Peer Review #2 of "Transcriptomic and metabolomic analysis of autumn leaf color change in Fraxinus angustifolia (v0.2)"
Yanlong WangJinpeng ZhenXiaoyu CheKang ZhangGuowei ZhangHuijuan YangJing WenJinxin WangJiming WangBo HeAilong YuYanhui LiZhigang WangJinxin WangJiming Wang
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Fraxinus angustifolia is a type of street tree and shade tree with ornamental value.It has a beautiful shape and yellow or reddish purple autumn leaves, but its leaf color formation mechanism and molecular regulation network need to be studied.In this study, we integrated the metabolomes and transcriptomes of stage 1 (green leaf) and stage 2 (redpurple leaf) leaves at two different developmental stages to screen differential candidate genes and metabolites related to leaf color variation.The results of stage 1 and stage 2 transcriptome analysis showed that a total of 5827 genes were differentially expressed, including 2249 upregulated genes and 3578 downregulated genes.Through functional enrichment analysis of differentially expressed genes, we found that they were involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, pigment metabolism, carotene metabolism, terpenoid biosynthesis, secondary metabolite biosynthesis, pigment accumulation, and other biological processes.By measuring the metabolites of Fraxinus angustifolia leaves, we found the metabolites closely related to the differentially expressed genes in two different periods of Fraxinus angustifolia, among which flavonoid compounds were the main differential metabolites.Through transcriptome and metabolomics data association analysis, we screened nine differentially expressed genes related to anthocyanins.Transcriptome and qRT-PCR results showed that these nine genes showed significant expression differences in different stages of the sample, and we speculate that they are likely to be the main regulatory factors in the molecular mechanism of leaf coloration.This is the first time that we have analyzed the transcriptome combination metabolome in the process of leaf coloration of Fraxinus angustifolia, which has importantMating triggers substantial changes in gene expression and leads to subsequent physiological and behavioral modifications. However, postmating transcriptomic changes responding to mating have not yet been fully understood. Here, we carried out RNA sequencing (RNAseq) analysis in the sweet potato whitefly, Bemisia tabaci MED, to identify genes in females in response to mating. We compared mRNA expression in virgin and mated females at 24 h. As a result, 434 differentially expressed gene transcripts (DEGs) were identified between the mated and unmated groups, including 331 up- and 103 down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that many of these DEGs encode binding-related proteins and genes associated with longevity. An RT-qPCR validation study was consistent with our transcriptomic analysis (14/15). Specifically, expression of P450s (Cyp18a1 and Cyp4g68), ubiquitin-protein ligases (UBR5 and RNF123), Hsps (Hsp68 and Hsf), carboxylase (ACC-2), facilitated trehalose transporters (Tret1-2), transcription factor (phtf), and serine-protein kinase (TLK2) were significantly elevated in mated females throughout seven assay days. These combined results offer a glimpe of postmating molecular modifications to facilitate reproduction in B. tabaci females.
KEGG
RNA-Seq
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Body plan
Organogenesis
Drosophila embryogenesis
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Penaeus vannamei is one of the commercially important aquaculture species in the world but sensitive to Vibrio anguillarum infection. To understand the immune response of P. vannamei against V. anguillarum infection, the transcriptomes of hepatopancreas and gills of P. vannamei were analysed before and after V. anguillarum infection. Total 6213 differentially expressed genes (DEGs) were obtained from the hepatopancreas, and 3780 were obtained from the gills. The DEGs of interest were screened to construct a heat map. The reliability and accuracy of the transcriptome data were verified using RT-qPCR. HSP70 and ARF6 were found highly expressed in both hepatopancreas and gills, while MLC2s encoded by two different gene sequences were found to be expressed in hepatopancreas and gills. Six immune-related DEGs were identified from the protein–protein interaction (PPI) network including the HSP70, ARF6 and MLC2s. The sub-network of PPI was constructed to explore the mode of interaction of immune-related DEGs with their neighbouring proteins. Based on the result of PPI network, we infer that phosphorylated MLC2-1 conducts signal transduction to induce leukocyte transendothelial migration in P. vannamei gills tissue while MLC2-2 plays a role in immunity of V. anguillarum infection not only through activating signal transduction to mediate immune responses but also through the formation of phagosomes in hepatopancreas tissue. HSP70 is associated with the transporting exogenous cargos through presenting antigenic peptides in the process of V. anguillarum infection in P. vannamei. ARF6 interacts with Rab proteins to regulate phagolysosome formation by regulating GTPase activity in P. vannamei gills tissue. In hepatopancreas tissue, ARF6 plays a role in immunity by interacting with cytohesin. This study will contribute to further exploring the immune mechanism of P. vannamei to V. anguillarum infection.
Hepatopancreas
Vibrio anguillarum
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Euphorbia motuogensis M. T. Li, X. Z. Lan, H. P. Deng & W. L. Zheng, sp. nov., a new species from Motuo, Tibet, China, is described and illustrated here. It is closely similar to Euphorbia sikkimensis in having terete root, alternate leaves, well-developed pseudoumbellate inflorescence, cyathium, smooth and glaborus capsule, but Euphorbia motuogensis is clealy distinguishable by its pilose stems, involucral leaves color, secondary involucral leaves absent, cyathophylls number and color, and five similar glands. Furthermore, molecular phylogenetic analyses of sequences from both nuclear ribosomal ITS confirm that this species is distinct from morphologically similar species in this subgenus.
Euphorbiaceae
Subgenus
Euphorbia
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Sexual Differentiation
Illumina dye sequencing
RNA-Seq
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In many animals, sperm competition and sexual conflict are thought to drive the rapid evolution of male-specific genes, especially those expressed in the testes. A potential exception occurs in the male pregnant pipefishes, where females transfer eggs to the males, eliminating testes from participating in these processes. Here, we show that testis-related genes differ dramatically in their rates of molecular evolution and expression patterns in pipefishes and seahorses (Syngnathidae) compared to other fish. Genes involved in testis or sperm function within syngnathids experience weaker selection in comparison to their orthologs in spawning and livebearing fishes. An assessment of gene turnover and expression in the testis transcriptome suggests that syngnathids have lost (or significantly reduced expression of) important classes of genes from their testis transcriptomes compared to other fish. Our results indicate that more than 50 million years of male pregnancy have removed syngnathid testes from the molecular arms race that drives the rapid evolution of male reproductive genes in other taxa.
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RNA-Seq
Sexual dimorphism
KEGG
Sexual Differentiation
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Wheat is one of the most important staple crops worldwide. Fusarium head blight severely reduces wheat yield and quality. Cultivation of a novel type of cleistogamous wheat mutant, ZK001, which was created by static magnetic field treatment, is a new strategy for controlling Fusarium head blight. However, little is known about the mechanism of cleistogamy in wheat. The present study demonstrated that anthers of ZK001 were retained on the glumes at all flowering stages, whereas those of YM18 were extruded from the paleae and lemmae. There was a clear difference in the morphological characteristics of lodicules between YM18 and ZK001. Lodicule calcium and potassium contents were significantly higher in YM18 than in ZK001 from white to yellow anther stages. In Fusarium head blight resistance, the diseased kernel rate and deoxynivalenol content of ZK001 were markedly lower than those of YM18 and QM725. Comparative transcriptome analysis of YM18 and ZK001 was performed to identify regulatory mechanisms of cleistogamy. The main differentially expressed genes identified in the spikelets of YM18 and ZK001 at the green anther stage were associated with cell walls, carbohydrates, phytohormones, water channel, and ion binding, transport, and homeostasis. These differentially expressed genes may play an important role in regulating cellular homeostasis, osmotic pressure, and lodicule development. The results indicate that ZK001 lost the ability to push the lemmae and paleae apart during the flowering stage because of the thin lodicules. ZK001 was speculated to provide structural barriers for Fusarium head blight during the flowering stage. The thin lodicule of ZK001 results from low levels of soluble sugar, calcium ions, and potassium ions in the lodicules. These levels are regulated by differentially expressed genes.
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