scholarly journals Comparative Transcriptome Analysis of Early- and Late-Bolting Traits in Chinese Cabbage (Brassica rapa)

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaochun Wei ◽  
Md. Abdur Rahim ◽  
Yanyan Zhao ◽  
Shuangjuan Yang ◽  
Zhiyong Wang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Transcriptome Profiling ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Heading Chinese Cabbage ◽  
Dh Lines

Chinese cabbage is one of the most important and widely consumed vegetables in China. The developmental transition from the vegetative to reproductive phase is a crucial process in the life cycle of flowering plants. In spring-sown Chinese cabbage, late bolting is desirable over early bolting. In this study, we analyzed double haploid (DH) lines of late bolting (“Y410-1” and “SY2004”) heading Chinese cabbage (Brassica rapa var. pekinensis) and early-bolting Chinese cabbage (“CX14-1”) (B. rapa ssp. chinensis var. parachinensis) by comparative transcriptome profiling using the Illumina RNA-seq platform. We assembled 721.49 million clean high-quality paired-end reads into 47,363 transcripts and 47,363 genes, including 3,144 novel unigenes. There were 12,932, 4,732, and 4,732 differentially expressed genes (DEGs) in pairwise comparisons of Y410-1 vs. CX14-1, SY2004 vs. CX14-1, and Y410-1 vs. SY2004, respectively. The RNA-seq results were confirmed by reverse transcription quantitative real-time PCR (RT-qPCR). A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs revealed significant enrichment for plant hormone and signal transduction as well as starch and sucrose metabolism pathways. Among DEGs related to plant hormone and signal transduction, six unigenes encoding the indole-3-acetic acid-induced protein ARG7 (BraA02g009130), auxin-responsive protein SAUR41 (BraA09g058230), serine/threonine-protein kinase BSK11 (BraA07g032960), auxin-induced protein 15A (BraA10g019860), and abscisic acid receptor PYR1 (BraA08g012630 and BraA01g009450), were upregulated in both late bolting Chinese cabbage lines (Y410-1 and SY2004) and were identified as putative candidates for the trait. These results improve our understanding of the molecular mechanisms underlying flowering in Chinese cabbage and provide a foundation for studies of this key trait in related species.

scholarly journals Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans

2019 ◽  
Vol 20 (24) ◽  
pp. 6138 ◽  
Author(s):  
Mbuya Sylvain Ntambo ◽  
Jian-Yu Meng ◽  
Philippe C. Rott ◽  
Robert J. Henry ◽  
Hui-Li Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Glutathione Metabolism ◽  
Bacterial Disease ◽  
Post Inoculation ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Leaf Scald ◽  
Xanthomonas Albilineans

Sugarcane (Saccharum spp. hybrids) is a major source of sugar and renewable bioenergy crop worldwide and suffers serious yield losses due to many pathogen infections. Leaf scald caused by Xanthomonas albilineans is a major bacterial disease of sugarcane in most sugarcane-planting countries. The molecular mechanisms of resistance to leaf scald in this plant are, however, still unclear. We performed a comparative transcriptome analysis between resistant (LCP 85-384) and susceptible (ROC20) sugarcane cultivars infected by X. albilineans using the RNA-seq platform. 24 cDNA libraries were generated with RNA isolated at four time points (0, 24, 48, and 72 h post inoculation) from the two cultivars with three biological replicates. A total of 105,783 differentially expressed genes (DEGs) were identified in both cultivars and the most upregulated and downregulated DEGs were annotated for the processes of the metabolic and single-organism categories, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the 7612 DEGs showed that plant–pathogen interaction, spliceosome, glutathione metabolism, protein processing in endoplasmic reticulum, and plant hormone signal transduction contributed to sugarcane’s response to X. albilineans infection. Subsequently, relative expression levels of ten DEGs determined by quantitative reverse transcription-PCR (qRT-PCR), in addition to RNA-Seq data, indicated that different plant hormone (auxin and ethylene) signal transduction pathways play essential roles in sugarcane infected by X. albilineans. In conclusion, our results provide, for the first time, valuable information regarding the transcriptome changes in sugarcane in response to infection by X. albilineans, which contribute to the understanding of the molecular mechanisms underlying the interactions between sugarcane and this pathogen and provide important clues for further characterization of leaf scald resistance in sugarcane.

Comparative transcriptome profiling in human bicuspid aortic valve disease using RNA sequencing

2015 ◽  
Vol 47 (3) ◽  
pp. 75-87 ◽  
Author(s):  
Ratnasari Padang ◽  
Richard D. Bagnall ◽  
Tatiana Tsoutsman ◽  
Paul G. Bannon ◽  
Christopher Semsarian
Keyword(s):  
Aortic Valve ◽  
Rna Sequencing ◽  
Bicuspid Aortic Valve ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Common Complication ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Calcific Aortic Stenosis ◽  
Phenotype Heterogeneity

Intrinsic valvular degeneration and dysfunction is the most common complication of bicuspid aortic valve (BAV) disease. Phenotypically, it ranges from calcific aortic stenosis to redundant or prolapsing regurgitant leaflets. The underlying molecular mechanism underpinning phenotype heterogeneity of valvular degeneration in BAV is poorly understood. We used RNA sequencing (RNA-seq) to identify genes and pathways responsible for the development of valvular degeneration in BAV, compared with tricuspid aortic valve (TAV). Comparative transcriptome analysis was performed on total RNA of aortic valve tissues of patients with diseased BAV ( n = 5) and calcified TAV ( n = 3). RNA-seq findings were validated by RT-qPCR. A total of 59 and 177 genes were significantly up- and downregulated, respectively, in BAV compared with TAV. Hierarchical clustering indicated heterogeneity within the BAV group, separating those with heavy calcification (BAVc) from those with redundant leaflets and/or minimal calcification (BAVr). Interestingly, the gene expression profile of the BAVc group closely resembled the TAV, with shared up- and downregulation of inflammatory and NOTCH1 signaling pathways, respectively. Downregulation of matrix protease ADAMTS9 and protein aggrecan were observed in BAVr compared with TAV. Dysregulation of fetal gene programs were also present, with notable downregulation of SEMA6B and SEMA3F in BAVr and BAVc compared with TAV, respectively. Upregulation of TBX20 was observed exclusively in BAVr compared with BAVc. In conclusion, diverging molecular mechanisms underpin phenotype heterogeneity of valvular degeneration in BAV and data from the present study suggest that there may be shared mechanisms leading to calcification in BAV and TAV. Recognition of these pathways is fundamental to improve our understanding of the molecular basis of human BAV disease.

scholarly journals Nitrogen Signaling Genes and SOC1 Determine the Flowering Time in a Reciprocal Negative Feedback Loop in Chinese Cabbage (Brassica rapa L.) Based on CRISPR/Cas9-Mediated Mutagenesis of Multiple BrSOC1 Homologs

2021 ◽  
Vol 22 (9) ◽  
pp. 4631
Author(s):  
Haemyeong Jung ◽  
Areum Lee ◽  
Seung Hee Jo ◽  
Hyun Ji Park ◽  
Won Yong Jung ◽  
...  
Keyword(s):  
Flowering Time ◽  
Brassica Rapa ◽  
Negative Feedback ◽  
Chinese Cabbage ◽  
Feedback Loop ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Negative Feedback Loop ◽  
Transcription Analysis ◽  
Nitrogen Levels

Precise flowering timing is critical for the plant life cycle. Here, we examined the molecular mechanisms and regulatory network associated with flowering in Chinese cabbage (Brassica rapa L.) by comparative transcriptome profiling of two Chinese cabbage inbred lines, “4004” (early bolting) and “50” (late bolting). RNA-Seq and quantitative reverse transcription PCR (qPCR) analyses showed that two positive nitric oxide (NO) signaling regulator genes, nitrite reductase (BrNIR) and nitrate reductase (BrNIA), were up-regulated in line “50” with or without vernalization. In agreement with the transcription analysis, the shoots in line “50” had substantially higher nitrogen levels than those in “4004”. Upon vernalization, the flowering repressor gene Circadian 1 (BrCIR1) was significantly up-regulated in line “50”, whereas the flowering enhancer genes named SUPPRESSOR OF OVEREXPRESSION OF CONSTANCE 1 homologs (BrSOC1s) were substantially up-regulated in line “4004”. CRISPR/Cas9-mediated mutagenesis in Chinese cabbage demonstrated that the BrSOC1-1/1-2/1-3 genes were involved in late flowering, and their expression was mutually exclusive with that of the nitrogen signaling genes. Thus, we identified two flowering mechanisms in Chinese cabbage: a reciprocal negative feedback loop between nitrogen signaling genes (BrNIA1 and BrNIR1) and BrSOC1s to control flowering time and positive feedback control of the expression of BrSOC1s.

scholarly journals Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia

2021 ◽  
Vol 22 (5) ◽  
pp. 2683
Author(s):  
Princess D. Rodriguez ◽  
Hana Paculova ◽  
Sophie Kogut ◽  
Jessica Heath ◽  
Hilde Schjerven ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
B Cell ◽  
Molecular Mechanisms ◽  
Lymphoblastic Leukemia ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Technological Developments ◽  
Cell Acute Lymphoblastic Leukemia

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

scholarly journals Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum)

2019 ◽  
Vol 20 (17) ◽  
pp. 4303 ◽  
Author(s):  
Hongyou Li ◽  
Qiuyu Lv ◽  
Jiao Deng ◽  
Juan Huang ◽  
Fang Cai ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Seed Development ◽  
Seed Size ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Fagopyrum Esculentum ◽  
Rna Seq ◽  
Common Buckwheat ◽  
Size Change ◽  
Key Genes

Seed development is an essential and complex process, which is involved in seed size change and various nutrients accumulation, and determines crop yield and quality. Common buckwheat (Fagopyrum esculentum Moench) is a widely cultivated minor crop with excellent economic and nutritional value in temperate zones. However, little is known about the molecular mechanisms of seed development in common buckwheat (Fagopyrum esculentum). In this study, we performed RNA-Seq to investigate the transcriptional dynamics and identify the key genes involved in common buckwheat seed development at three different developmental stages. A total of 4619 differentially expressed genes (DEGs) were identified. Based on the results of Gene Ontology (GO) and KEGG analysis of DEGs, many key genes involved in the seed development, including the Ca2+ signal transduction pathway, the hormone signal transduction pathways, transcription factors (TFs), and starch biosynthesis-related genes, were identified. More importantly, 18 DEGs were identified as the key candidate genes for seed size through homologous query using the known seed size-related genes from different seed plants. Furthermore, 15 DEGs from these identified as the key genes of seed development were selected to confirm the validity of the data by using quantitative real-time PCR (qRT-PCR), and the results show high consistency with the RNA-Seq results. Taken together, our results revealed the underlying molecular mechanisms of common buckwheat seed development and could provide valuable information for further studies, especially for common buckwheat seed improvement.

Transcriptome Profiling of Dehydration Stress in the Chinese Cabbage (Brassica rapa L. ssp. pekinensis) by Tag Sequencing

2011 ◽  
Vol 30 (1) ◽  
pp. 17-28 ◽  
Author(s):  
Shuancang Yu ◽  
Fenglan Zhang ◽  
Yangjun Yu ◽  
Deshuang Zhang ◽  
Xiuyun Zhao ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Transcriptome Profiling ◽  
Dehydration Stress

Identification of conserved microRNAs and their targets in Chinese cabbage (Brassica rapa subsp. pekinensis)

Genome ◽  
2011 ◽  
Vol 54 (12) ◽  
pp. 1029-1040 ◽  
Author(s):  
Jinyan Wang ◽  
Xilin Hou ◽  
Xuedong Yang
Keyword(s):  
Signal Transduction ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Acid Metabolism ◽  
Protein Translation ◽  
Transcriptional Level ◽  
Regulate Gene Expression ◽  
New Class ◽  
Plant Pathogen Interaction ◽  
Cellular Components

The microRNAs (miRNAs) are a new class of small nonprotein-coding RNAs that have been identified to regulate gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Until now, thousands of miRNAs have been identified in many plants species. However, only 23 miRNAs have been reported from the microRNA database in Chinese cabbage ( Brassica rapa subsp. pekinensis ), one of the most widely cultivated vegetables in China and East Asia. In the present study, 168 potential miRNAs, derived from 22 EST and 119 GSS sequences in Chinese cabbage were identified and classified into 38 miRNA families by well-defined computational analysis, in which most belonged to the miRNA1533, miRNA156, and miRNA2911 families. Totally, there are 129 identified miRNAs potentially targeting 1386 Chinese cabbage EST genes, which play roles in multiple biological and metabolic processes including metabolism, cell growth, signal transduction, stress response, and plant development. Gene ontology analysis, based on these target proteins, showed that 688, 532, and 287 genes were involved in molecular functions, biological processes, and cellular components, respectively. KEGG pathway analysis demonstrated that these miRNAs participated in 214 metabolism pathways, including, amongst others, plant–pathogen interaction, fatty acid metabolism, amino acid metabolism, nitrogen metabolism, plant hormone signal transduction.

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