scholarly journals Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 86
Author(s):  
Padmapriya Swaminathan ◽  
Michelle Ohrtman ◽  
Abigail Carinder ◽  
Anup Deuja ◽  
Cankun Wang ◽  
...  
Keyword(s):  
United States ◽  
Water Deficit ◽  
De Novo ◽  
Ornamental Plants ◽  
Molecular Function ◽  
Rna Sequences ◽  
Process Networks ◽  
Tamarix Spp ◽  
Northern United States ◽  
Cellular Components

Tamarix spp. (saltcedar) were introduced from Asia to the southern United States as windbreak and ornamental plants and have spread into natural areas. This study determined differential gene expression responses to water deficit (WD) in seedlings of T. chinensis and T. ramosissima from established invasive stands in New Mexico and Montana, respectively. A reference de novo transcriptome was developed using RNA sequences from WD and well-watered samples. Blast2GO analysis of the resulting 271,872 transcripts yielded 89,389 homologs. The reference Tamarix (Tamaricaceae, Carophyllales order) transcriptome showed homology with 14,247 predicted genes of the Beta vulgaris subsp. vulgaris (Amaranthaceae, Carophyllales order) genome assembly. T. ramosissima took longer to show water stress symptoms than T. chinensis. There were 2068 and 669 differentially expressed genes (DEG) in T. chinensis and T. ramosissima, respectively; 332 were DEG in common between the two species. Network analysis showed large biological process networks of similar gene content for each of the species under water deficit. Two distinct molecular function gene ontology networks (binding and transcription factor-related) encompassing multiple up-regulated transcription factors (MYB, NAC, and WRKY) and a cellular components network containing many down-regulated photosynthesis-related genes were identified in T. chinensis, in contrast to one small molecular function network in T. ramosissima.

scholarly journals De Novo Genome Sequence of a Fusarium xylarioides Race Pathogenic to Robusta Coffee (Coffea canephora) in Uganda

2019 ◽  
Vol 8 (31) ◽  
Author(s):  
Sammy Olal ◽  
Daphne N. Bitalo ◽  
Nicholas D. Olango ◽  
Julius Mulindwa ◽  
Silver Ochwo ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Genome Assembly ◽  
De Novo ◽  
Coffea Canephora ◽  
Whole Genome ◽  
Molecular Function ◽  
Biological Processes ◽  
Gene Ontology Analysis ◽  
Robusta Coffee ◽  
Cellular Components

Here, we report the first whole-genome assembly of a Fusarium xylarioides race pathogenic to robusta coffee in Uganda. It comprises 55,122,624 bases and 14,552 genes. Gene ontology analysis assigned 5,720 genes to biological processes, 4,545 genes to cellular components, and 6,021 genes to molecular function.

The North American Species in Group VII of Ips De Geer (Coleoptera: Scolytidae)

1965 ◽  
Vol 97 (2) ◽  
pp. 193-198 ◽  
Author(s):  
G. R. Hopping
Keyword(s):  
United States ◽  
New Species ◽  
North American ◽  
North American Species ◽  
The North ◽  
Northern United States

AbstractGroup VII of North American Ips contains I. thomasi, new species, I. borealis Swaine and I. swainei R. Hopping. They are less than 4.0 mm. long and females have the front of the head or at least the vertex smooth and shining, impunctate, or with very fine sparse punctures; males are more coarsely granulate-punctate on the frons. The species are described and a key is given. All breed in Picea in Canada and northern United States.

De novo protein synthesis in relation to ammonia and proline accumulation in water stressed white clover

2004 ◽  
Vol 31 (8) ◽  
pp. 847 ◽  
Author(s):  
Tae-Hwan Kim ◽  
Bok-Rye Lee ◽  
Woo-Jin Jung ◽  
Kil-Yong Kim ◽  
Jean-Christophe Avice ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Water Deficit ◽  
White Clover ◽  
De Novo ◽  
Proline Accumulation ◽  
Leaf Water ◽  
Total N ◽  
Water Parameters ◽  
Leaves And Roots ◽  
De Novo Protein Synthesis

The kinetics of protein incorporation from newly-absorbed nitrogen (N, de novo protein synthesis) was estimated by 15N tracing in 18-week-old white clover plants (Trifolium repens L. cv. Regal) during 7 d of water-deficit treatment. The physiological relationship between kinetics and accumulation of proline and ammonia in response to the change in leaf-water parameters was also assessed. All leaf-water parameters measured decreased gradually under water deficit. Leaf and root dry mass was not significantly affected during the first 3 d when decreases in leaf-water parameters were substantial. However, metabolic parameters such as total N, proline and ammonia were significantly affected within 1 d of commencement of water-deficit treatment. Water-deficit treatment significantly increased the proline and NH3–NH4+ concentrations in both leaves and roots. There was a marked reduction in the amount of N incorporated into the protein fraction from the newly absorbed N (NANP) in water-deficit stressed plants, particularly in leaf tissue. This reduction in NANP was strongly associated with an increased concentration of NH3–NH4+ in roots (P≤0.05) and proline (P≤0.01) in leaves and roots. These results suggest that proline accumulation may be a sensitive biochemical indicator of plant water status and of the dynamics of de novo protein synthesis in response to stress severity.

scholarly journals On the dynamics of some small structural motifs in rRNA upon ligand binding

2008 ◽  
Vol 73 (1) ◽  
pp. 41-53
Author(s):  
Aleksandra Rakic ◽  
Petar Mitrasinovic
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Binding Sites ◽  
De Novo ◽  
Reference Structure ◽  
Base Pairs ◽  
Rna Sequences ◽  
Conformational Model ◽  
Thermodynamic Variables ◽  
Dynamics Simulations

The present study characterizes using molecular dynamics simulations the behavior of the GAA (1186-1188) hairpin triloops with their closing c-g base pairs in large ribonucleoligand complexes (PDB IDs: 1njn, 1nwy, 1jzx). The relative energies of the motifs in the complexes with respect to that in the reference structure (unbound form of rRNA; PDB ID: 1njp) display the trends that agree with those of the conformational parameters reported in a previous study1 utilizing the de novo pseudotorsional (?,?) approach. The RNA regions around the actual RNA-ligand contacts, which experience the most substantial conformational changes upon formation of the complexes were identified. The thermodynamic parameters, based on a two-state conformational model of RNA sequences containing 15, 21 and 27 nucleotides in the immediate vicinity of the particular binding sites, were evaluated. From a more structural standpoint, the strain of a triloop, being far from the specific contacts and interacting primarily with other parts of the ribosome, was established as a structural feature which conforms to the trend of the average values of the thermodynamic variables corresponding to the three motifs defined by the 15-, 21- and 27-nucleotide sequences. From a more functional standpoint, RNA-ligand recognition is suggested to be presumably dictated by the types of ligands in the complexes.

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