scholarly journals Insight into the Phylogenetic Relationships among Three Subfamilies within Heptageniidae (Insecta: Ephemeroptera) along with Low-Temperature Selection Pressure Analyses Using Mitogenomes

Insects ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 656
Author(s):  
Xiao-Dong Xu ◽  
Jia-Yin Guan ◽  
Zi-Yi Zhang ◽  
Yu-Rou Cao ◽  
Yin-Yin Cai ◽  
...  
Keyword(s):  
Low Temperature ◽  
Positive Selection ◽  
Temperature Stress ◽  
Selection Pressure ◽  
Gene Rearrangement ◽  
Phylogenetic Analyses ◽  
Low Temperature Stress ◽  
Protein Coding ◽  
Site Model ◽  
Branch Site

We determined 15 complete and two nearly complete mitogenomes of Heptageniidae belonging to three subfamilies (Heptageniinae, Rhithrogeninae, and Ecdyonurinae) and six genera (Afronurus, Epeorus, Leucrocuta, Maccaffertium, Stenacron, and Stenonema). Species of Rhithrogeninae and Ecdyonurinae had the same gene rearrangement of CR-I-M-Q-M-ND2, whereas a novel gene rearrangement of CR-I-M-Q-NCR-ND2 was found in Heptageniinae. Non-coding regions (NCRs) of 25–47 bp located between trnA and trnR were observed in all mayflies of Heptageniidae, which may be a synapomorphy for Heptageniidae. Both the BI and ML phylogenetic analyses supported the monophyly of Heptageniidae and its subfamilies (Heptageniinae, Rhithrogeninae, and Ecdyonurinae). The phylogenetic results combined with gene rearrangements and NCR locations confirmed the relationship of the subfamilies as (Heptageniinae + (Rhithrogeninae + Ecdyonurinae)). To assess the effects of low-temperature stress on Heptageniidae species from Ottawa, Canada, we found 27 positive selection sites in eight protein-coding genes (PCGs) using the branch-site model. The selection pressure analyses suggested that mitochondrial PCGs underwent positive selection to meet the energy requirements under low-temperature stress.

scholarly journals Comparative Proteomic Analysis on Chloroplast Proteins Provides New Insights Into the Effects of Low Temperature in Sugar Beet

2021 ◽  
Author(s):  
Jiali Long ◽  
Wang Xing ◽  
Yuguang Wang ◽  
Zedong Wu ◽  
Wenjing Li ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Low Temperature ◽  
Sugar Beet ◽  
Temperature Stress ◽  
Phylogenetic Analyses ◽  
Marker Gene ◽  
Low Temperature Stress ◽  
Chloroplast Envelope ◽  
Pcr Analysis ◽  
Sugar Beets

Abstract Background: Low temperature, which is one of the main environmental factors that limits geographical distribution and sucrose yield, is a common abiotic stress during the growth and development of sugar beet. As a regulatory hub of plant response to abiotic stress, activity in the chloroplasts is related to many molecular and physiological processes, particularly in response to low temperature stress. Results: The contents of chlorophyll (Chl) and malondialdehyde (MDA), relative electrical conductivity (REL), and superoxide dismutase (SOD) activity were measured. The results showed that sugar beet could manage low temperature stress by regulating the levels of Chl, REL and MDA, and the activity of SOD. The physiological responses indicated that sugar beets respond positively to low temperature treatments and are not significantly damaged. Moreover, to determine the precise time to response low temperature in sugar beet, well-known abiotic stresses-responsive transcript factor family, namely DEHYDRATION RESPONSIVE ELEMENT BINDING PROTEIN (DREB), was selected as the marker gene. The results of phylogenetic analyses showed that BvDREBA1 and BvDREBA4 were in the same branch as the cold- and drought-responsive AtDREB gene. In addition, the expression of BvDREBs reached its maximum level at 24 h after low temperature by RNA-Seq and qRT-PCR analysis. Furthermore, the changes in chloroplast proteome after low temperature at 24 h were detected using a label-free technique. A total of 416 differentially expressed proteins were identified. GO enrichment analysis showed that 16 GO terms were significantly enriched, particularly chloroplast stroma, chloroplast envelope, and chloroplast thylakoid membrane. It is notable that the transport of photosynthetic proteins (BvLTD, BvTOC100, and Toc-Tic complex), the formation of starch granules (BvPU1, BvISA3, and BvGWD3) and the scavenging of reactive oxygen species (BvCu/Zn-SOD, BvCAT, BvPrx, and BvTrx) were the pathways used by sugar beets to respond to low temperatures at an early stage.Conclusions: These results provide a preliminarily analysis of how chloroplasts of sugar beet respond to low temperature stress at the translational level and provide a theoretical basis for breeding low temperature resistant varieties of sugar beet.

scholarly journals Dietary Diversification and Specialisation in New World Bats Facilitated by Early Molecular Evolution

2021 ◽  
Author(s):  
Joshua H T Potter ◽  
Kalina T J Davies ◽  
Laurel R Yohe ◽  
Miluska K R Sanchez ◽  
Edgardo M Rengifo ◽  
...  
Keyword(s):  
Positive Selection ◽  
Food Sources ◽  
Published Data ◽  
Protein Coding ◽  
Ecological Diversification ◽  
Site Model ◽  
Branch Site ◽  
Complex Picture ◽  
Dietary Diversification ◽  
Dietary Shifts

Abstract Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources, including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species, and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodelling, a trait previously linked to phyllostomid dietary specialisation. Finally, using simulations, we show that the widely-used branch-site model is likely to be misspecified, with the implication that it is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specialisations has been facilitated by early adaptations combined with the generation of new genetic variation.

Effects of low-temperature stress on histone modification in ZF4 cells

2019 ◽  
Vol 26 (2) ◽  
pp. 280
Author(s):  
Penglei JIANG ◽  
Yingdi SHI ◽  
Yanwen HOU ◽  
Bingshe HAN ◽  
Junfang ZHANG
Keyword(s):  
Low Temperature ◽  
Histone Modification ◽  
Temperature Stress ◽  
Low Temperature Stress

Effects of low temperature stress on photosynthesis in potato leaves

2014 ◽  
Vol 39 (1) ◽  
pp. 26-30 ◽  
Author(s):  
Yu-zhi QIN ◽  
Jue CHEN ◽  
Zhen XING ◽  
Chang-zheng HE ◽  
Xing-yao XIONG
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Low Temperature Stress

A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution

2019 ◽  
Vol 69 (4) ◽  
pp. 722-738 ◽  
Author(s):  
Christopher T Jones ◽  
Noor Youssef ◽  
Edward Susko ◽  
Joseph P Bielawski
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Evolutionary History ◽  
Life History Trait ◽  
Molecular Adaptation ◽  
Simulation Studies ◽  
Site Model ◽  
Branch Site ◽  
A Site ◽  
Post Hoc

Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega > 1$. As it is becoming increasingly clear that $\omega > 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]

scholarly journals Zinc Seed Priming Improves Spinach Germination at Low Temperature

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 271
Author(s):  
Muhammad Imran ◽  
Asim Mahmood ◽  
Günter Neumann ◽  
Birte Boelt
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Multispectral Imaging ◽  
Germination Rate ◽  
Cost Effective ◽  
Seed Priming ◽  
Seedling Development ◽  
Low Temperature Stress ◽  
Early Seedling ◽  
Early Seedling Development

Low temperature during germination hinders germination speed and early seedling development. Zn seed priming is a useful and cost-effective tool to improve germination rate and resistance to low temperature stress during germination and early seedling development. Spinach was tested to improve germination and seedling development with Zn seed priming under low temperature stress conditions. Zn priming increased seed Zn concentration up to 48 times. The multispectral imaging technique with VideometerLab was used as a non-destructive method to differentiate unprimed, water- and Zn-primed spinach seeds successfully. Localization of Zn in the seeds was studied using the 1,5-diphenyl thiocarbazone (DTZ) dying technique. Active translocation of primed Zn in the roots of young seedlings was detected with laser confocal microscopy. Zn priming of spinach seeds at 6 mM Zn showed a significant increase in germination rate and total germination under low temperature at 8 °C.

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