Comparative transcriptome analysis of differential expression in different tissues of Prunella vulgaris / 中草药

Objective: To compare and analyze the transcriptome of ears, leaves and stems of Prunella vulgaris, and excavate the key enzyme genes related to the secondary metabolism biosynthesis of P. vulgaris. Methods: The transcriptome of ears, leaves and stems of P. vulgaris were sequenced by Illumina high-throughput sequencing technology. Additionally biosynthesis related enzyme gene of secondary metabolism were identified from differentially expressed genes. Results: In the transcripts of three different tissues of P. vulgaris, a total of 8 270 Unigenes differed significantly between at least two tissues. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of genes differentially expressed in different tissues showed that the expression of phenylpropanoid biosynthesis genes varied greatly. A total of 31 triterpenoid biosynthesis-related Unigenes, 16 phenolic acid biosynthesis-related Unigenes, and 113 P450s-related Unigenes were identified in the differentially expressed genes. Conclusion: This study provides a basis for the subsequent discovery of functional genes related to the secondary metabolism synthesis pathway of P. vulgaris, and plays a foundation for the regulation of secondary metabolism biosynthesis of P. vulgaris.

Transcriptome analysis reveals key enzyme genes involved in lignin biosynthesis pathway in Arctium lappa / 中草药

Objective: To obtain the functional genes in Arctium lappa and analyze the key enzyme genes involved in biosynthesis pathway of lignin. Methods: The transcriptome dataset of roots of A. lappa was obtained by using the BGISEQ-500 sequencing platform. Unigenes were de novo assembled and annotated according to the existing nucleic acids and protein databases. The key enzyme genes involved in lignin biosynthesis pathway were analyzed and the three-dimensional model of phenylalanine ammonialyase (AlPAL) was generated by the SWISS-MODEL and PyMol. Results: A total of 54 215 Unigenes were obtained by de novo assembly, and 42 003 Unigenes were annotated in at least one public database. A total of 1 668 Unigenes were identified to be plant transcription factors (TFs), which belong to 54 TF families, and 423 Unigenes were found to be involved in the biosynthesis pathway of lignin. Structure model indicated that AlPAL was a homotypic tetramer, and each monomer was consisted of three domains, including 4-methyl-imidazole-5-ketone (MIO) domain, core domain and shield domain. The MIO domain contained three conserved amino acids (ASG), which formed the catalytic activity center of the enzyme. Conclusion: This study was the first de novo transcriptome assembly of A. lappa, which will lay the foundation for the identification of functional genes, secondary metabolic pathway and the study of regulation mechanism of biosynthesis pathway of lignin in A. lappa in the future.

Transcriptome profiling and digital gene expression analysis of genes associated with salinity resistance in peanut

Background: Soil salinity can significantly reduce crop production, but the molecular mechanism of salinity tolerance in peanut is poorly understood. A mutant (S1) with higher salinity resistance than its mutagenic parent HY22 (S3) was obtained. Transcriptome sequencing and digital gene expression (DGE) analysis were performed with leaves of S1 and S3 before and after plants were irrigated with 250 mM NaCl. Results: A total of 107,725 comprehensive transcripts were assembled into 67,738 unigenes using TIGR Gene Indices clustering tools (TGICL). All unigenes were searched against the euKaryotic Ortholog Groups (KOG), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and these unigenes were assigned to 26 functional KOG categories, 56 GO terms, 32 KEGG groups, respectively. In total 112 differentially expressed genes (DEGs) between S1 and S3 after salinity stress were screened, among them, 86 were responsive to salinity stress in S1 and/or S3. These 86 DEGs included genes that encoded the following kinds of proteins that are known to be involved in resistance to salinity stress: late embryogenesis abundant proteins (LEAs), major intrinsic proteins (MIPs) or aquaporins, metallothioneins (MTs), lipid transfer protein (LTP), calcineurin B-like protein-interacting protein kinases (CIPKs), 9-cis-epoxycarotenoid dioxygenase (NCED) and oleosins, etc. Of these 86 DEGs, 18 could not be matched with known proteins. Conclusion: The results from this study will be useful for further research on the mechanism of salinity resistance and will provide a useful gene resource for the variety breeding of salinity resistance in peanut.

High-throughput transcriptome sequencing of roots of Dictamnus dasycarpus and data analyses / 中草药

Objective To obtain the transcriptome dataset of roots of Dictamnus dasycarpus. Methods The root transcriptome dataset of D. dasycarpus was obtained using the high-throughput sequencing platform Illumina HiSeqTM 2000 150PE, followed by systemic bioinformatics analyses. Results A great number of 69 643 286 high quality clean reads were obtained by the transcriptome sequencing analyses. Using Trinity de novo assembling, a total of 49 050 unigenes were finally obtained, with an average length of 841 nt. BLAST analysis indicated that 31 636 (accounting 64.49% of the total unigenes), 22 367 (45.60%), 19 246 (39.23%), 12 595 (25.68%) unigenes were successfully annotated in the NR, Swiss-port, KOG, and KEGG databases, respectively. And GO classification contained the basic three major groups, including biological process, cellular component, and molecular function with 42 subgroups. A total of 132 KEGG standard metabolic pathways were designated, 18 of which were defied as the secondary metabolism. Further analysis revealed that a total of 90 unigenes were involved in the biosynthesis of various alkaloids. Of all unigenes, 1 908 were predicted to have CDS, and 55 families of plant transcription factors were also identified. Using MISA prediction, 4 579 simple sequence repeats (SSRs) were obtained, among which the tri-nucleotide SSRs were abundant with 2 021 (44.1%), whereas the penta-nucleotide SSRs accounted for 3.5%. Conclusion The root transcriptome of D. dasycarpus revealed by the high-throughput sequencing technology will be important for gene functional characterization, secondary metabolism pathway exploration, and regulation mechanism research in this species.

Transcriptome differences between 20- and 3, 000-year-old Platycladus orientalis reveal that ROS are involved in senescence regulation

Background: Platycladus orientalis has an extremely long life span of several thousands of years, attracting great interests in the mechanisms involved in such successful senescence regulation and resistance at physiological and molecular levels. Results: The levels of reactive oxygen species (ROS) were higher in 3,000-year-old than in 20-year-old P. orientalis, and the activities of GR and GSH demonstrated the same trend. We produced and analyzed massive sequence information from pooled samples of P. orientalis through transcriptome sequencing, which generated 51,664 unigenes with an average length of 475 bp. We then used RNA-seq analysis to obtain a high-resolution age­course profile of gene expression in 20- and 3,000-year-old P. orientalis individuals. Totally, 106 differentially expressed genes were obtained, of which 47 genes were downregulated and 59 upregulated in the old tree. These genes were involved in transcription factors, hormone-related responses, ROS scavengers, senescence-related responses, stress response, and defense and possibly play crucial roles in tackling various stresses in the 3,000-year-old P. orientalis during its life time. The expression patterns of genes related to ROS homeostasis further indicated that the high ability of ROS scavenging could be helpful for the 3,000-year-old P. orientalis to resist senescence. Conclusions: This study provides a foundation for the elucidation of senescence resistance through molecular studies and the discovery of useful genes in P. orientalis.

Transcriptome analysis of Cinnamomum longepaniculatum by high-throughput sequencing

Background: Cinnamomum longepaniculatum is an important commercial crop and the main source of volatile terpenoids. The biosynthesis of key bioactive metabolites of C. longepaniculatum is not well understood because of the lack of available genomic and transcriptomic information. To address this issue, we performed transcriptome sequencing of C. longepaniculatum leaves to identify factors involved in terpenoid metabolite biosynthesis. Results: Transcriptome sequencing of C. longepaniculatum leaves generated over 56 million raw reads. The transcriptome was assembled using the Trinity software and yielded 82,061 unigenes with an average length of 879.43 bp and N50 value of 1387 bp. Furthermore, Benchmarking Universal Single-Copy Orthologs analysis indicated that our assembly is 91% complete. The unigenes were used to query the nonredundant database depending on sequence similarity; 42,809 unigenes were homologous to known genes in different species, with an annotation rate of 42.87%. The transcript abundance and Gene Ontology analyses revealed that numerous unigenes were associated with metabolism, while others were annotated in functional categories including transcription, signal transduction, and secondary metabolism. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that 19,260 unigenes were involved in 385 metabolic pathways, with 233 unigenes found to be involved in terpenoid metabolism. Moreover, 23,463 simple sequence repeats were identified using the microsatellite identification tool. Conclusion: This is the first detailed transcriptome analysis of C. longepaniculatum. The findings provide insights into the molecular basis of terpenoid biosynthesis and a reference for future studies on the genetics and breeding of C. longepaniculatum.

Sequencing and de novo assembly of the Asian gypsy moth transcriptome using the Illumina platform

Abstract The Asian gypsy moth (Lymantria dispar) is a serious pest of forest and shade trees in many Asian and some European countries. However, there have been few studies of L. dispar genetic information and comprehensive genetic analyses of this species are needed in order to understand its genetic and metabolic sensitivities, such as the molting mechanism during larval development. In this study, high-throughput sequencing technology was used to sequence the transcriptome of the Asian subspecies of the gyspy moth, after which a comprehensive analysis of chitin metabolism was undertaken. We generated 37,750,380 high-quality reads and assembled them into contigs. A total of 37,098 unigenes were identified, of which 15,901 were annotated in the NCBI non-redundant protein database and 9,613 were annotated in the Swiss-Prot database. We mapped 4,329 unigenes onto 317 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. Chitin metabolism unigenes were found in the transcriptome and the data indicated that a variety of enzymes was involved in chitin catabolic and biosynthetic pathways.