transcriptome analyses
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2022 ◽  
Vol 15 ◽  
Author(s):  
Yuan-Bo Pan ◽  
Yiyu Sun ◽  
Hong-Jiang Li ◽  
Lai-Yang Zhou ◽  
Jianmin Zhang ◽  
...  

The function of glial cells in axonal regeneration after injury has been the subject of controversy in recent years. Thus, deeper insight into glial cells is urgently needed. Many studies on glial cells have elucidated the mechanisms of a certain gene or cell type in axon regeneration. However, studies that manipulate a single variable may overlook other changes. Here, we performed a series of comprehensive transcriptome analyses of the optic nerve head over a period of 90 days after optic nerve crush (ONC), showing systematic molecular changes in the optic nerve head (ONH). Furthermore, using weighted gene coexpression network analysis (WGCNA), we established gene module programs corresponding to various pathological events at different times post-ONC and found hub genes that may be potential therapeutic targets. In addition, we analyzed the changes in different glial cells based on their subtype markers. We revealed that the transition trend of different glial cells depended on the time course, which provides clues for modulating glial function in further research.


Horticulturae ◽  
2022 ◽  
Vol 8 (1) ◽  
pp. 57
Author(s):  
Xinxin Lu ◽  
Lei Zhang ◽  
Wenyue Huang ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
...  

Turnip mosaic virus (TuMV), which is distributed almost all over the world and has a wide range of hosts, mainly brassica crops, was first described in Brassica rapa in the USA. Plant volatile compounds play an important role in the host searching behavior of natural enemies of herbivorous insects. In this study, TuMV-inoculated resistant and susceptible B. rapa lines were tested using volatile metabolome and transcriptome analyses. In volatile metabolome analysis, the volatile organic compounds (VOCs) were different after inoculation with TuMV in resistant B80124 and susceptible B80461, and the degree of downregulation of differentially expressed metabolites was more obvious than the degree of upregulation. Through transcriptome analysis, 70% of differentially expressed genes were in biological process, especially focusing on defense response, flavonoid biosynthetic process, and toxin metabolic process, which indicates that TuMV stress maybe accelerate the increase of VOCs. Integrating the metabolome and transcriptome analyses, after inoculating with TuMV, auxin regulation was upregulated, and ARF, IAA and GH3 were also upregulated, which accelerated cell enlargement and plant growth in tryptophan metabolism. The different genes in zeatin biosynthesis pathways were downregulated, which reduced cell division and shoot initiation. However, the metabolite pathways showed upregulation in brassinosteroid biosynthesis and α-linolenic acid metabolism, which could cause cell enlargement and a stress response. This study determined the difference in volatiles between normal plants and infected plants and may lay a foundation for anti-TuMV research in B. rapa.


2022 ◽  
Vol 67 (1) ◽  
pp. 163-180
Author(s):  
Franziska Beran ◽  
Georg Petschenka

Plant defense compounds play a key role in the evolution of insect–plant associations by selecting for behavioral, morphological, and physiological insect adaptations. Sequestration, the ability of herbivorous insects to accumulate plant defense compounds to gain a fitness advantage, represents a complex syndrome of adaptations that has evolved in all major lineages of herbivorous insects and involves various classes of plant defense compounds. In this article, we review progress in understanding how insects selectively accumulate plant defense metabolites and how the evolution of specific resistance mechanisms to these defense compounds enables sequestration. These mechanistic considerations are further integrated into the concept of insect–plant coevolution. Comparative genome and transcriptome analyses, combined with approaches based on analytical chemistry that are centered in phylogenetic frameworks, will help to reveal adaptations underlying the sequestration syndrome, which is essential to understanding the influence of sequestration on insect–plant coevolution.


2022 ◽  
Vol 292 ◽  
pp. 110652
Author(s):  
Qi Kai-Jie ◽  
Wu Xiao ◽  
Gao Xin ◽  
Li Lu-Fei ◽  
Xie Zhi-Hua ◽  
...  

2021 ◽  
Author(s):  
B Gemeinholzer ◽  
O Rupp ◽  
A Becker ◽  
M. Strickert ◽  
C-M Müller

AbstractThe important worldwide forage crop red clover (Trifolium pratense L.) is widely cultivated as cattle feed and for soil improvement. Wild populations and landraces have great natural diversity that could be used to improve cultivated red clover. However, to date, there is still insufficient knowledge about the natural genetic and phenotypic diversity of the species. Here, we developed a low-cost transcriptome analysis (mRNA-GBS) with reduced complexity and compared the results with population genetic (GBS) and previously published mRNA-Seq data, to assess whether analysis of intraspecific variation within and between populations and transcriptome responses is possible simultaneously. The mRNA-GBS approach was successful. SNP analyses from the mRNA-GBS approach revealed comparable patterns to the GBS results, but it was not possible to link transcriptome analyses with reduced complexity and sequencing depth to previously published greenhouse and field expression studies. The use of short sequences upstream of the poly(A) tail of mRNA to reduce complexity are promising approaches that combine population genetics and expression profiling to analyze many individuals with trait differences simultaneously and cost-effectively, even in non-model species. Our mRNA-GBS approach revealed too many additional short mRNA sequences, hampering sequence alignment depth and SNP recovery. Optimizations are being discussed. Nevertheless, our study design across different regions in Germany was also challenging as the use of differential expression analyses with reduced complexity, in which mRNA is fragmented at specific sites rather than randomly, is most likely counteracted under natural conditions by highly complex plant reactions at low sequencing depth.


2021 ◽  
Vol 226 ◽  
pp. 112798
Author(s):  
Yongfeng Wang ◽  
Zhiquan Yu ◽  
Zunpan Fan ◽  
Yiwei Fang ◽  
Liting He ◽  
...  

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