scholarly journals The Full-Length Transcriptome Provides New Insights Into the Transcript Complexity of Abdominal Adipose and Subcutaneous Adipose in Pekin Ducks

2021 ◽  
Vol 12 ◽  
Author(s):  
Dandan Sun ◽  
Xiaoqin Li ◽  
Zhongtao Yin ◽  
Zhuocheng Hou
Keyword(s):  
Alternative Splicing ◽  
Expression Profiles ◽  
Full Length ◽  
Pekin Duck ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Next Generation Sequencing Technology ◽  
Pekin Ducks ◽  
Alternative Splicing Events ◽  
Subcutaneous Adipose

Adipose tissues have a central role in organisms, and adipose content is a crucial economic trait of poultry. Pekin duck is an ideal model to study the mechanism of abdominal and subcutaneous adipose deposition for its high ability of adipose synthesis and deposition. Alternative splicing contributes to functional diversity in abdominal and subcutaneous adipose. However, there has been no systematic analysis of the dynamics of differential alternative splicing of abdominal and subcutaneous adipose in Pekin duck. In our study, the Pacific Biosciences (PacBio) Iso-Seq technology was applied to explore the transcriptional complexity of abdominal and subcutaneous adipose in Pekin ducks. In total, 143,931 and 111,337 full-length non-chimeric transcriptome sequences of abdominal and subcutaneous adipocytes were obtained from 41.78 GB raw data, respectively. These data led us to identify 19,212 long non-coding RNAs (lncRNAs) and 74,571 alternative splicing events. In addition, combined with the next-generation sequencing technology, we correlated the structure and function annotation with the differential expression profiles of abdominal and subcutaneous adipose transcripts. This study identified lots of novel alternative splicing events and major transcripts of transcription factors related to adipose synthesis. STAT3 was reported as a vital gene for adipogenesis, and we found that its major transcript is STAT3-1, which may play a considerable role in the process of adipose synthesis in Pekin duck. This study greatly increases our understanding of the gene models, genome annotations, genome structures, and the complexity and diversity of abdominal and subcutaneous adipose in Pekin duck. These data provide insights into the regulation of alternative splicing events, which form an essential part of transcript diversity during adipogenesis in poultry. The results of this study provide an invaluable resource for studying alternative splicing and tissue-specific expression.

scholarly journals Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity

2005 ◽  
Vol 6 (Suppl 4) ◽  
pp. S20 ◽  
Author(s):  
Luciano Milanesi ◽  
Mauro Petrillo ◽  
Leandra Sepe ◽  
Angelo Boccia ◽  
Nunzio D'Agostino ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Structural Diversity ◽  
Systematic Analysis ◽  
Human Kinase ◽  
Number Of Genes ◽  
Alternative Splicing Events

scholarly journals The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing

DNA Research ◽  
2019 ◽  
Vol 26 (4) ◽  
pp. 301-311 ◽  
Author(s):  
Yue Zhang ◽  
Tonny Maraga Nyong'A ◽  
Tao Shi ◽  
Pingfang Yang
Keyword(s):  
Alternative Splicing ◽  
Real Time ◽  
Single Molecule ◽  
Intron Retention ◽  
Critical Role ◽  
Full Length ◽  
Specific Expression ◽  
Splice Isoforms ◽  
Tissue Specific ◽  
Genomic Studies

Abstract Alternative splicing (AS) plays a critical role in regulating different physiological and developmental processes in eukaryotes, by dramatically increasing the diversity of the transcriptome and the proteome. However, the saturation and complexity of AS remain unclear in lotus due to its limitation of rare obtainment of full-length multiple-splice isoforms. In this study, we apply a hybrid assembly strategy by combining single-molecule real-time sequencing and Illumina RNA-seq to get a comprehensive insight into the lotus transcriptomic landscape. We identified 211,802 high-quality full-length non-chimeric reads, with 192,690 non-redundant isoforms, and updated the lotus reference gene model. Moreover, our analysis identified a total of 104,288 AS events from 16,543 genes, with alternative 3ʹ splice-site being the predominant model, following by intron retention. By exploring tissue datasets, 370 tissue-specific AS events were identified among 12 tissues. Both the tissue-specific genes and isoforms might play important roles in tissue or organ development, and are suitable for ‘ABCE’ model partly in floral tissues. A large number of AS events and isoform variants identified in our study enhance the understanding of transcriptional diversity in lotus, and provide valuable resource for further functional genomic studies.

scholarly journals Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

2020 ◽  
Vol 21 (19) ◽  
pp. 7180
Author(s):  
Hongfeng Wang ◽  
Hongjiao Jiang ◽  
Yiteng Xu ◽  
Yan Wang ◽  
Lin Zhu ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Feedback Regulation ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Model Legume ◽  
Genome Wide ◽  
A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

scholarly journals Analysis of Multiple Occurrences of Alternative Splicing Events in Arabidopsis thaliana Using Novel Sequenced Full-Length cDNAs

DNA Research ◽  
2009 ◽  
Vol 16 (3) ◽  
pp. 155-164 ◽  
Author(s):  
K. Iida ◽  
K. Fukami-Kobayashi ◽  
A. Toyoda ◽  
Y. Sakaki ◽  
M. Kobayashi ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Alternative Splicing ◽  
Full Length ◽  
Alternative Splicing Events

scholarly journals Computer Analysis of Glioma Transcriptome Profiling: Alternative Splicing Events

2017 ◽  
Vol 14 (3) ◽  
Author(s):  
Vladimir N. Babenko ◽  
Natalya V. Gubanova ◽  
Anatoly O. Bragin ◽  
Irina V. Chadaeva ◽  
Gennady V. Vasiliev ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Alternative Splicing ◽  
Expression Profiles ◽  
Rna Extraction ◽  
Transcriptome Profiling ◽  
Laboratory Animals ◽  
Normal Brain ◽  
Computer Tools ◽  
Alternative Splicing Events

AbstractHere we present the analysis of alternative splicing events on an example of glioblastoma cell culture samples using a set of computer tools in combination with database integration. The gene expression profiles of glioblastoma were obtained from cell culture samples of primary glioblastoma which were isolated and processed for RNA extraction. Transcriptome profiling of normal brain samples and glioblastoma were done by Illumina sequencing. The significant differentially expressed exon-level probes and their corresponding genes were identified using a combination of the splicing index method. Previous studies indicated that tumor-specific alternative splicing is important in the regulation of gene expression and corresponding protein functions during cancer development. Multiple alternative splicing transcripts have been identified as progression markers, including generalized splicing abnormalities and tumor- and stage-specific events. We used a set of computer tools which were recently applied to analysis of gene expression in laboratory animals to study differential splicing events. We found 69 transcripts that are differentially alternatively spliced. Three cancer-associated genes were considered in detail, in particular: APP (amyloid beta precursor protein), CASC4 (cancer susceptibility candidate 4) and TP53. Such alternative splicing opens new perspectives for cancer research.

scholarly journals A comparative transcriptional landscape of two castor cultivars obtained by single-molecule sequencing comparative analysis

2020 ◽  
Author(s):  
Wei Zhou ◽  
Yaxing Zhou ◽  
Guoli Zhu ◽  
Yun Wang ◽  
Zhibiao He ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Comparative Analysis ◽  
Alternative Splicing ◽  
Rna Sequencing ◽  
Transcriptome Sequencing ◽  
Full Length ◽  
Transcriptional Analysis ◽  
Sequencing Analysis ◽  
Short Read ◽  
Alternative Splicing Events

AbstractBackground and ObjectivesCastor (Ricinus communis L.) is an important non-edible oilseed crop. Lm type female strains and normal amphiprotic strains are important castor cultivars, and are mainly different in inflorescence structures and leaf shapes. To better understand the mechanisums underling these differences at the molecular level, we performed comparative transcriptional analysis.Materials and MethodsFull-length transcriptome sequencing and short-read RNA sequencing were employed.ResultsA total of 76,068 and 44,223 non-redundant transcripts were obtained from high-quality transcripts of Lm type female strains and normal amphiprotic strains, respectively. In Lm female strain and normal amphiprotic strains 51,613 and 20,152 alternative splicing events were found, respectively. There were 13,239 transcription factors identified from the full-length transcriptomes. Comparative analysis showed great different gene expression of common and unique transcription factors between the two cultivars. Meanwhile, functional analysis of isoform was conducted. Full-length sequences were used as a reference genome, and short-read RNA sequencing analysis was performed to conduct differential gene analysis. Furthermore, the function of DEGs were performed to annotation analysis.ConclusionsThe results revealed considerable difference and expression diversity between two cultivars, well beyond what was reported in previous studies, likely reflecting the differences in architecture between these two cultivars.HighlightUsing the full-length transcriptome sequencing technology, we performed comparative analysis of transcription factors of two castor cultivars, analyzed alternative splicing events, and identified their lncRNAs.

scholarly journals Global Survey of the Full-Length Cabbage Transcriptome (Brassica oleracea Var. capitata L.) Reveals Key Alternative Splicing Events Involved in Growth and Disease Response

2021 ◽  
Vol 22 (19) ◽  
pp. 10443
Author(s):  
Yong Wang ◽  
Jialei Ji ◽  
Long Tong ◽  
Zhiyuan Fang ◽  
Limei Yang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Brassica Oleracea ◽  
Single Molecule ◽  
Alternative Polyadenylation ◽  
Full Length ◽  
Genomic Research ◽  
Accurate Information ◽  
Sequencing Data ◽  
Specific Expression ◽  
Global Survey

Cabbage (Brassica oleracea L. var. capitata L.) is an important vegetable crop cultivated around the world. Previous studies of cabbage gene transcripts were primarily based on next-generation sequencing (NGS) technology which cannot provide accurate information concerning transcript assembly and structure analysis. To overcome these issues and analyze the whole cabbage transcriptome at the isoform level, PacBio RS II Single-Molecule Real-Time (SMRT) sequencing technology was used for a global survey of the full-length transcriptomes of five cabbage tissue types (root, stem, leaf, flower, and silique). A total of 77,048 isoforms, capturing 18,183 annotated genes, were discovered from the sequencing data generated through SMRT. The patterns of both alternative splicing (AS) and alternative polyadenylation (APA) were comprehensively analyzed. In total, we detected 13,468 genes which had isoforms containing APA sites and 8978 genes which underwent AS events. Moreover, 5272 long non-coding RNAs (lncRNAs) were discovered, and most exhibited tissue-specific expression. In total, 3147 transcription factors (TFs) were detected and 10 significant gene co-expression network modules were identified. In addition, we found that Fusarium wilt, black rot and clubroot infection significantly influenced AS in resistant cabbage. In summary, this study provides abundant cabbage isoform transcriptome data, which promotes reannotation of the cabbage genome, deepens our understanding of their post-transcriptional regulation mechanisms, and can be used for future functional genomic research.

scholarly journals Single cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing

2021 ◽  
Author(s):  
Heon Seok Kim ◽  
Susan M Grimes ◽  
Anna C Hooker ◽  
Billy T Lau ◽  
Hanlee P Ji
Keyword(s):  
Alternative Splicing ◽  
Single Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Splicing Factors ◽  
Transcript Isoforms ◽  
Long Read ◽  
Cell Gene Expression ◽  
Transcript Structure ◽  
Alternative Splicing Events

Transcript isoforms are mRNAs that arise from alternative splicing events. During RNA processing, different combinations of a gene's exons lead to a diverse set of isoforms. Polymorphisms or mutations at splice junctions can generate alternative splicing events. Various splicing factors also impact the representation of a gene's transcript isoforms. To assess how these two features contribute to alternative splicing, we developed a single cell approach to introduce CRISPR edits that modify mRNA transcript structure. Our method combines (1) long-read sequencing to characterize the expressed transcripts and identify the edit at single cell resolution; (2) short-read sequencing to match the single cell gene expression profiles of the cells with the altered isoform. First, we modify target exon-intron segments with CRISPR-Cas9. Second, using cDNAs with cell barcodes, we use long read sequencing to directly identify the changes in transcript isoforms from the targeted CRISPR edits. As a variation on this approach, we also determined how modifying specific splicing factors influence isoform expression and structure. Overall, we demonstrate how the integration of single cell long read analysis and CRISPR engineering can be used to directly confirm transcript isoform and target genomic edits at single cell resolution. This approach will improve our understanding of the role of alternative splicing in transcriptional regulation.

scholarly journals The Full-Length Transcriptome of Spartina alterniflora Reveals the Complexity of High Salt Tolerance in Monocotyledonous Halophyte

2020 ◽  
Vol 61 (5) ◽  
pp. 882-896
Author(s):  
Wenbin Ye ◽  
Taotao Wang ◽  
Wei Wei ◽  
Shuaitong Lou ◽  
Faxiu Lan ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Alternative Splicing ◽  
Salt Tolerance ◽  
Spartina Alterniflora ◽  
High Salt ◽  
Full Length ◽  
High Salt Tolerance ◽  
High Salt Stress ◽  
Alternative Splicing Events

Abstract Spartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used Pacific Biosciences (PacBio) full-length single-molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt gradient experiments. High-quality unigenes, transcription factors, non-coding RNA and Spartina-specific transcripts were identified. Co-expression network analysis found that protein kinase-encoding genes (SaOST1, SaCIPK10 and SaLRRs) are hub genes in the salt tolerance regulatory network. High salt stress induced the expression of transcription factors but repressed the expression of long non-coding RNAs. The Spartina transcriptome is closer to rice than Arabidopsis, and a higher proportion of transporter and transcription factor-encoding transcripts have been found in Spartina. Transcriptome analysis showed that high salt stress induced the expression of carbohydrate metabolism, especially cell-wall biosynthesis-related genes in Spartina, and repressed its expression in rice. Compared with rice, high salt stress highly induced the expression of stress response, protein modification and redox-related gene expression and greatly inhibited translation in Spartina. High salt stress also induced alternative splicing in Spartina, while differentially expressed alternative splicing events associated with photosynthesis were overrepresented in Spartina but not in rice. Finally, we built the SAPacBio website for visualizing full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes and alternative splicing events in Spartina. Overall, this study suggests that the salt tolerance mechanism in Spartina is different from rice in many aspects and is far more complex than expected.

The full-length cDNA cloning and expression profiles of 14-3-3 genes from the mud crab Scylla paramamosain Estampador, 1949

Crustaceana ◽  
2015 ◽  
Vol 88 (10-11) ◽  
pp. 1065-1078 ◽  
Author(s):  
Miao-An Shu ◽  
Chen Long ◽  
Wei-Ren Dong ◽  
Pan Zhang ◽  
Bin-Peng Xu ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Full Length ◽  
Cloning And Expression ◽  
Scylla Paramamosain ◽  
Mud Crab ◽  
Phylogenetic Tree Analysis ◽  
Specific Expression ◽  
Full Length Cdna ◽  
Cdna Sequences

Two full-length cDNA sequences of 14-3-3 genes were isolated from the mud crab, Scylla paramamosain Estampador, 1949, using RT-PCR and RACE (rapid-amplification of cDNA ends). Sequence analysis indicates that both 14-3-3 genes contain an open reading frame of 744 bp with a deduced 247-amino-acid protein. The gene and protein sequences of Sp14-3-3 genes show 96 and 97% identity, respectively, and both Sp14-3-3 cluster together with other animal 14-3-3 proteins in phylogenetic tree analysis. Tissue specific expression analysis reveals that both Sp14-3-3 genes are ubiquitously expressed, however, their expression patterns are different from each other. Expressions of both Sp14-3-3 genes are sensitive to salinity decrease, even a 5 ppt drop from 30 ppt to 25 ppt, indicating that Sp14-3-3 genes are involved in osmoregulation. Our observations may contribute to a better understanding of the molecular and functional evolution of the 14-3-3 family in both crustaceans and (in)vertebrates as a whole.

Sign in / Sign up

Export Citation Format

Share Document