scholarly journals The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Hilary S. Ireland ◽  
Chen Wu ◽  
Cecilia H. Deng ◽  
Elena Hilario ◽  
Ali Saei ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Negative Control ◽  
Fleshy Fruit ◽  
Ancestral Genome ◽  
Important Species ◽  
Syntenic Conservation ◽  
Rosaceae Family ◽  
Improved Model ◽  
Dry Fruit ◽  
Growth And Reproduction

AbstractThe Rosaceae family has striking phenotypic diversity and high syntenic conservation. Gillenia trifoliata is sister species to the Maleae tribe of apple and ~1000 other species. Gillenia has many putative ancestral features, such as herb/sub-shrub habit, dry fruit-bearing and nine base chromosomes. This coalescence of ancestral characters in a phylogenetically important species, positions Gillenia as a ‘rosetta stone’ for translational science within Rosaceae. We present genomic and phenological resources to facilitate the use of Gillenia for this purpose. The Gillenia genome is the first fully annotated chromosome-level assembly with an ancestral genome complement (x = 9), and with it we developed an improved model of the Rosaceae ancestral genome. MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fleshy fruit development in Rosaceae.

scholarly journals Detection and evaluation of selection signatures in sheep

2018 ◽  
Vol 53 (5) ◽  
pp. 527-539 ◽  
Author(s):  
Tiago do Prado Paim ◽  
Patrícia Ianella ◽  
Samuel Rezende Paiva ◽  
Alexandre Rodrigues Caetano ◽  
Concepta Margaret McManus Pimentel
Keyword(s):  
Statistical Methods ◽  
Phenotypic Diversity ◽  
Selection Process ◽  
Genomic Data ◽  
Research Field ◽  
Economic Traits ◽  
Selection Signatures ◽  
Important Species ◽  
Challenges And Opportunities ◽  
Genomic Regions

Abstract: The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field.

scholarly journals Evolution with a seed bank: the population genetic consequences of microbial dormancy

2017 ◽  
Author(s):  
WR Shoemaker ◽  
JT Lennon
Keyword(s):  
Seed Bank ◽  
Population Genetic ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Seed Banks ◽  
Hedging Strategy ◽  
Term Survival ◽  
Evolutionary Forces ◽  
Growth And Reproduction

ABSTRACTDormancy is a bet-hedging strategy that allows organisms to persist through conditions that are sub-optimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long-term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence microbial evolutionary dynamics.

Identification and expression analysis of the LRR-RLK gene family in tomato (Solanum lycopersicum) Heinz 1706

Genome ◽  
2015 ◽  
Vol 58 (4) ◽  
pp. 121-134 ◽  
Author(s):  
Zhirong Wei ◽  
Jiehua Wang ◽  
Shaohui Yang ◽  
Yingjin Song
Keyword(s):  
Gene Family ◽  
Solanum Lycopersicum ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Developmental Stages ◽  
Sequence Similarity ◽  
Functional Divergence ◽  
Fleshy Fruit ◽  
Important Species ◽  
Preferential Expression

As the largest subfamily of receptor-like kinases (RLKs), leucine-rich repeat receptor-like kinases (LRR-RLKs) regulate the growth, development, and stress responses of plants. Through a reiterative process of sequence analysis and re-annotation, 234 LRR-RLK genes were identified in the genome of tomato (Solanum lycopersicum) ‘Heinz 1706’, which were further grouped into 10 major groups based on their sequence similarity. In comparison to the significant role of tandem duplication in the expansion process of this gene family in other species, only approximately 12% (29 out of 234) of SlLRR-RLK genes arose from tandem duplication. Using the multiple expectation maximization for motif elicitation (MEME) method, the motif composition and arrangement were found to be variably conserved within each SlLRR-RLK group, indicating their different extent of functional divergence. Expression profiling analyses by qRT-PCR data revealed that SlLRR-RLK genes were differentially expressed in various tomato organs and tissues, and some SlLRR-RLK genes exhibited preferential expression in fruits at distinct developmental stages, suggesting that SlLRR-RLK may take important roles in fruit development and ripening process. The results of this study provide an overview of the LRR-RLK gene family in tomato Heinz 1706, one important species of Solanaceae, and will be helpful for future functional analysis of this important protein family in fleshy fruit-bearing species.

scholarly journals Genetic and Phenotypic Diversity of Rhizobia Isolated from Trifolium rubens Root Nodules

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1286
Author(s):  
Anna Marzec-Grządziel ◽  
Anna Gałązka ◽  
Monika Marek-Kozaczuk ◽  
Anna Skorupska
Keyword(s):  
Trifolium Pratense ◽  
Phenotypic Diversity ◽  
Root Nodules ◽  
Red Clover ◽  
Nitrogen Sources ◽  
Negative Control ◽  
Strong Positive Correlation ◽  
16S Rrna Sequence ◽  
Experimental Conditions ◽  
High Genetic Diversity

The aim of this study was to analyse the genetic and phenotypic differentiation of bacteria isolated from root nodules of Trifolium rubens, a rare clover species. The symbiotic compatibility of selected isolates was investigated using two agronomically important plants, red clover (Trifolium pratense L.) and pea (Pisum sativum L.). A high genetic diversity of analysed strains was shown using the Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) method. Most of the strains showed a high similarity to R. leguminosarum in the 16S rRNA sequence. Two strains were identified as Agrobacterium spp. There was a strong positive correlation between fresh clover weight and the number of root nodules and a statistically significant increase in the number of the root nodules in selected strains compared to the negative control. Phenotypic tests and BIOLOG analysis showed the ability of the analysed strains to grow in different experimental conditions (pH = 6–10, 0.5–3% NaCl, different carbon and nitrogen sources), which makes them suitable for application as an agronomically important factor.

scholarly journals Molecular characterization and expression of mandibular organ-inhibiting hormone, a recently discovered neuropeptide involved in the regulation of growth and reproduction in the crab Cancer pagurus

1999 ◽  
Vol 343 (2) ◽  
pp. 355-360 ◽  
Author(s):  
Chenhui TANG ◽  
Weiqun LU ◽  
Geoffrey WAINWRIGHT ◽  
Simon G. WEBSTER ◽  
Huw H. REES ◽  
...  
Keyword(s):  
Blot Analysis ◽  
Southern Blotting ◽  
Negative Control ◽  
Sinus Gland ◽  
Methyl Farnesoate ◽  
Putative Signal Peptide ◽  
Cancer Pagurus ◽  
Rapid Amplification ◽  
Regulation Of Growth ◽  
Growth And Reproduction

Methyl farnesoate, the crustacean juvenoid, is synthesized and secreted from the mandibular organs of crustaceans under the negative control of the sinus gland-derived mandibular organ-inhibiting hormone (MO-IH). Previously we isolated and sequenced two isoforms, MO-IH-1 and MO-IH-2, differing by just one amino acid, from sinus glands of the edible crab, Cancer pagurus. We now report the isolation of cDNAs encoding MO-IH-1 and MO-IH-2 by a combination of reverse-transcriptase-mediated PCR in conjunction with 5′ and 3′ rapid amplification of cDNA ends (‘RACE’). Full-length clones of MO-IH-1 and MO-IH-2 encoded a 34-residue putative signal peptide and the mature 78-residue MO-IH sequences. Northern blot analysis of various tissues showed that MO-IH expression is confined to the X-organ (a cluster of perikarya within the eye). Southern blot analysis indicated that there are approx. 10 copies of the gene for MO-IH in C. pagurus. Additional Southern blotting experiments detected MO-IH-hybridizing bands in another Cancer species, C. antennarius. In support of this, an HPLC-radioimmunoassay analysis of sinus gland extracts of C. antennarius and C. magister also revealed MO-IH-like immunoreactivity.

scholarly journals Wild Himalayan Cherry (Prunus cerasoides) as a Natural Host of Prunus necrotic ringspot virus in India

Plant Disease ◽  
2007 ◽  
Vol 91 (12) ◽  
pp. 1686-1686 ◽  
Author(s):  
V. Chandel ◽  
T. Rana ◽  
V. Hallan ◽  
A. A. Zaidi
Keyword(s):  
Coat Protein ◽  
Coat Protein Gene ◽  
Protein Gene ◽  
Negative Control ◽  
Ringspot Virus ◽  
Pcr Analysis ◽  
Additional Tool ◽  
Prunus Cerasoides ◽  
Prunus Necrotic Ringspot Virus ◽  
Rosaceae Family

Prunus cerasoides, also known as wild Himalayan cherry, grows naturally in the Himalayas. A member of the Rosaceae family, the tree has medicinal (astringent) and other (beads, dye, wood) uses. During surveys in the northwestern Himalayan Region of India, necrotic spots were observed on leaves of P. cerasoides. Since the symptoms were typical of Prunus necrotic ringspot virus (PNRSV), preliminary detection was done by double-antibody sandwich (DAS)-ELISA (Agdia, Elkhart, IN). Positive results were obtained three times more than the negative control which is provided in the kit. To further confirm its presence, reverse transcription (RT)-PCR analysis was performed using a primer pair (upstream 5′-AACTGCAGATGGTTTGCCGAATTTGCAA-3′; downstream 5′-GCTCTAGACTAGATCTCAAGCAGGTC-3′) specific for the coat protein gene (GenBank Accession Nos. AJ619984 and AJ619983). Amplification of the expected 675-bp fragment was obtained. The sequence of a cloned copy of the amplified product showed 99% similarity to the PNRSV coat protein gene (GenBank Accession No. AF170165), confirming the presence of PNRSV in P. cerasoides (sequence submitted as Accession No. AM493717). The cloned DNA has the potential for utilization as an additional tool, and an early PNRSV screening (both pollen and seed transmitted) will be highly useful to ensure healthy rootstocks are used for grafting purposes (1). PNRSV mainly infects members of the Rosaceae family, including stone fruits and ornamental plants such as peach, plum, cherry, apricot, nectarines, and roses, and was first reported in P. persica (1). Proper management of PNRSV at this level can prevent its transmission and disease development in grafted scions of commercial Prunus spp. Reference: (1) A. A. Brunt et al. Page 1047 in: Viruses of Plants. CAB International, Wallingford, UK. 1996.

A scanning electron microscopic study of the eggs of Culicoides variipennis (Diptera: Ceratopogonidae)

1987 ◽  
Vol 45 ◽  
pp. 884-885 ◽  
Author(s):  
R. A. Nunamaker ◽  
C. E. Nunamaker ◽  
B. C. Wick
Keyword(s):  
Distinct Species ◽  
Hemorrhagic Disease ◽  
Insect Vector ◽  
Electron Microscopic ◽  
Important Species ◽  
Scanning Electron Microscopic Study ◽  
Laboratory Colony ◽  
Culicoides Variipennis ◽  
Morphological Differences ◽  
Scanning Electron

Culicoides variipennis (Coquillett) is probably the most economically important species of biting midge in the U.S. due to its involvement in the transmission of bluetongue (BT) disease of sheep, cattle and ruminant wildlife, and epizootic hemorrhagic disease (EHD) of deer. Proposals have been made to recognize the eastern and western populations of this insect vector as distinct species. Others recommend use of the term “variipennis complex” until such time that the necessary biosystematic studies have been made to determine the genetic nature and/or minute morphological differences within the population structure over the entire geographic range of the species. Increasingly, students of ootaxonomy are relying on scanning electron microscopy (SEM) to assess chorionic features. This study was undertaken to provide comparative chorionic data for the C. variipennis complex.Culicoides variipennis eggs were collected from a laboratory colony maintained in Laramie, Wyoming.

Oral Immune Activation by Disgust and Disease-Related Pictures

2015 ◽  
Vol 29 (3) ◽  
pp. 119-129 ◽  
Author(s):  
Richard J. Stevenson ◽  
Deborah Hodgson ◽  
Megan J. Oaten ◽  
Luba Sominsky ◽  
Mehmet Mahmut ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune Responses ◽  
Innate Immune Response ◽  
Negative Control ◽  
Innate Immune ◽  
Innate Immune Responses ◽  
Immune Markers ◽  
Before And After ◽  
Secondary Analyses ◽  
Image Set

Abstract. Both disgust and disease-related images appear able to induce an innate immune response but it is unclear whether these effects are independent or rely upon a common shared factor (e.g., disgust or disease-related cognitions). In this study we directly compared these two inductions using specifically generated sets of images. One set was disease-related but evoked little disgust, while the other set was disgust evoking but with less disease-relatedness. These two image sets were then compared to a third set, a negative control condition. Using a wholly within-subject design, participants viewed one image set per week, and provided saliva samples, before and after each viewing occasion, which were later analyzed for innate immune markers. We found that both the disease related and disgust images, relative to the negative control images, were not able to generate an innate immune response. However, secondary analyses revealed innate immune responses in participants with greater propensity to feel disgust following exposure to disease-related and disgusting images. These findings suggest that disgust images relatively free of disease-related themes, and disease-related images relatively free of disgust may be suboptimal cues for generating an innate immune response. Not only may this explain why disgust propensity mediates these effects, it may also imply a common pathway.

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