scholarly journals Opsin Evolution in Flower-Visiting Beetles

2021 ◽  
Vol 9 ◽  
Author(s):  
Camilla R. Sharkey ◽  
Gareth S. Powell ◽  
Seth M. Bybee
Keyword(s):  
Visual Cues ◽  
Potential Role ◽  
Flower Color ◽  
Rna Seq ◽  
Flower Visitor ◽  
Visual Systems ◽  
Wavelength Sensitivity ◽  
Color Signals ◽  
Flower Visiting ◽  
Insect Visitors

Flowers have evolved signals that exploit the sensory systems of insect visitors. In the case of visual cues, color signals are thought to have been shaped in large part by the spectral sensitivity of key pollinators, such as hymenopterans. Beetles were some of the first plant pollinators, pre-dating the angiosperm radiation but with the exception of a few well-studied species, the evolution of flower-visiting beetle visual systems is poorly understood. Thus, the ability of beetles to detect and distinguish flower color signals and perhaps their potential role in shaping flower coloration is not well understood. Traditional models of pollinator visual systems often assume a putative tri- or tetrachromatic flower-visitor, as is found in bees, flies and butterflies. Beetles are unique among modern pollinators as ancestrally they did not possess the machinery for trichromatic vision, lacking the blue-sensitive photoreceptor class. Research on the evolution of visual genes responsible for wavelength sensitivity (opsins) has revealed that beetles with putative tri- and tetrachromatic visual systems have evolved independently, along multiple lineages. We explore the evolution of beetle visual genes using newly generated and publicly available RNA-seq data from 25 species with flower associations, including previously unexplored key flower-visitor groups and 20 non-flower visiting relatives. Our findings serve as a resource to inform and guide future studies on beetle-flower interactions, where insight from both signal and receiver is needed to better understand these poorly explored systems.

scholarly journals Machine learning, transcriptome, and genotyping chip analyses provide insights into SNP markers identifying flower color in Platycodon grandiflorus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Go-Eun Yu ◽  
Younhee Shin ◽  
Sathiyamoorthy Subramaniyam ◽  
Sang-Ho Kang ◽  
Si-Myung Lee ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Feature Selection Method ◽  
Flower Color ◽  
Classification Performance ◽  
Snp Markers ◽  
Rna Seq ◽  
Color Classification ◽  
Dna Pcr ◽  
Selection Of

AbstractBellflower is an edible ornamental gardening plant in Asia. For predicting the flower color in bellflower plants, a transcriptome-wide approach based on machine learning, transcriptome, and genotyping chip analyses was used to identify SNP markers. Six machine learning methods were deployed to explore the classification potential of the selected SNPs as features in two datasets, namely training (60 RNA-Seq samples) and validation (480 Fluidigm chip samples). SNP selection was performed in sequential order. Firstly, 96 SNPs were selected from the transcriptome-wide SNPs using the principal compound analysis (PCA). Then, 9 among 96 SNPs were later identified using the Random forest based feature selection method from the Fluidigm chip dataset. Among six machines, the random forest (RF) model produced higher classification performance than the other models. The 9 SNP marker candidates selected for classifying the flower color classification were verified using the genomic DNA PCR with Sanger sequencing. Our results suggest that this methodology could be used for future selection of breeding traits even though the plant accessions are highly heterogeneous.

scholarly journals Transcriptome Sequencing and Biochemical Analysis of Perianths and Coronas Reveal Flower Color Formation in Narcissus pseudonarcissus

2018 ◽  
Vol 19 (12) ◽  
pp. 4006 ◽  
Author(s):  
Xi Li ◽  
Dongqin Tang ◽  
Hui Du ◽  
Yimin Shi
Keyword(s):  
Flower Color ◽  
Carotenoid Biosynthesis ◽  
Carotenoid Content ◽  
Rna Seq ◽  
Color Formation ◽  
Light Yellow ◽  
Color Fading ◽  
Narcissus Pseudonarcissus ◽  
Bulbous Plant ◽  
Β Carotene

Narcissus pseudonarcissus is an important bulbous plant with white or yellow perianths and light yellow to orange-red coronas, but little is known regarding the biochemical and molecular basis related to flower color polymorphisms. To investigate the mechanism of color formation, RNA-Seq of flower of two widely cultured cultivars (‘Slim Whitman’ and ‘Pinza’) with different flower color was performed. A total of 84,463 unigenes were generated from the perianths and coronas. By parallel metabolomic and transcriptomic analyses, we provide an overview of carotenoid biosynthesis, degradation, and accumulation in N. pseudonarcissus. The results showed that the content of carotenoids in the corona was higher than that in the perianth in both cultivars. Accordingly, phytoene synthase (PSY) transcripts have a higher abundance in the coronas than that in perianths. While the expression levels of carotenoid biosynthetic genes, like GGPPS, PSY, and LCY-e, were not significantly different between two cultivars. In contrast, the carotenoid degradation gene NpCCD4 was highly expressed in white-perianth cultivars, but was hardly detected in yellow-perianth cultivars. Silencing of NpCCD4 resulted in a significant increase in carotenoid accumulation, especially in all-trans-β-carotene. Therefore, we presume that NpCCD4 is a crucial factor that causes the low carotenoid content and color fading phenomenon of ‘Slim Whitman’ by mediating carotenoid turnover. Our findings provide mass RNA-seq data and new insights into carotenoid metabolism in N. pseudonarcissus.

A comparison of flower-visiting insects to rare Symphyotrichum sericeum and common Solidago nemoralis (Asteraceae)

Botany ◽  
2010 ◽  
Vol 88 (3) ◽  
pp. 241-249 ◽  
Author(s):  
Diana Bizecki Robson
Keyword(s):  
Seed Set ◽  
Visitation Rate ◽  
Hand Pollination ◽  
Insect Visitation ◽  
The Common ◽  
Insect Activity ◽  
Flower Visiting ◽  
Common Plant ◽  
Insect Visitors ◽  
Over Time

Flower-visiting insect activity to the rare Symphyotrichum sericeum (Vent.) G.L. Nesom and the common Solidago nemoralis Ait. var. longipetiolata (Mack. & Bush) Pal. & Steyerm. was examined to detect compositional and temporal similarities. A hand pollination experiment was conducted to determine whether pollen was limiting seed set. Of the 31 insect taxa that visited these plants, Bombus bifarius Cresson was the most common visitor to both species. More insect visitors of the Halictidae and Bombyliidae were received by S. sericeum than S. nemoralis, which received more visitors of the Syrphidae and Tachinidae. The insect visitation rate was not significantly different between the two plant species. Solidago nemoralis was visited by fewer insect taxa per day than S. sericeum, but the constancy of its visitors was higher. The insect visitor composition changed over time, with B. bifarius ignoring S. sericeum plants initially, then visiting them more frequently as the number of receptive S. nemoralis capitula declined. Hand pollination increased seed set in the earliest flowering capitula of S. sericeum, but not for those flowering during the peak. This research shows that the quantity of insect visits to the rare plant is comparable with that of the common plant but that pollination quality may be lower, particularly for early blooming capitula.

scholarly journals Biogenesis and Function of Small Non-Coding RNAs Derived from Eukaryotic Ribosomal RNA

2018 ◽  
Author(s):  
Marine Lambert ◽  
Abderrahim Benmoussa ◽  
Patrick Provost
Keyword(s):  
Ribosomal Rna ◽  
Potential Role ◽  
A Priori ◽  
Biological Significance ◽  
Rna Seq ◽  
New Class ◽  
Scientific Mind ◽  
Non Coding Rnas ◽  
And Function ◽  
Rrna Sequences

The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will discuss about the biogenesis and function of small non-coding RNAs derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs), and their potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because we could not believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.

scholarly journals RNA‐seq–based profiling of extracellular vesicles in plasma reveals a potential role of miR‐122‐5p in asthma

Allergy ◽  
2020 ◽  
Vol 76 (1) ◽  
pp. 366-371
Author(s):  
Thomas Bahmer ◽  
Susanne Krauss‐Etschmann ◽  
Dominik Buschmann ◽  
Jochen Behrends ◽  
Henrik Watz ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Potential Role ◽  
Rna Seq

scholarly journals Chemical Basis of Floral Color Signals in Gesneriaceae: The Effect of Alternative Anthocyanin Pathways

2020 ◽  
Vol 11 ◽  
Author(s):  
Ezgi Ogutcen ◽  
Karine Durand ◽  
Marina Wolowski ◽  
Laura Clavijo ◽  
Catherine Graham ◽  
...  
Keyword(s):  
High Performance ◽  
Flower Color ◽  
Pollination Syndromes ◽  
Angiosperm Evolution ◽  
Ecological Diversification ◽  
Floral Color ◽  
Wide Range ◽  
Hummingbird Pollination ◽  
Color Signals ◽  
Physical And Chemical

Changes in floral pigmentation can have dramatic effects on angiosperm evolution by making flowers either attractive or inconspicuous to different pollinator groups. Flower color largely depends on the type and abundance of pigments produced in the petals, but it is still unclear whether similar color signals rely on same biosynthetic pathways and to which extent the activation of certain pathways influences the course of floral color evolution. To address these questions, we investigated the physical and chemical aspects of floral color in the Neotropical Gesnerioideae (ca. 1,200 spp.), in which two types of anthocyanins, hydroxyanthocyanins, and deoxyanthocyanins, have been recorded as floral pigments. Using spectrophotometry, we measured flower reflectance for over 150 species representing different clades and pollination syndromes. We analyzed these reflectance data to estimate how the Gesnerioideae flowers are perceived by bees and hummingbirds using the visual system models of these pollinators. Floral anthocyanins were further identified using high performance liquid chromatography coupled to mass spectrometry. We found that orange/red floral colors in Gesnerioideae are produced either by deoxyanthocyanins (e.g., apigenidin, luteolinidin) or hydroxyanthocyanins (e.g., pelargonidin). The presence of deoxyanthocyanins in several lineages suggests that the activation of the deoxyanthocyanin pathway has evolved multiple times in the Gesnerioideae. The hydroxyanthocyanin-producing flowers span a wide range of colors, which enables them to be discriminated by hummingbirds or bees. By contrast, color diversity among the deoxyanthocyanin-producing species is lower and mainly represented at longer wavelengths, which is in line with the hue discrimination optima for hummingbirds. These results indicate that Gesnerioideae have evolved two different biochemical mechanisms to generate orange/red flowers, which is associated with hummingbird pollination. Our findings also suggest that the activation of the deoxyanthocyanin pathway has restricted flower color diversification to orange/red hues, supporting the potential constraining role of this alternative biosynthetic pathway on the evolutionary outcome of phenotypical and ecological diversification.

The potential role of visual cues for microhabitat selection during the early life phase of a coral reef fish (Lutjanus fulviflamma)

2011 ◽  
Vol 401 (1-2) ◽  
pp. 118-125 ◽  
Author(s):  
M.M. Igulu ◽  
I. Nagelkerken ◽  
R. Fraaije ◽  
R. van Hintum ◽  
H. Ligtenberg ◽  
...  
Keyword(s):  
Coral Reef ◽  
Reef Fish ◽  
Coral Reef Fish ◽  
Early Life ◽  
Visual Cues ◽  
Potential Role ◽  
Microhabitat Selection ◽  
Life Phase

scholarly journals Inhibition of Osteoblast Proliferation and Migration by Exogenous and Endogenous Formaldehyde

2019 ◽  
Author(s):  
Xu Teng ◽  
Wei Huang ◽  
Hefeng Yu ◽  
Pei Wang ◽  
Weishi Li ◽  
...  
Keyword(s):  
Cell Growth ◽  
Potential Role ◽  
Expression Patterns ◽  
Cell Counting ◽  
Rna Seq ◽  
Cell Growth And Migration ◽  
Naturally Occurring ◽  
Significant Enrichment ◽  
And Migration ◽  
Proliferation And Migration

AbstractExogenous and endogenous formaldehyde (FA) plays an important role in cell growth and migration; however, its potential role in osteoblasts remains largely unclear. Cell counting kit-8 (CCK-8) and wound healing assays revealed that FA exposure at naturally occurring concentrations inhibited the proliferation and migration of mouse preosteoblast MC3T3-E1 cells. Moreover, RNA sequencing (RNA-seq) analysis revealed that FoxO1 signaling pathway components displayed distinct expression patterns upon FA exposure, reflected through significant enrichment of cell migration. In particular, FoxO1 Sirt1 and FA-induced related protein expression which were closely with cell proliferation and migration were confirmed by western blotting. The present results indicate that the FoxO1 pathway is involved in FA-induced inhibition of cell growth and migration.

scholarly journals Insect visitors to avocado flowers in the Bay of Plenty, New Zealand

2017 ◽  
Vol 70 ◽  
pp. 38-44 ◽  
Author(s):  
S.F.J. Read ◽  
B.G. Howlett ◽  
L.K. Jesson ◽  
D.E. Pattemore
Keyword(s):  
New Zealand ◽  
Honey Bee ◽  
Honey Bees ◽  
Insect Species ◽  
Insect Pollination ◽  
Flower Visitor ◽  
Production Area ◽  
Abundance And Diversity ◽  
Stocking Rates ◽  
Insect Visitors

Insect pollination is key to ensuring adequate fruit yields within avocado orchards. Various bee and non-bee insect species have been considered as potential pollinators of avocado worldwide, but in New Zealand there has been little research into which insect species visit avocado flowers. In the Bay of Plenty, an important avocado production area, flower visitor abundance and diversity data were obtained by conducting observational surveys in four orchards in November 2015. Honey bees were the dominant flower visitors in all orchards surveyed, representing 92.9% of all insects recorded, but there was high variation in numbers among sites. Other common insects observed included the beetle, Zorion guttigerum (3.4%), and bumblebees Bombus spp. (1.6%). A better understanding of the interaction between honey bee stocking rates and flower visitor abundances within orchards could assist in improving pollination recommendations.

scholarly journals Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis

2018 ◽  
Author(s):  
Jin Li ◽  
Peng Yu
Keyword(s):  
Alternative Splicing ◽  
Computational Analysis ◽  
Potential Role ◽  
Exon Skipping ◽  
Chronic Inflammatory Disease ◽  
Splicing Factors ◽  
The Novel ◽  
Rna Seq ◽  
Genome Wide

AbstractPsoriasis is a chronic inflammatory disease that affects the skin, nails, and joints. For understanding the mechanism of psoriasis, though, alternative splicing analysis has received relatively little attention in the field. Here, we developed and applied several computational analysis methods to study psoriasis. Using psoriasis mouse and human datasets, our differential alternative splicing analyses detected hundreds of differential alternative splicing changes. Our analysis of conservation revealed many exon-skipping events conserved between mice and humans. In addition, our splicing signature comparison analysis using the psoriasis datasets and our curated splicing factor perturbation RNA-Seq database, SFMetaDB, identified nine candidate splicing factors that may be important in regulating splicing in the psoriasis mouse model dataset. Three of the nine splicing factors were confirmed upon analyzing the human data. Our computational methods have generated predictions for the potential role of splicing in psoriasis. Future experiments on the novel candidates predicted by our computational analysis are expected to provide a better understanding of the molecular mechanism of psoriasis and to pave the way for new therapeutic treatments.

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