RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum

ABSTRACT Fusarium graminearum floral infections are a major risk to the global supply of safe cereal grains. We report updates to the PH-1 reference genome and significant improvements to the annotation. Changes include introduction of legacy annotation identifiers, new gene models, secretome and effectorP predictions, and inclusion of extensive untranslated region (UTR) annotations.

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SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

Genome Biology ◽

10.1186/gb-2012-13-1-r4 ◽

2012 ◽

Vol 13 (1) ◽

pp. R4 ◽

Cited By ~ 92

Author(s):

Mark F Rogers ◽

Julie Thomas ◽

Anireddy SN Reddy ◽

Asa Ben-Hur

Keyword(s):

Alternative Splicing ◽

Rna Seq ◽

Gene Models

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RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing

10.1101/010116 ◽

2014 ◽

Author(s):

Vikas Gupta ◽

April Dawn Estrada ◽

Ivory Clabaugh Blakley ◽

Rob Reid ◽

Ketan Patel ◽

...

Keyword(s):

Alternative Splicing ◽

Candidate Genes ◽

Bioactive Compounds ◽

Genome Assembly ◽

Metabolic Pathway ◽

Fruit Ripening ◽

Rna Seq ◽

Developmentally Regulated ◽

Specific Alternative ◽

Gene Models

Background: Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable breeding berry varieties with enhanced health benefits. Results: Toward this end, we annotated a draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape Vitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up and down regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3? end formation. Conclusions: We report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry. RNA-Seq data are freely available for visualization in Integrated Genome Browser, and analysis code is available from the git repository at http://bitbucket.org/lorainelab/blueberrygenome.

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Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae)

Genes ◽

10.3390/genes12060896 ◽

2021 ◽

Vol 12 (6) ◽

pp. 896

Author(s):

Yuenan Zhou ◽

Pei Yang ◽

Shuang Xie ◽

Min Shi ◽

Jianhua Huang ◽

...

Keyword(s):

Alternative Splicing ◽

Adult Development ◽

Sexual Development ◽

Molecular Mechanisms ◽

Parasitic Wasp ◽

Differentially Expressed Gene ◽

Regulation Mechanism ◽

Rna Seq ◽

Male And Female ◽

Cotesia Vestalis

The endoparasitic wasp Cotesia vestalis is an important biological agent for controlling the population of Plutella xylostella, a major pest of cruciferous crops worldwide. Though the genome of C. vestalis has recently been reported, molecular mechanisms associated with sexual development have not been comprehensively studied. Here, we combined PacBio Iso-Seq and Illumina RNA-Seq to perform genome-wide profiling of pharate adult and adult development of male and female C. vestalis. Taking advantage of Iso-Seq full-length reads, we identified 14,466 novel transcripts as well as 8770 lncRNAs, with many lncRNAs showing a sex- and stage-specific expression pattern. The differentially expressed gene (DEG) analyses showed 2125 stage-specific and 326 sex-specific expressed genes. We also found that 4819 genes showed 11,856 alternative splicing events through combining the Iso-Seq and RNA-Seq data. The results of comparative analyses showed that most genes were alternatively spliced across developmental stages, and alternative splicing (AS) events were more prevalent in females than in males. Furthermore, we identified six sex-determining genes in this parasitic wasp and verified their sex-specific alternative splicing profiles. Specifically, the characterization of feminizer and doublesex splicing between male and female implies a conserved regulation mechanism of sexual development in parasitic wasps.

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A Novel NFIX-STAT6 Gene Fusion in Solitary Fibrous Tumor: A Case Report

International Journal of Molecular Sciences ◽

10.3390/ijms22147514 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7514

Author(s):

David S. Moura ◽

Juan Díaz-Martín ◽

Silvia Bagué ◽

Ruth Orellana-Fernandez ◽

Ana Sebio ◽

...

Keyword(s):

Solitary Fibrous Tumor ◽

Gene Fusion ◽

Wide Spectrum ◽

Bioinformatic Analysis ◽

Fusion Partner ◽

Rna Seq ◽

Genomic Location ◽

Nuclear Factor I ◽

New Gene ◽

Fibrous Tumor

Solitary fibrous tumor is a rare subtype of soft-tissue sarcoma with a wide spectrum of histopathological features and clinical behaviors, ranging from mildly to highly aggressive tumors. The defining genetic driver alteration is the gene fusion NAB2–STAT6, resulting from a paracentric inversion within chromosome 12q, and involving several different exons in each gene. STAT6 (signal transducer and activator of transcription 6) nuclear immunostaining and/or the identification of NAB2–STAT6 gene fusion is required for the diagnostic confirmation of solitary fibrous tumor. In the present study, a new gene fusion consisting of Nuclear Factor I X (NFIX), mapping to 19p13.2 and STAT6, mapping to 12q13.3 was identified by targeted RNA-Seq in a 74-year-old female patient diagnosed with a deep-seated solitary fibrous tumor in the pelvis. Histopathologically, the neoplasm did not display nuclear pleomorphism or tumor necrosis and had a low proliferative index. A total of 378 unique reads spanning the NFIXexon8–STAT6exon2 breakpoint with 55 different start sites were detected in the bioinformatic analysis, which represented 59.5% of the reads intersecting the genomic location on either side of the breakpoint. Targeted RNA-Seq results were validated by RT-PCR/ Sanger sequencing. The identification of a new gene fusion partner for STAT6 in solitary fibrous tumor opens intriguing new hypotheses to refine the role of STAT6 in the sarcomatogenesis of this entity.

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Deciphering the Monilinia fructicola Genome to Discover Effector Genes Possibly Involved in Virulence

Genes ◽

10.3390/genes12040568 ◽

2021 ◽

Vol 12 (4) ◽

pp. 568

Author(s):

Laura Vilanova ◽

Claudio A. Valero-Jiménez ◽

Jan A.L. van Kan

Keyword(s):

Brown Rot ◽

Biological Properties ◽

Effector Proteins ◽

Stone Fruit ◽

Rna Seq ◽

Sequencing Technology ◽

Pathogen Virulence ◽

Effector Genes ◽

Gene Models ◽

High Quality Genome

Brown rot is the most economically important fungal disease of stone fruits and is primarily caused by Monilinia laxa and Monlinia fructicola. Both species co-occur in European orchards although M. fructicola is considered to cause the most severe yield losses in stone fruit. This study aimed to generate a high-quality genome of M. fructicola and to exploit it to identify genes that may contribute to pathogen virulence. PacBio sequencing technology was used to assemble the genome of M. fructicola. Manual structural curation of gene models, supported by RNA-Seq, and functional annotation of the proteome yielded 10,086 trustworthy gene models. The genome was examined for the presence of genes that encode secreted proteins and more specifically effector proteins. A set of 134 putative effectors was defined. Several effector genes were cloned into Agrobacterium tumefaciens for transient expression in Nicotiana benthamiana plants, and some of them triggered necrotic lesions. Studying effectors and their biological properties will help to better understand the interaction between M. fructicola and its stone fruit host plants.

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Characterization of alternative splicing events and prognostic signatures in breast cancer

BMC Cancer ◽

10.1186/s12885-021-08305-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Pihua Han ◽

Jingjun Zhu ◽

Guang Feng ◽

Zizhang Wang ◽

Yanni Ding

Keyword(s):

Breast Cancer ◽

Alternative Splicing ◽

Proportional Hazards ◽

Pearson Correlation ◽

Original Data ◽

Cox Proportional Hazards ◽

Prognostic Indicators ◽

Splicing Factors ◽

Rna Seq

Abstract Background Breast cancer (BRCA) is one of the most common cancers worldwide. Abnormal alternative splicing (AS) frequently observed in cancers. This study aims to demonstrate AS events and signatures that might serve as prognostic indicators for BRCA. Methods Original data for all seven types of splice events were obtained from TCGA SpliceSeq database. RNA-seq and clinical data of BRCA cohorts were downloaded from TCGA database. Survival-associated AS events in BRCA were analyzed by univariate COX proportional hazards regression model. Prognostic signatures were constructed for prognosis prediction in patients with BRCA based on survival-associated AS events. Pearson correlation analysis was performed to measure the correlation between the expression of splicing factors (SFs) and the percent spliced in (PSI) values of AS events. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to demonstrate pathways in which survival-associated AS event is enriched. Results A total of 45,421 AS events in 21,232 genes were identified. Among them, 1121 AS events in 931 genes significantly correlated with survival for BRCA. The established AS prognostic signatures of seven types could accurately predict BRCA prognosis. The comprehensive AS signature could serve as independent prognostic factor for BRCA. A SF-AS regulatory network was therefore established based on the correlation between the expression levels of SFs and PSI values of AS events. Conclusions This study revealed survival-associated AS events and signatures that may help predict the survival outcomes of patients with BRCA. Additionally, the constructed SF-AS networks in BRCA can reveal the underlying regulatory mechanisms in BRCA.

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GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-seq data

Genome Biology ◽

10.1186/gb-2013-14-7-r74 ◽

2013 ◽

Vol 14 (7) ◽

pp. R74 ◽

Cited By ~ 56

Author(s):

Keyan Zhao ◽

Zhi-xiang Lu ◽

Juw Park ◽

Qing Zhou ◽

Yi Xing

Keyword(s):

Alternative Splicing ◽

Statistical Model ◽

Rna Seq ◽

Regulatory Variation

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Plant buffering against the high-light stress-induced accumulation of CsGA2ox8 transcripts via alternative splicing to finely tune gibberellin levels and maintain hypocotyl elongation

Horticulture Research ◽

10.1038/s41438-020-00430-w ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Bin Liu ◽

Shuo Zhao ◽

Pengli Li ◽

Yilu Yin ◽

Qingliang Niu ◽

...

Keyword(s):

Alternative Splicing ◽

Light Intensity ◽

Intron Retention ◽

Light Stress ◽

Photosynthetic Photon Flux Density ◽

Photon Flux ◽

Photon Flux Density ◽

Rna Seq ◽

Multiple Transcripts ◽

Novel Transcript

AbstractIn plants, alternative splicing (AS) is markedly induced in response to environmental stresses, but it is unclear why plants generate multiple transcripts under stress conditions. In this study, RNA-seq was performed to identify AS events in cucumber seedlings grown under different light intensities. We identified a novel transcript of the gibberellin (GA)-deactivating enzyme Gibberellin 2-beta-dioxygenase 8 (CsGA2ox8). Compared with canonical CsGA2ox8.1, the CsGA2ox8.2 isoform presented intron retention between the second and third exons. Functional analysis proved that the transcript of CsGA2ox8.1 but not CsGA2ox8.2 played a role in the deactivation of bioactive GAs. Moreover, expression analysis demonstrated that both transcripts were upregulated by increased light intensity, but the expression level of CsGA2ox8.1 increased slowly when the light intensity was >400 µmol·m−2·s−1 PPFD (photosynthetic photon flux density), while the CsGA2ox8.2 transcript levels increased rapidly when the light intensity was >200 µmol·m−2·s−1 PPFD. Our findings provide evidence that plants might finely tune their GA levels by buffering against the normal transcripts of CsGA2ox8 through AS.

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