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Plant genomics

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https://www.readbyqxmd.com/read/28340469/characterization-and-expression-patterns-of-key-c4-photosynthetic-pathway-genes-in-bread-wheat-triticum-aestivum-l-under-field-conditions
#1
Daoura Goudia Bachir, Iqbal Saeed, Quanhao Song, Tay Zar Linn, Liang Chen, Yin-Gang Hu
Wheat is a C3 plant with relatively low photosynthetic efficiency and is a potential target for C4 photosynthetic pathway engineering. Here we reported the characterization of four key C4 pathway genes and assessed their expression patterns and enzymatic activities at three growth stages in flag leaves of 59 bread wheat genotypes. The C4-like genes homologous to PEPC, NADP-ME, MDH, and PPDK in maize were identified in the A, B, and D sub-genomes of bread wheat, located on the long arms of chromosomes 3 and 5 (TaPEPC), short arms of chromosomes 1 and 3 (TaNADP-ME), long arms of chromosomes 1 and 7 (TaMDH), and long arms of chromosome 1 (TaPPDK), respectively...
March 9, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28339862/a-new-insight-into-the-evolution-and-functional-divergence-of-sweet-transporters-in-chinese-white-pear-pyrus-bretschneideri
#2
Jiaming Li, Mengfan Qin, Xin Qiao, Yinsheng Cheng, Xiaolong Li, Huping Zhang, Jun Wu
SWEET genes are a recently identified plant gene family that play an indispensable role in sugar efflux. However, no systematic study has been performed in pear. In this research, 18 SWEET transporters identified in pear, almost twice the number found in woodland strawberry and Japanese apricot, were divided into four clades. Conserved motifs and six exons of the SWEET transporters were found in six species. SWEET transporters contained seven transmembrane segments (TMSs) that evolved from an internal duplication of an ancestral three-TMSs unit, connected by TMS4...
March 1, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28339484/a-high-throughput-qpcr-system-for-simultaneous-quantitative-detection-of-dairy-lactococcus-lactis-and-leuconostoc-bacteriophages
#3
Musemma K Muhammed, Lukasz Krych, Dennis S Nielsen, Finn K Vogensen
Simultaneous quantitative detection of Lactococcus (Lc.) lactis and Leuconostoc species bacteriophages (phages) has not been reported in dairies using undefined mixed-strain DL-starters, probably due to the lack of applicable methods. We optimized a high-throughput qPCR system that allows simultaneous quantitative detection of Lc. lactis 936 (now SK1virus), P335, c2 (now C2virus) and Leuconostoc phage groups. Component assays are designed to have high efficiencies and nearly the same dynamic detection ranges, i...
2017: PloS One
https://www.readbyqxmd.com/read/28339482/a-genome-wide-identification-and-analysis-of-the-dyw-deaminase-genes-in-the-pentatricopeptide-repeat-gene-family-in-cotton-gossypium-spp
#4
Bingbing Zhang, Guoyuan Liu, Xue Li, Liping Guo, Xuexian Zhang, Tingxiang Qi, Hailin Wang, Huini Tang, Xiuqin Qiao, Jinfa Zhang, Chaozhu Xing, Jianyong Wu
The RNA editing occurring in plant organellar genomes mainly involves the change of cytidine to uridine. This process involves a deamination reaction, with cytidine deaminase as the catalyst. Pentatricopeptide repeat (PPR) proteins with a C-terminal DYW domain are reportedly associated with cytidine deamination, similar to members of the deaminase superfamily. PPR genes are involved in many cellular functions and biological processes including fertility restoration to cytoplasmic male sterility (CMS) in plants...
2017: PloS One
https://www.readbyqxmd.com/read/28338992/identification-of-the-eucalyptus-grandis-chitinase-gene-family-and-expression-characterization-under-different-biotic-stress-challenges
#5
Peri A Tobias, Nanette Christie, Sanushka Naidoo, David I Guest, Carsten Külheim
Eucalyptus grandis (W. Hill ex Maiden) is an Australian Myrtaceae tree grown for timber in many parts of the world and for which the annotated genome sequence is available. Known to be susceptible to a number of pests and diseases, E. grandis is a useful study organism for investigating defense responses in woody plants. Chitinases are widespread in plants and cleave glycosidic bonds of chitin, the major structural component of fungal cell walls and arthropod exoskeletons. They are encoded by an important class of genes known to be up-regulated in plants in response to pathogens...
March 13, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28338970/woody-plant-ecosystems-under-climate-change-and-air-pollution-response-consistencies-across-zonobiomes
#6
R Matyssek, A R Kozovits, G Wieser, J King, H Rennenberg
Forests store the largest terrestrial pools of carbon (C), helping to stabilize the global climate system, yet are threatened by climate change (CC) and associated air pollution (AP, highlighting ozone (O3) and nitrogen oxides (NOx)). We adopt the perspective that CC-AP drivers and physiological impacts are universal, resulting in consistent stress responses of forest ecosystems across zonobiomes. Evidence supporting this viewpoint is presented from the literature on ecosystem gross/net primary productivity and water cycling...
March 14, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28338960/organellar-genomes-from-a-%C3%A2-5-000-years-old-archaeological-maize-sample-are-closely-related-to-nb-genotype
#7
Bernardo Pérez-Zamorano, Miguel Vallebueno-Estrada, Javier Martínez González, Angel García Cook, Rafael Montiel, Jean-Philippe Vielle-Calzada, Luis Delaye
The story of how pre-Columbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, México. Accelerator mass spectrometry dated the maize sample to be 5,040 to 5,300 years before present (95% probability). Phylogenetic analysis of the mitochondrial genome shows that the archaeological sample branches basal to the other Zea mays genomes, as expected...
March 17, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338896/rapid-evolution-of-microrna-loci-in-the-brown-algae
#8
J Mark Cock, Fuli Liu, Delin Duan, Simon Bourdareau, Agnieszka Lipinska, Susana M Coelho, James E Tarver
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on analysis of a single species, the filamentous brown alga Ectocarpus sp. Here we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families...
March 3, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338876/subcellular-localization-of-arabidopsis-arogenate-dehydratases-suggests-novel-and-non-enzymatic-roles
#9
Crystal D Bross, Travis R Howes, Sara Abolhassani Rad, Ornela Kljakic, Susanne E Kohalmi
Arogenate dehydratases (ADTs) catalyze the final step in phenylalanine biosynthesis in plants. The Arabidopsis thaliana genome encodes a family of six ADTs capable of decarboxylating/dehydrating arogenate into phenylalanine. Using cyan fluorescent protein (CFP)-tagged proteins, the subcellular localization patterns of all six A. thaliana ADTs were investigated in intact Nicotiana benthamiana and A. thaliana leaf cells. We show that A. thaliana ADTs localize to stroma and stromules (stroma-filled tubules) of chloroplasts...
March 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338826/the-evolutionary-fate-of-the-chloroplast-and-nuclear-rps16-genes-as-revealed-through-the-sequencing-and-comparative-analyses-of-four-novel-legume-chloroplast-genomes-from-lupinus
#10
J Keller, M Rousseau-Gueutin, G E Martin, J Morice, J Boutte, E Coissac, M Ourari, M Aïnouche, A Salmon, F Cabello-Hurtado, A Aïnouche
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins...
February 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338823/transporters-involved-in-ph-and-k-homeostasis-affect-pollen-wall-formation-male-fertility-and-embryo-development
#11
Senthilkumar Padmanaban, Daniel D Czerny, Kara A Levin, Alexander R Leydon, Robert T Su, Timothy K Maugel, Yanjiao Zou, Salil Chanroj, Alice Y Cheung, Mark A Johnson, Heven Sze
Flowering plant genomes encode multiple cation/H+ exchangers (CHXs) whose functions are largely unknown. AtCHX17, AtCHX18, and AtCHX19 are membrane transporters that modulate K+ and pH homeostasis and are localized in the dynamic endomembrane system. Loss of function reduced seed set, but the particular phase(s) of reproduction affected was not determined. Pollen tube growth and ovule targeting of chx17chx18chx19 mutant pollen appeared normal, but reciprocal cross experiments indicate a largely male defect...
February 23, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338805/deciphering-the-genetic-control-of-fruit-texture-in-apple-by-multiple-family-based-analysis-and-genome-wide-association
#12
Mario Di Guardo, Marco C A M Bink, Walter Guerra, Thomas Letschka, Lidia Lozano, Nicola Busatto, Lara Poles, Alice Tadiello, Luca Bianco, Richard G F Visser, Eric van de Weg, Fabrizio Costa
Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions...
February 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338802/cross-species-genome-wide-identification-of-evolutionary-conserved-microproteins
#13
Daniel Straub, Stephan Wenkel
MicroProteins are small single-domain proteins that act by engaging their targets into different, sometimes non-productive protein complexes. In order to identify novel microProteins in any sequenced genome of interest, we have developed miPFinder, a program that identifies and classifies potential microProteins. In the past years, several microProteins have been discovered in plants where they are mainly involved in the regulation of development by fine-tuning transcription factor activities. The miPFinder algorithm identifies all up to date known plant microProteins and extends the microProtein concept beyond transcription factors to other protein families...
March 2, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338762/redox-and-reactive-oxygen-species-network-in-acclimation-for-salinity-tolerance-in-sugar-beet
#14
M Sazzad Hossain, Abdelaleim Ismail ElSayed, Marten Moore, Karl-Josef Dietz
Fine-tuned and coordinated regulation of transport, metabolism and redox homeostasis allows plants to acclimate to osmotic and ionic stress caused by high salinity. Sugar beet is a highly salt tolerant crop plant and is therefore an interesting model to study sodium chloride (NaCl) acclimation in crops. Sugar beet plants were subjected to a final level of 300 mM NaCl for up to 14 d in hydroponics. Plants acclimated to NaCl stress by maintaining its growth rate and adjusting its cellular redox and reactive oxygen species (ROS) network...
February 18, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338712/molecular-mechanisms-of-flowering-under-long-days-and-stem-growth-habit-in-soybean
#15
Dong Cao, Ryoma Takeshima, Chen Zhao, Baohui Liu, Abe Jun, Fanjiang Kong
Precise timing of flowering is critical to crop adaptation and productivity in a given environment. A number of classical E genes controlling flowering time and maturity have been identified in soybean [Glycine max (L.) Merr.]. The public availability of the soybean genome sequence has accelerated the identification of orthologues of Arabidopsis flowering genes and their functional analysis, and has allowed notable progress towards understanding the molecular mechanisms of flowering in soybean. Great progress has been made particularly in identifying genes and modules that inhibit flowering in long-day conditions, because a reduced or absent inhibition of flowering by long daylengths is an essential trait for soybean, a short-day (SD) plant, to expand its adaptability toward higher latitude environments...
October 20, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338020/epigenetic-regulation-of-intronic-transgenes-in-arabidopsis
#16
Kenji Osabe, Yoshiko Harukawa, Saori Miura, Hidetoshi Saze
Defense mechanisms of plant genomes can epigenetically inactivate repetitive sequences and exogenous transgenes. Loss of mutant phenotypes in intronic T-DNA insertion lines by interaction with another T-DNA locus, termed T-DNA suppression, has been observed in Arabidopsis thaliana, although the molecular basis of establishment and maintenance of T-DNA suppression is poorly understood. Here we show that maintenance of T-DNA suppression requires heterochromatinisation of T-DNA sequences and the nuclear proteins, INCREASED IN BONSAI METHYLATION 2 (IBM2) and ENHANCED DOWNY MILDEW 2 (EDM2), which prevent ectopic 3' end processing of mRNA in atypically long introns containing T-DNA sequences...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337996/protein-interaction-evolution-from-promiscuity-to-specificity-with-reduced-flexibility-in-an-increasingly-complex-network
#17
T Alhindi, Z Zhang, P Ruelens, H Coenen, H Degroote, N Iraci, K Geuten
A key question regarding protein evolution is how proteins adapt to the dynamic environment in which they function and how in turn their evolution shapes the protein interaction network. We used extant and resurrected ancestral plant MADS-domain transcription factors to understand how SEPALLATA3, a protein with hub and glue properties, evolved and takes part in network organization. Although the density of dimeric interactions was saturated in the network, many new interactions became mediated by SEPALLATA3 after a whole genome triplication event...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337544/complete-genome-sequences-of-cowpea-polerovirus-1-and-cowpea-polerovirus-2-infecting-cowpea-plants-in-burkina-faso
#18
Essowè Palanga, Darren P Martin, Serge Galzi, Jean Zabré, Zakaria Bouda, James Bouma Neya, Mahamadou Sawadogo, Oumar Traore, Michel Peterschmitt, Philippe Roumagnac, Denis Filloux
The full-length genome sequences of two novel poleroviruses found infecting cowpea plants, cowpea polerovirus 1 (CPPV1) and cowpea polerovirus 2 (CPPV2), were determined using overlapping RT-PCR and RACE-PCR. Whereas the 5845-nt CPPV1 genome was most similar to chickpea chlorotic stunt virus (73% identity), the 5945-nt CPPV2 genome was most similar to phasey bean mild yellow virus (86% identity). The CPPV1 and CPPV2 genomes both have a typical polerovirus genome organization. Phylogenetic analysis of the inferred P1-P2 and P3 amino acid sequences confirmed that CPPV1 and CPPV2 are indeed poleroviruses...
March 23, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28337069/detection-of-alien-genetic-introgressions-in-bread-wheat-using-dot-blot-genomic-hybridisation
#19
María-Dolores Rey, Pilar Prieto
Simple, reliable methods for the identification of alien genetic introgressions are required in plant breeding programmes. The use of genomic dot-blot hybridisation allows the detection of small Hordeum chilense genomic introgressions in the descendants of genetic crosses between wheat and H. chilense addition or substitution lines in wheat when molecular markers are difficult to use. Based on genomic in situ hybridisation, DNA samples from wheat lines carrying putatively H. chilense introgressions were immobilised on a membrane, blocked with wheat genomic DNA and hybridised with biotin-labelled H...
2017: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/28336770/ptac10-a-key-subunit-of-plastid-encoded-rna-polymerase-promotes-chloroplast-development
#20
Sun Hyun Chang, Sangyool Lee, Tae Young Um, Ju-Kon Kim, Yang Do Choi, Geupil Jang
Regulation of photosynthetic gene expression by plastid-encoded RNA polymerase (PEP) is essential for chloroplast development. The activity of PEP largely relies on at least 12 PEP-associated proteins (PAPs) encoded in the nuclear genome of plant cells. A recent model proposed that these PAPs regulate the establishment of the PEP complex through broad PAP-PEP or PAP-PAP interactions. In this study, we identified the Arabidopsis thaliana seedling lethal mutant ptac10-1, which has defects in chloroplast development, and found that the mutant phenotype is caused by the suppression of PLASTID S1 RNA-BINDING DOMAIN PROTEIN (pTAC10/PAP3)...
March 23, 2017: Plant Physiology
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