile medicinal herb via particle gun method. The vector KNTc, harbouring aadA as a selectable marker and egfp as a reporter gene which were under the control of synthetic promoter pNG1014a, targets inverted repeats, trnR/trnN of the plastid genome. By use of this heterologous vector, recovery of transplastomic lines with suitable selection protocol have been successfully established with overall efficiency of two transgenic lines for 25 bombarded leaf explants...
October 2016: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/27924129/interplay-of-genes-in-plant-pathogen-interactions-in-planta-expression-and-docking-studies-of-a-beta-1-3-glucanase-gene-from-piper-colubrinum-and-a-glucanase-inhibitor-gene-from-phytophthora-capsici
#4
K Johnson George, O Rosana Babu, I P Vijesh Kumar, J Santhosh Eapen, M Anandaraj
Oomycete pathogen, Phytophthora capsici is devastating for black pepper (Piper nigrum L.) and causes foot rot disease at all stages of plant growth. Phytophthora secretes a glucanase inhibitor protein (GIP), which is capable of inhibiting defence proteins like endoglucanases. In this particular study Quantitative PCR analysis, molecular docking studies and analysis of sequences of Glucanase inhibitor protein and beta-1,3 glucanse genes were done mainly depending on the data derived from Phytophthora capsici whole genome sequencing and Piper colubrinum RNA-sequencing (RNA-Seq)...
October 2016: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/27924042/planttfdb-4-0-toward-a-central-hub-for-transcription-factors-and-regulatory-interactions-in-plants
#5
Jinpu Jin, Feng Tian, De-Chang Yang, Yu-Qi Meng, Lei Kong, Jingchu Luo, Ge Gao
With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923985/the-get-system-inserts-the-tail-anchored-syp72-protein-into-endoplasmic-reticulum-membranes
#6
Renu Srivistava, Benjamin E Zalisko, Robert J Keenan, Stephen H Howell
The Arabidopsis genome encodes homologs of the Guided Entry of Tail anchored proteins (GET) system for the post-translational insertion of tail-anchored (TA) proteins into endoplasmic reticulum (ER) membranes. In yeast, TA proteins are loaded onto the cytosolic targeting factor Get3 and then delivered to the membrane-associated Get1/2 complex for insertion into ER membranes. The role of the GET system in Arabidopsis was investigated by monitoring the membrane insertion of a tail-anchored protein, SYP72, a syntaxin...
December 6, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27923736/genomic-and-phenotypic-analyses-of-serratia-fonticola-strain-gs2-a-rhizobacterium-isolated-from-sesame-rhizosphere-that-promotes-plant-growth-and-produces-n-acyl-homoserine-lactone
#7
Byung Kwon Jung, Abdur Rahim Khan, Sung-Jun Hong, Gun-Seok Park, Yeong-Jun Park, Chang Eon Park, Hwang-Ju Jeon, Sung-Eun Lee, Jae-Ho Shin
The genus Serratia incorporates many agriculturally important species. Serratia fonticola strain GS2, isolated from a sesame rhizosphere, can produce N-acyl homoserine lactone quorum sensing signal molecules and indole-3-acetic acid (IAA). Here we report the complete genome sequence and phenotypic characteristics based on genomic information of this bacterium. The complete genome sequence of S. fonticola strain GS2 consists of a chromosome of 6.1 Mbp and two plasmids of 132 kbp and 94 kbp. The genome clusters for IAA and N-acyl homoserine lactone biosynthesis were identified in the genome...
December 3, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27922098/comparison-of-432-pseudomonas-strains-through-integration-of-genomic-functional-metabolic-and-expression-data
#8
Jasper J Koehorst, Jesse C J van Dam, Ruben G A van Heck, Edoardo Saccenti, Vitor A P Martins Dos Santos, Maria Suarez-Diez, Peter J Schaap
Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922095/co-expression-network-analyses-identify-functional-modules-associated-with-development-and-stress-response-in-gossypium-arboreum
#9
Qi You, Liwei Zhang, Xin Yi, Kang Zhang, Dongxia Yao, Xueyan Zhang, Qianhua Wang, Xinhua Zhao, Yi Ling, Wenying Xu, Fuguang Li, Zhen Su
Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922076/identification-of-bnayucca6-as-a-candidate-gene-for-branch-angle-in-brassica-napus-by-qtl-seq
#10
Hui Wang, Hongtao Cheng, Wenxiang Wang, Jia Liu, Mengyu Hao, Desheng Mei, Rijin Zhou, Li Fu, Qiong Hu
Oilseed rape (Brassica napus L.) is one of the most important oil crops in China as well as worldwide. Branch angle as a plant architecture component trait plays an important role for high density planting and yield performance. In this study, bulked segregant analysis (BSA) combined with next generation sequencing technology was used to fine map QTL for branch angle. A major QTL, designated as branch angle 1 (ba1) was identified on A06 and further validated by Indel marker-based classical QTL mapping in an F2 population...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922066/de-novo-transcriptome-characterization-of-dracaena-cambodiana-and-analysis-of-genes-involved-in-flavonoid-accumulation-during-formation-of-dragon-s-blood
#11
Jia-Hong Zhu, Tian-Jun Cao, Hao-Fu Dai, Hui-Liang Li, Dong Guo, Wen-Li Mei, Shi-Qing Peng
Dragon's blood is a red resin mainly extracted from Dracaena plants, and has been widely used as a traditional medicine in East and Southeast Asia. The major components of dragon's blood are flavonoids. Owing to a lack of Dracaena plants genomic information, the flavonoids biosynthesis and regulation in Dracaena plants remain unknown. In this study, three cDNA libraries were constructed from the stems of D. cambodiana after injecting the inducer. Approximately 266.57 million raw sequencing reads were de novo assembled into 198,204 unigenes, of which 34,873 unique sequences were annotated in public protein databases...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921404/genome-wide-profiling-of-genetic-variation-in-agrobacterium-transformed-rice-plants
#12
Wen-Xu Li, San-Ling Wu, Yan-Hua Liu, Gu-Lei Jin, Hai-Jun Zhao, Long-Jiang Fan, Qing-Yao Shu
Agrobacterium-mediated transformation has been widely used in producing transgenic plants, and was recently used to generate "transgene-clean" targeted genomic modifications coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Although tremendous variation in morphological and agronomic traits, such as plant height, seed fertility, and grain size, was observed in transgenic plants, the underlying mechanisms are not yet well understood, and the types and frequency of genetic variation in transformed plants have not been fully disclosed...
2016: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/27921396/frequency-and-type-of-inheritable-mutations-induced-by-%C3%AE-rays-in-rice-as-revealed-by-whole-genome-sequencing
#13
Shan Li, Yun-Chao Zheng, Hai-Rui Cui, Hao-Wei Fu, Qing-Yao Shu, Jian-Zhong Huang
Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M2 rice plants were sequenced; a total of 144-188 million high-quality (Q>20) reads were generated for each M2 plant, resulting in genome coverage of >45 times for each plant...
2016: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/27920771/evidence-for-ecological-flexibility-in-the-cosmopolitan-genus-curtobacterium
#14
Alexander B Chase, Philip Arevalo, Martin F Polz, Renaud Berlemont, Jennifer B H Martiny
Assigning ecological roles to bacterial taxa remains imperative to understanding how microbial communities will respond to changing environmental conditions. Here we analyze the genus Curtobacterium, as it was found to be the most abundant taxon in a leaf litter community in southern California. Traditional characterization of this taxon predominantly associates it as the causal pathogen in the agricultural crops of dry beans. Therefore, we sought to investigate whether the abundance of this genus was because of its role as a plant pathogen or another ecological role...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920767/ecophysiology-and-comparative-genomics-of-nitrosomonas-mobilis-ms1-isolated-from-autotrophic-nitrifying-granules-of-wastewater-treatment-bioreactor
#15
Soe Myat Thandar, Norisuke Ushiki, Hirotsugu Fujitani, Yuji Sekiguchi, Satoshi Tsuneda
Ammonia-oxidizing bacteria (AOB), which oxidize ammonia to nitrite in the first step of nitrification, play an important role in biological wastewater treatment systems. Nitrosomonas mobilis is an important and dominant AOB in various wastewater treatment systems. However, the detailed physiological and genomic properties of N. mobilis have not been thoroughly investigated because of limited success isolating pure cultures. This study investigated the key physiological characteristics of N. mobilis Ms1, which was previously isolated into pure culture from the nitrifying granules of wastewater treatment bioreactor...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27919652/sequencing-of-individual-chromosomes-of-plant-pathogenic-fusarium-oxysporum
#16
Takeshi Kashiwa, Toshinori Kozaki, Kazuo Ishii, B Gillian Turgeon, Tohru Teraoka, Ken Komatsu, Tsutomu Arie
A small chromosome in reference isolate 4287 of F. oxysporum f. sp. lycopersici (Fol) has been designated as a 'pathogenicity chromosome' because it carries several pathogenicity related genes such as the Secreted In Xylem (SIX) genes. Sequence assembly of small chromosomes in other isolates, based on a reference genome template, is difficult because of karyotype variation among isolates and a high number of sequences associated with transposable elements. These factors often result in misassembly of sequences, making it unclear whether other isolates possess the same pathogenicity chromosome harboring SIX genes as in the reference isolate...
December 2, 2016: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/27918628/phenotypic-and-genome-wide-association-analysis-of-spike-ethylene-in-diverse-wheat-genotypes-under-heat-stress
#17
Ravi Valluru, Matthew P Reynolds, William J Davies, Sivakumar Sukumaran
The gaseous phytohormone ethylene plays an important role in spike development in wheat (Triticum aestivum). However, the genotypic variation and the genomic regions governing spike ethylene (SET) production in wheat under long-term heat stress remain unexplored. We investigated genotypic variation in the production of SET and its relationship with spike dry weight (SDW) in 130 diverse wheat elite lines and landraces under heat-stressed field conditions. We employed an Illumina iSelect 90K single nucleotide polymorphism (SNP) genotyping array to identify the genetic loci for SET and SDW through a genome-wide association study (GWAS) in a subset of the Wheat Association Mapping Initiative (WAMI) panel...
December 5, 2016: New Phytologist
https://www.readbyqxmd.com/read/27918076/genome-wide-association-analyses-of-54-traits-identified-multiple-loci-for-the-determination-of-floret-fertility-in-wheat
#18
Zifeng Guo, Dijun Chen, Ahmad M Alqudah, Marion S Röder, Martin W Ganal, Thorsten Schnurbusch
Increasing grain yield is still the main target of wheat breeding; yet today's wheat plants utilize less than half of their yield potential. Owing to the difficulty of determining grain yield potential in a large population, few genetic factors regulating floret fertility (i.e. the difference between grain yield potential and grain number) have been reported to date. In this study, we conducted a genome-wide association study (GWAS) by quantifying 54 traits (16 floret fertility traits and 38 traits for assimilate partitioning and spike morphology) in 210 European winter wheat accessions...
December 5, 2016: New Phytologist
https://www.readbyqxmd.com/read/27917953/the-core-subunit-of-a-chromatin-remodeling-complex-zmchb101-plays-essential-roles-in-maize-growth-and-development
#19
Xiaoming Yu, Lili Jiang, Rui Wu, Xinchao Meng, Ai Zhang, Ning Li, Qiong Xia, Xin Qi, Jinsong Pang, Zheng-Yi Xu, Bao Liu
ATP-dependent chromatin remodeling complexes play essential roles in the regulation of diverse biological processes by formulating a DNA template that is accessible to the general transcription apparatus. Although the function of chromatin remodelers in plant development has been studied in A. thaliana, how it affects growth and development of major crops (e.g., maize) remains uninvestigated. Combining genetic, genomic and bioinformatic analyses, we show here that the maize core subunit of chromatin remodeling complex, ZmCHB101, plays essential roles in growth and development of maize at both vegetative and reproductive stages...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917576/karyotype-diversity-and-genome-size-variation-in-neotropical-maxillariinae-orchids
#20
A P Moraes, S Koehler, J S Cabral, S S L Gomes, L F Viccini, F Barros, L P Felix, M Guerra, E R Forni-Martins
(1) Orchidaceae is a widely distributed plant family with a very diverse vegetative and floral morphology and such variability is also reflected in their karyotypes. However, since only a low proportion of Orchidaceae has been analysed for chromosome data, a greater diversity may await to be unveiled. Here we analyse both genome size (GS) and karyotype in two subtribes recently included in the broadened Maxillariineae to detect how much chromosome and GS variation there are in these groups and to evaluate which genome rearrangements were involved in the species evolution...
December 5, 2016: Plant Biology
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