High-Throughput Sequencing and <i>De Novo</i> Assembly of the <i>Isatis indigotica</i> Transcriptome

<div><p>Background</p><p><i>Isatis indigotica</i>, the source of the traditional Chinese medicine Radix isatidis (Ban-Lan-Gen), is an extremely important economical crop in China. To facilitate biological, biochemical and molecular research on the medicinal chemicals in <i>I. indigotica</i>, here we report the first <i>I. indigotica</i> transcriptome generated by RNA sequencing (RNA-seq).</p><p>Results</p><p>RNA-seq library was created using RNA extracted from a mixed sample including leaf and root. A total of 33,238 unigenes were assembled from more than 28 million of high quality short reads. The quality of the assembly was experimentally examined by cDNA sequencing of seven randomly selected unigenes. Based on blast search 28,184 unigenes had a hit in at least one of the protein and nucleotide databases used in this study, and 8 unigenes were found to be associated with biosynthesis of indole and its derivatives. According to Gene Ontology classification, 22,365 unigenes were categorized into 48 functional groups. Furthermore, Clusters of Orthologous Group and Swiss-Port annotation were assigned for 7,707 and 18,679 unigenes, respectively. Analysis of repeat motifs identified 6,400 simple sequence repeat markers in 4,509 unigenes.</p><p>Conclusion</p><p>Our data provide a comprehensive sequence resource for molecular study of <i>I. indigotica</i>. Our results will facilitate studies on the functions of genes involved in the indole alkaloid biosynthesis pathway and on metabolism of nitrogen and indole alkaloids in <i>I. indigotica</i> and its related species.</p></div

Histogram of COG clusters of the <i>I.indigotica</i> unigenes.

<p>Out of the 33,238 <i>de novo</i> assembled unigenes, 7,707 had a match in COG and were grouped into 24 clusters.</p

Distribution of different types of simple sequence repeats (SSRs) identified in the <i>I. indigotica</i> unigenes that are longer than 1000 bp.

<p>Distribution of different types of simple sequence repeats (SSRs) identified in the <i>I. indigotica</i> unigenes that are longer than 1000 bp.</p

Pathway assignment based on KEGG mapping.

<p>Pathway assignment based on KEGG mapping.</p

MOESM1 of Responses of zinc recovery to temperature and mineral composition during sphalerite bioleaching process

Additional file 1. Supporting materials including supporting experimental methods,  figures and tables

Histogram of GO classifications of the assembled <i>I. indigotica</i> unigenes.

<p>Results are summarized in three main GO categories: biological process, cellular component and molecular function.</p

Additional file 1 of OsVPE2, a Member of Vacuolar Processing Enzyme Family, Decreases Chilling Tolerance of Rice

Supplementary Material 1. Table S1: Primers used in this study. Table S2: The low-temperature seedling survivability (LTSS) of rice varieties with the two main haplotypes of OsVPE

Image_1_Integrative transcriptomic analysis deciphering the role of rice bHLH transcription factor Os04g0301500 in mediating responses to biotic and abiotic stresses.pdf

Understanding the signaling pathways activated in response to these combined stresses and their crosstalk is crucial to breeding crop varieties with dual or multiple tolerances. However, most studies to date have predominantly focused on individual stress factors, leaving a significant gap in understanding plant responses to combined biotic and abiotic stresses. The bHLH family plays a multifaceted regulatory role in plant response to both abiotic and biotic stresses. In order to comprehensively identify and analyze the bHLH gene family in rice, we identified putative OsbHLHs by multi-step homolog search, and phylogenic analysis, molecular weights, isoelectric points, conserved domain screening were processed using MEGAX version 10.2.6. Following, integrative transcriptome analysis using 6 RNA-seq data including Xoo infection, heat, and cold stress was processed. The results showed that 106 OsbHLHs were identified and clustered into 17 clades. Os04g0301500 and Os04g0489600 are potential negative regulators of Xoo resistance in rice. In addition, Os04g0301500 was involved in non-freezing temperatures (around 4°C) but not to 10°C cold stresses, suggesting a complex interplay with temperature signaling pathways. The study concludes that Os04g0301500 may play a crucial role in integrating biotic and abiotic stress responses in rice, potentially serving as a key regulator of plant resilience under changing environmental conditions, which could be important for further multiple stresses enhancement and molecular breeding through genetic engineering in rice.</p

Additional file 1: of Comparison of microbial taxonomic and functional shift pattern along contamination gradient

Table S1. Sediment properties and ANOVA analysis among three groups. Table S2. Shannon diversity and Pielou evenness of samples based on sequencing data and Geochip hybridization data respectively. Table S3. Correlation between microbial composition and function. Table S4. (a) Mantel test of sequencing data with environmental attributes at the genus level; (b) Mantel test of GeoChip hybridization data with environmental attributes. (DOCX 41 kb

Genome-based models for the oxidation of inorganic sulfur compounds (ISCs).

<p>Schematic representation of enzymes and electron transfer proteins involved in the oxidation of ISCs. Electrons from SQR, TQR, HDR are transferred to the electron transfer chain by the quinone, then are used by NADH complex I to generate reducing power or by terminal oxidases <i>bd</i> or <i>bo₃</i> to form a proton gradient. Abbreviations: TTH, tetrathionate hydrolase; SQR, sulfide quinone reductase; TQR, thiosulfate quinone oxidoreductase; SOR, sulfur oxygenase reductase; SAT, sulfate adenylyltransferase; HDR, heterodisulfide reductase; Omp, outer membrane protein.</p