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https://www.readbyqxmd.com/read/29244768/identification-and-expression-profiling-of-the-auxin-response-factors-in-capsicum-annuum-l-under-abiotic-stress-and-hormone-treatments
#1
Chenliang Yu, Yihua Zhan, Xuping Feng, Zong-An Huang, Chendong Sun
Auxin response factors (ARFs) play important roles in regulating plant growth and development and response to environmental stress. An exhaustive analysis of the CaARF family was performed using the latest publicly available genome for pepper (Capsicum annuum L.). In total, 22 non-redundant CaARF gene family members in six classes were analyzed, including chromosome locations, gene structures, conserved motifs of proteins, phylogenetic relationships and Subcellular localization. Phylogenetic analysis of the ARFs from pepper (Capsicum annuum L...
December 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29242292/comparative-oligo-fish-mapping-an-efficient-and-powerful-methodology-to-reveal-karyotypic-and-chromosomal-evolution
#2
Guilherme T Braz, Li He, Hainan Zhao, Tao Zhang, Kassandra Semrau, Jean-Marie Rouillard, Giovana A Torres, Jiming Jiang
Developing the karyotype of a eukaryotic species relies on identification of individual chromosomes, which has been a major challenge for most non-model plant and animal species. We developed a novel chromosome identification system by selecting and labeling oligonucleotides (oligos) located in specific regions on every chromosome. We selected a set of 54,672 oligos (45 nt) based on single copy DNA sequences in the potato genome. These oligos generated 26 distinct FISH signals that can be used as a 'barcode' or a 'banding pattern' to uniquely label each of the 12 chromosomes from both diploid and polyploid (4x and 6x) potato species...
December 13, 2017: Genetics
https://www.readbyqxmd.com/read/29240795/the-msmx-atpase-plays-a-crucial-role-in-pectin-mobilization-by-bacillus-subtilis
#3
Mário J Ferreira, Aristides L Mendes, Isabel de Sá-Nogueira
Carbohydrates from plant cell walls are often found as heteropolysaccharides intertwined with each other. For competitive advantage against other microorganisms, and ability to fully exploit available carbon and energy sources, Bacillus subtilis possesses a high number of proteins dedicated to the uptake of mono- and oligosaccharides. Here, we characterize transporter complexes, belonging to the ATP-binding cassette (ABC) superfamily, involved in the uptake of oligosaccharides commonly found in pectin. The uptake of these carbohydrates is shown to be MsmX-dependent, assigning a key role in pectin mobilization for MsmX, a multipurpose ATPase serving several distinct ABC-type I sugar importers...
2017: PloS One
https://www.readbyqxmd.com/read/29237241/the-p-patens-chromosome-scale-assembly-reveals-moss-genome-structure-and-evolution
#4
Daniel Lang, Kristian K Ullrich, Florent Murat, Jörg Fuchs, Jerry Jenkins, Fabian B Haas, Mathieu Piednoel, Heidrun Gundlach, Michiel Van Bel, Rabea Meyberg, Cristina Vives, Jordi Morata, Aikaterini Symeonidi, Manuel Hiss, Wellington Muchero, Yasuko Kamisugi, Omar Saleh, Guillaume Blanc, Eva L Decker, Nico van Gessel, Jane Grimwood, Richard D Hayes, Sean W Graham, Lee E Gunter, Stuart McDaniel, Sebastian N W Hoernstein, Anders Larsson, Fay-Wei Li, Pierre-Francois Perroud, Jeremy Phillips, Priya Ranjan, Daniel S Rokshar, Carl J Rothfels, Lucas Schneider, Shengqiang Shu, Dennis W Stevenson, Fritz Thümmler, Michael Tillich, Juan Carlos Villarreal A, Thomas Widiez, Gane Ka-Shu Wong, Ann Wymore, Yong Zhang, Andreas D Zimmer, Ralph S Quatrano, Klaus F X Mayer, David Goodstein, Josep M Casacuberta, Klaas Vandepoele, Ralf Reski, Andrew C Cuming, Jerry Tuskan, Florian Maumus, Jérome Salse, Jeremy Schmutz, Stefan A Rensing
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2,000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes...
December 13, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29237140/high-density-snp-mapping-reveals-closely-linked-qtl-for-resistance-to-stagonospora-nodorum-blotch-snb-in-flag-leaf-and-glume-of-hexaploid-wheat
#5
Michael Francki, Esther Walker, Dora Li, Kerrie Forrest
The genetic control of adult plant resistance to Stagonospora nodorum blotch (SNB) is complex consisting of genes with minor effects interacting in an additive manner. Earlier studies detected quantitative trait loci (QTL) for flag leaf resistance in successive years on chromosomes 1B, 2A, 2D, 5B using SSR- and DArT-based genetic maps of progeny from the crosses EGA Blanco/Millewa, 6HRWSN125/WAWHT2074 and P92201D5/P91193D1. Similarly, QTL for glume resistance detected in successive years and multiple environments were identified on chromosomes 2D and 4B from genetic maps of P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively...
December 13, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29237079/fine-tuning-of-the-setting-of-critical-day-length-by-two-casein-kinases-in-rice-photoperiodic-flowering
#6
Yasue Nemoto, Kiyosumi Hori, Takeshi Izawa
Many short-day plants have a critical day length that fixes the schedule for flowering time, limiting the range of natural growth habitats (or growth and cultivation areas). Thus, fine-tuning of the critical day-length setting in photoperiodic flowering determines ecological niches within latitudinal clines; however, little is known about the molecular mechanisms controlling the fine-tuning of the critical day-length setting in plants. Previously, we determined that florigen genes are regulated by day length, and identified several key genes involved in setting the critical day length in rice...
December 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29236867/karyotype-analysis-in-bignonieae-bignoniaceae-chromosome-numbers-and-heterochromatin
#7
Joel M P Cordeiro, Miriam Kaehler, Gustavo Souza, Leonardo P Felix
Chromosome numbers and heterochromatin banding pattern variability have been shown to be useful for taxonomic and evolutionary studies of different plant taxa. Bignonieae is the largest tribe of Bignoniaceae, composed mostly by woody climber species whose taxonomies are quite complicated. We reviewed and added new data concerning chromosome numbers in Bignonieae and performed the first analyses of heterochromatin banding patterns in that tribe based on the fluorochromes chromomycin A3 (CMA) and 4'-6-diamidino-2-phenylindole (DAPI)...
December 11, 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/29236185/genome-wide-identification-and-cadmium-induced-expression-profiling-of-sulfate-transporter-sultr-genes-in-sorghum-sorghum-bicolor-l
#8
M Aydın Akbudak, Ertugrul Filiz, Kubra Kontbay
Sulfur is an essential element for all living organisms. Plants can convert inorganic sulfur into organic sulfur compounds by complex enzymatic steps. In this study, we conducted a genome-wide analysis of sulfate transporter genes (SULTRs) in the sorghum (Sorghum bicolor) genome and examined expression profiles of SbSULTR genes under 200 µM cadmium (Cd) exposure. As a result of sorghum genome analysis, 11 SULTR genes were identified, including SbSULTR1;1, SbSULTR1;2, SbSULTR1;3, SbSULTR2;1, SbSULTR2;2, SbSULTR3;1, SbSULTR3;2, SbSULTR3;3, SbSULTR3;4, SbSULTR3;5, and SbSULTR4...
December 13, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/29234880/reorganization-of-wheat-and-rye-genomes-in-octoploid-triticale-%C3%A3-%C3%A2-triticosecale
#9
Anna Kalinka, Magdalena Achrem
The analysis of early generations of triticale showed numerous rearrangements of the genome. Complexed transformation included loss of chromosomes, t-heterochromatin content changes and the emergence of retrotransposons in new locations. This study investigated certain aspects of genomic transformations in the early generations (F5 and F8) of the primary octoploid triticale derived from the cross of hexaploid wheat with the diploid rye. Most of the plants tested were hypoploid; among eliminated chromosomes were rye chromosomes 4R and 5R and variable number of wheat chromosomes...
December 12, 2017: Planta
https://www.readbyqxmd.com/read/29233089/de-novo-transcriptome-assembly-from-flower-buds-of-dioecious-gynomonoecious-and-chemically-masculinized-female-coccinia-grandis-reveals-genes-associated-with-sex-expression-and-modification
#10
Ravi Suresh Devani, Sangram Sinha, Jayeeta Banerjee, Rabindra Kumar Sinha, Abdelhafid Bendahmane, Anjan Kumar Banerjee
BACKGROUND: Coccinia grandis (ivy gourd), is a dioecious member of Cucurbitaceae having heteromorphic sex chromosomes. Chromosome constitution of male and female plants of C. grandis is 22A + XY and 22A + XX respectively. Earlier we showed that a unique gynomonoecious form of C. grandis (22A + XX) also exists in nature bearing morphologically hermaphrodite flowers (GyM-H). Additionally, application of silver nitrate (AgNO3) on female plants induces stamen development leading to the formation of morphologically hermaphrodite flowers (Ag-H) despite the absence of Y-chromosome...
December 12, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29232688/genotype-and-cell-specific-dynamics-of-tandem-repeat-patterns-in-aegilops-speltoides-tausch-poaceae-triticeae
#11
Olga Raskina
In wild plant populations, chromosome rearrangements lead to the wide intraspecific polymorphisms in the abundance and patterns of highly repetitive DNA. However, despite the large amount of accumulated data, the impact of the complex repetitive DNA fraction on genome reorganization and functioning and the mechanisms balancing and maintaining the structural integrity of the genome are not fully understood. Homologous recombination is thought to play a key role in both genome reshuffling and stabilization, while the contribution of nonhomologous recombination seems to be undervalued...
December 13, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/29231813/evolutionary-transitions-between-beneficial-and-phytopathogenic-rhodococcus-challenge-disease-management
#12
Elizabeth A Savory, Skylar L Fuller, Alexandra J Weisberg, William J Thomas, Michael I Gordon, Danielle M Stevens, Allison L Creason, Michael S Belcher, Maryna Serdani, Michele S Wiseman, Niklaus J Grünwald, Melodie L Putnam, Jeff H Chang
Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks...
December 12, 2017: ELife
https://www.readbyqxmd.com/read/29230584/mapping-of-a-major-quantitative-trait-locus-for-bakanae-disease-resistance-in-rice-by-genome-resequencing
#13
Hyeonso Ji, Tae-Ho Kim, Gang-Seob Lee, Hyun-Ju Kang, Seung-Bum Lee, Seok Cheol Suh, Song Lim Kim, Inchan Choi, Jeongho Baek, Kyung-Hwan Kim
Bakanae disease (BD) has emerged as a serious threat in almost all rice cultivation regions worldwide. Nampyeong is a Korean japonica rice variety known to be resistant to BD. In this study, quantitative trait locus (QTL) mapping was performed with F2 and F3 plants derived from a cross between the Nampyeong variety and a susceptible Korean japonica line, DongjinAD. First, resequencing of Nampyeong and DongjinAD was performed, which identified 171,035 single nucleotide polymorphisms (SNPs) between the two parental varieties...
December 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29228374/quantitative-trait-loci-mapping-of-western-corn-rootworm-coleoptera-chrysomelidae-host-plant-resistance-in-two-populations-of-doubled-haploid-lines-in-maize-zea-mays-l
#14
Martin O Bohn, Juan J Marroquin, Sherry Flint-Garcia, Kenton Dashiell, David B Willmot, Bruce E Hibbard
Over the last 70 yr, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae), larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Selected genotypes were mostly characterized by large root systems and superior root regrowth after root damage caused by western corn rootworm larvae. However, no hybrids claiming native (i...
December 8, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/29228286/cut-and-paste-transposons-in-fungi-with-diverse-lifestyles
#15
Anna Muszewska, Kamil Steczkiewicz, Marta Stepniewska-Dziubinska, Krzysztof Ginalski
Transposons (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighbourhoods and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut and paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches...
December 8, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29225728/the-complete-genome-sequence-of-the-rumen-bacterium-butyrivibrio-hungatei-mb2003
#16
Nikola Palevich, William J Kelly, Sinead C Leahy, Eric Altermann, Jasna Rakonjac, Graeme T Attwood
Butyrivibrio hungatei MB2003 was isolated from the plant-adherent fraction of rumen contents from a pasture-grazed New Zealand dairy cow, and was selected for genome sequencing in order to examine its ability to degrade plant polysaccharides. The genome of MB2003 is 3.39 Mb and consists of four replicons; a chromosome, a secondary chromosome or chromid, a megaplasmid and a small plasmid. The genome has an average G + C content of 39.7%, and encodes 2983 putative protein-coding genes. MB2003 is able to use a variety of monosaccharide substrates for growth, with acetate, butyrate and formate as the principal fermentation end-products, and the genes encoding these metabolic pathways have been identified...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29224171/genetic-mapping-and-validation-of-the-loci-controlling-7s-%C3%AE-and-11s-a-type-storage-protein-subunits-in-soybean-glycine-max-l-merr
#17
Jeffrey D Boehm, Vi Nguyen, Rebecca M Tashiro, Dale Anderson, Chun Shi, Xiaoguang Wu, Lorna Woodrow, Kangfu Yu, Yuhai Cui, Zenglu Li
Four soybean storage protein subunit QTLs were mapped using bulked segregant analysis and an F2 population, which were validated with an F5 RIL population. The storage protein globulins β-conglycinin (7S subunit) and glycinin (11S subunits) can affect the quantity and quality of proteins found in soybean seeds and account for more than 70% of the total soybean protein. Manipulating the storage protein subunits to enhance soymeal nutrition and for desirable tofu manufacturing characteristics are two end-use quality goals in soybean breeding programs...
December 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29223850/genome-wide-analysis-of-carotenoid-cleavage-oxygenase-genes-and-their-responses-to-various-phytohormones-and-abiotic-stresses-in-apple-malus-domestica
#18
Hongfei Chen, Xiya Zuo, Hongxia Shao, Sheng Fan, Juanjuan Ma, Dong Zhang, Caiping Zhao, Xiangyan Yan, Xiaojie Liu, Mingyu Han
Carotenoid cleavage oxygenases (CCOs) are able to cleave carotenoids to produce apocarotenoids and their derivatives, which are important for plant growth and development. In this study, 21 apple CCO genes were identified and divided into six groups based on their phylogenetic relationships. We further characterized the apple CCO genes in terms of chromosomal distribution, structure and the presence of cis-elements in the promoter. We also predicted the cellular localization of the encoded proteins. An analysis of the synteny within the apple genome revealed that tandem, segmental, and whole-genome duplication events likely contributed to the expansion of the apple carotenoid oxygenase gene family...
December 5, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29223068/comprehensive-analysis-and-transcript-profiling-of-arabidopsis-thaliana-and-oryza-sativa-catalase-gene-family-suggests-their-specific-roles-in-development-and-stress-responses
#19
Nazmir Binta Alam, Ajit Ghosh
Stress induces the generation of Reactive Oxygen Species (ROS) that ultimately hampers the growth, development, and productivity of the plant. As an antioxidant enzyme, catalase converts hydrogen peroxide to water and keeps ROS level down to protect cells from stress-induced apoptosis. Here, a genome-wide analysis of catalase gene family has been performed in two model plants- Arabidopsis thaliana and Oryza sativa. Both Arabidopsis and rice has a small family of three and four genes, respectively; that code for seven proteins each...
December 1, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29223067/dissection-of-resistance-to-microdochium-nivale-in-lolium-multiflorum-festuca-arundinacea-introgression-forms
#20
Agnieszka Płażek, Ewa Pociecha, Adam Augustyniak, Katarzyna Masajada, Michał Dziurka, Joanna Majka, Dawid Perlikowski, Izabela Pawłowicz, Arkadiusz Kosmala
The potential of resistance to Microdochium nivale is still not recognized for numerous plant species. The forage grasses of Lolium-Festuca complex are important for grass-biomass production in the temperate regions. Lolium multiflorum is a grass with a high forage quality and productivity but also a relatively low resistance to M. nivale. On the contrary, F. arundinacea has a higher potential of resistance but simultaneously a significantly lower forage quality. These two species cross with each other and the intergeneric hybrids possess complementary characters of both genera...
December 5, 2017: Plant Physiology and Biochemistry: PPB
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