17 research outputs found
Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China
<div><p>Wheat blue dwarf (WBD) disease is an important disease that has caused heavy losses in wheat production in northwestern China. This disease is caused by WBD phytoplasma, which is transmitted by <i>Psammotettix striatus</i>. Until now, no genome information about WBD phytoplasma has been published, seriously restricting research on this obligate pathogen. In this paper, we report a new sequencing and assembling strategy for phytoplasma genome projects. This strategy involves differential centrifugation, pulsed-field gel electrophoresis, whole genome amplification, shotgun sequencing, <i>de novo</i> assembly, screening of contigs from phytoplasma and the connection of phytoplasma contigs. Using this scheme, the WBD phytoplasma draft genome was obtained. It was comprised of six contigs with a total size of 611,462 bp, covering ∼94% of the chromosome. Five-hundred-twenty-five protein-coding genes, two operons for rRNA genes and 32 tRNA genes were identified. Comparative genome analyses between WBD phytoplasma and other phytoplasmas were subsequently carried out. The results showed that extensive arrangements and inversions existed among the WBD, OY-M and AY-WB phytoplasma genomes. Most protein-coding genes in WBD phytoplasma were found to be homologous to genes from other phytoplasmas; only 22 WBD-specific genes were identified. KEGG pathway analysis indicated that WBD phytoplasma had strongly reduced metabolic capabilities. However, 46 transporters were identified, which were involved with dipeptides/oligopeptides, spermidine/putrescine, cobalt and Mn/Zn transport, and so on. A total of 37 secreted proteins were encoded in the WBD phytoplasma chromosome and plasmids. Of these, three secreted proteins were similar to the reported phytoplasma virulence factors TENGU, SAP11 and SAP54. In addition, WBD phytoplasma possessed several proteins that were predicted to play a role in its adaptation to diverse environments. These results will provide clues for research on the pathogenic mechanisms of WBD phytoplasma and will also provide a perspective about the genome sequencing of other phytoplasmas and obligate organisms.</p></div
Alignments between WBD phytoplasma secreted proteins and published phytoplasma virulence factors.
<p>Alignments between WBD phytoplasma secreted proteins and published phytoplasma virulence factors.</p
Synteny plots of WBD and other phytoplasma genomes.
<p>Shown are alignments of the WBD assembly and ‘<i>Ca.</i> P. australiense’ (A), ‘<i>Ca.</i> P. mali’(B), OY-M (C) and AY-WB (D). E, alignment between OY-M and AY-WB.</p
Placement of WBD contigs in the OY-M and AY-WB genomes.
<p>Ring 1, similar sequences to the WBD contigs in the OY-M sense strand; ring 2, similar sequences to the WBD contigs in the OY-M antisense strand; ring 3, WBD contigs; ring 4, similar sequences to the WBD contigs in the AY-WB sense strand; ring 4, similar sequences to the WBD contigs in the AY-WB antisense strand.</p
Map of the WBD draft genome.
<p>Rings from the outside to inside are as follows: ring 1, contigs of the WBD draft genome; ring 2, predicted ORFs on the sense strand; ring 3, predicted ORFs on the antisense strand; ring 4, ORFs of predicted secreted proteins; ring 5, ORFs of predicted secreted membrane proteins; ring 6, ORFs of predicted transport proteins; ring 7, locations of rRNA genes (purple) and tRNA genes (gray).</p
The arrangements of 13 genes involved in glycolysis and gluconeogenesis in the WBD, OY-M and AY-WB genomes.
<p>The arrangements of 13 genes involved in glycolysis and gluconeogenesis in the WBD, OY-M and AY-WB genomes.</p
Amino acid sequence identity of 13 proteins involved in glycolysis and gluconeogenesis between WBD and four other phytoplasmas.
<p>Amino acid sequence identity of 13 proteins involved in glycolysis and gluconeogenesis between WBD and four other phytoplasmas.</p
Number of homologous genes and genome-specific genes.
<p>A, comparative analysis of the COG functional category between WBD phytoplasma genes and phytoplasmas-shared genes; B, comparison among WBD, OY-M, AY-WB, ‘<i>Ca</i>. P. mali’ and ‘<i>Ca.</i> P. australiense’; C, comparison among WBD, OY-M and AY-WB; D, comparison among WBD, ‘<i>Ca</i>. P. mali’ and ‘<i>Ca.</i> P. australiense’. J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; D: Cell cycle control, cell division, chromosome partitioning; V: Defense mechanisms; T: Signal transduction mechanisms; M: Cell wall/membrane/envelope biogenesis; U: Intracellular trafficking, secretion, and vesicular transport; O: Posttranslational modification, protein turnover, chaperones; C: Energy production and conversion; G: Carbohydrate transport and metabolism; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; P: Inorganic ion transport and metabolism; Q: Secondary metabolite biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown; X: no functional category assignment.</p
Efficient preparation of icariin from epimedin C by recyclable biphasic enzymatic hydrolysis
Icariin is the most bioactive ingredient of Epimedium L. and a quality marker of Herba Epimedii. Conventional methods for production of Icariin are known to be inefficient, resulting in low yields and significant environmental pollution. This study aimed to develop a sustainable and effective biphasic enzymatic hydrolysis system for the efficient conversion of epimedin C to icariin. The biphasic system was created using butyl acetate and phosphate buffer (pH 4.5) at a ratio of 3:1 (V/V) along with α-L-rhamnosidase/epimedin C (2 U/1 mg) at 50 °C for 12 h. Consequently, 98.21% of epimedin C was hydrolysed to icariin, with 95.62% of the product being transferred to the organic phase. Even after four cycles of use, the conversion ratio remained high at 75.28%. Furthermore, this novel strategy was also used for the conversion of Epimedium brevicornu Maxim. extracts. The biphasic system represents a sustainable and effective method for icariin production, offering potential benefits for industrial applications.</p
Table_3_Identification, characterization and expression analysis of wheat RSH family genes under abiotic stress.xlsx
Guanosine pentaphosphate and guanosine tetraphosphate are collectively called (p)ppGpp (Guanosine tetraphosphate and pentaphosphate). (p)ppGpp content in plants is affected by conditions such as light, salt, pH, UV light, and environmental phytohormones. The synthesis and hydrolysis of (p)ppGpp in plants is accomplished by a class of proteins called RSH (RelA/SpoT homologs). To date, a systematic and comprehensive genome-wide analysis of the RSH gene family in wheat and its closely related species has not been conducted. In this study, 15, 14, 12, and 8 members of RSH were identified in wheat (Triticum aestivum), Triticum dicoccoides, Triticum urartu and Aegilops tauschii respectively. Based on the conserved structural domains of the RSH genes, the TaRSHs have been categorized into TaRSH and TaCRSH. The gene duplications in the TaRSH gene family were all identified as segmental duplications indicating that the TaRSH family plays a significant role in expansion and that segmental duplications maintain a degree of genetic stability. Through the analysis of transcriptome data and RT-qPCR experiments, it was observed that the expression levels of TaRSHs were upregulated in response to abiotic stress. This upregulation suggests that TaRSHs play a crucial role in enhancing the resilience of wheat to adverse environmental conditions during its growth and development. Their increased expression likely contributes to the acquisition of stress tolerance mechanisms in wheat. Especially under NaCl stress, the expression levels increased most significantly. The more detailed systematic analysis provided in this article will help us understand the role of TaRSHs and provide a reference for further research on its molecular biological functions in wheat.</p