scholarly journals Identification and Analysis of Micro-Exon Genes in the Rice Genome

2019 ◽  
Vol 20 (11) ◽  
pp. 2685 ◽  
Author(s):  
Qi Song ◽  
Fang Lv ◽  
Muhammad Tahir ul Qamar ◽  
Feng Xing ◽  
Run Zhou ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Stop Codon ◽  
Indica Rice ◽  
Rice Genome ◽  
Protein Structures ◽  
Wide Distribution ◽  
Rna Seq ◽  
Rice Varieties ◽  
Genome Wide ◽  
Alternatively Spliced

Micro-exons are a kind of exons with lengths no more than 51 nucleotides. They are generally ignored in genome annotation due to the short length, whereas recent studies indicate that they have special splicing properties and important functions. Considering that there has been no genome-wide study of micro-exons in plants up to now, we screened and analyzed genes containing micro-exons in two indica rice varieties in this study. According to the annotation of Zhenshan 97 (ZS97) and Minghui 63 (MH63), ~23% of genes possess micro-exons. We then identified micro-exons from RNA-seq data and found that >65% micro-exons had been annotated and most of novel micro-exons were located in gene regions. About 60% micro-exons were constitutively spliced, and the others were alternatively spliced in different tissues. Besides, we observed that approximately 54% of genes harboring micro-exons tended to be ancient genes, and 13% were Oryza genus-specific. Micro-exon genes were highly conserved in Oryza genus with consistent domains. In particular, the predicted protein structures showed that alternative splicing of in-frame micro-exons led to a local structural recombination, which might affect some core structure of domains, and alternative splicing of frame-shifting micro-exons usually resulted in premature termination of translation by introducing a stop codon or missing functional domains. Overall, our study provided the genome-wide distribution, evolutionary conservation, and potential functions of micro-exons in rice.

scholarly journals Variation in seed longevity among diverse Indica rice varieties

2019 ◽  
Vol 124 (3) ◽  
pp. 447-460 ◽  
Author(s):  
Jae-Sung Lee ◽  
Marlina Velasco-Punzalan ◽  
Myrish Pacleb ◽  
Rocel Valdez ◽  
Tobias Kretzschmar ◽  
...  
Keyword(s):  
Indica Rice ◽  
A Priori ◽  
Rice Genome ◽  
Sugar Metabolism ◽  
Probit Analysis ◽  
Seed Longevity ◽  
Rice Varieties ◽  
Genome Wide ◽  
Group A ◽  
Harvest Moisture

Abstract Background and Aims Understanding variation in seed longevity, especially within closely related germplasm, will lead to better understanding of the molecular basis of this trait, which is particularly important for seed genebanks, but is also relevant to anyone handling seeds. We therefore set out to determine the relative seed longevity of diverse Indica rice accessions through storage experiments. Since antioxidants are purported to play a role in seed storability, the antioxidant activity and phenolic content of caryopses were determined. Methods Seeds of 299 Indica rice accessions harvested at 31, 38 and 45 d after heading (DAH) between March and May 2015 and differing in harvest moisture content (MC) were subsequently stored at 10.9 % MC and 45 °C. Samples were taken at regular intervals and sown for germination. Germination data were subjected to probit analysis and the resulting parameters that describe the loss of viability during storage were used for genome-wide association (GWA) analysis. Key Results The seed longevity parameters, Ki [initial viability in normal equivalent deviates (NED)], −σ−1 (σ is the time for viability to fall by 1 NED in experimental storage) and p50 [time for viability to fall to 50 % (0 NED)], varied considerably across the 299 Indica accessions. Seed longevity tended to increase as harvest MC decreased and to decrease as harvest MC increased. Eight major loci associated with seed longevity parameters were identified through GWA analysis. The favourable haplotypes on chromosomes 1, 3, 4, 9 and 11 enhanced p50 by ratios of 0.22–1.86. Conclusions This is the first study to describe the extent of variation in σ within a species’ variety group. A priori candidate genes selected based on rice genome annotation and gene network ontology databases suggested that the mechanisms conferring high seed longevity might be related to DNA repair and transcription, sugar metabolism, reactive oxygen species scavenging and embryonic/root development.

scholarly journals Detection of alternative splicing in Diabrotica virgifera virgifera LeConte, in association with Bt resistance using RNA-seq and PacBio Iso-Seq

2020 ◽  
Author(s):  
Zixiao Zhao ◽  
Christine G. Elsik ◽  
Bruce E. Hibbard ◽  
Kent S. Shelby
Keyword(s):  
Alternative Splicing ◽  
Matrix Protein ◽  
Diabrotica Virgifera Virgifera ◽  
Western Corn Rootworm ◽  
Corn Rootworm ◽  
Diabrotica Virgifera ◽  
Rna Seq ◽  
Bt Resistance ◽  
Bt Toxins ◽  
Alternatively Spliced

AbstractBackgroundAlternative splicing is one of the major mechanisms that increases transcriptome diversity in eukaryotes, including insect species that have gained resistance to pesticides and Bt toxins. In western corn rootworm (Diabrotica virgifera virgifera LeConte), neither alternative splicing nor its role in resistance to Bt toxins has been studied.ResultsTo investigate the mechanisms of Bt resistance we carried out single-molecule real-time (SMRT) transcript sequencing and Iso-seq analysis on resistant, eCry3.1Ab-selected and susceptible, unselected, western corn rootworm neonate midguts which fed on seedling maize with and without eCry3.1Ab for 12 and 24 hours. We present transcriptome-wide alternative splicing patterns of western corn rootworm midgut in response to feeding on eCry3.1Ab-expressing corn using a comprehensive approach that combines both RNA-seq and SMRT transcript sequencing techniques. We found that 67.73% of multi-exon genes are alternatively spliced, which is consistent with the high transposable element content of the genome. One of the alternative splicing events we identified was a novel peritrophic matrix protein with two alternative splicing isoforms. Analysis of differential exon usage between resistant and susceptible colonies showed that in eCry3.1Ab-resistant western corn rootworm, expression of one isoform was significantly higher than in the susceptible colony, while no significant differences between colonies were observed with the other isoform.ConclusionOur results provide the first survey of alternative splicing in western corn rootworm and suggest that the observed alternatively spliced isoforms of peritrophic matrix protein may be associated with eCry3.1Ab resistance in western corn rootworm.

scholarly journals The gene structure and hypervariability of the complete Penaeus monodon Dscam gene

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kantamas Apitanyasai ◽  
Shiao-Wei Huang ◽  
Tze Hann Ng ◽  
Shu-Ting He ◽  
Yu-Hsun Huang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Gene Structure ◽  
Transmembrane Domain ◽  
Stop Codon ◽  
Penaeus Monodon ◽  
Cytoplasmic Tail ◽  
Extracellular Region ◽  
Alternatively Spliced ◽  
Alternatively Spliced Exons ◽  
Selection Of

Abstract Using two advanced sequencing approaches, Illumina and PacBio, we derive the entire Dscam gene from an M2 assembly of the complete Penaeus monodon genome. The P. monodon Dscam (PmDscam) gene is ~266 kbp, with a total of 44 exons, 5 of which are subject to alternative splicing. PmDscam has a conserved architectural structure consisting of an extracellular region with hypervariable Ig domains, a transmembrane domain, and a cytoplasmic tail. We show that, contrary to a previous report, there are in fact 26, 81 and 26 alternative exons in N-terminal Ig2, N-terminal Ig3 and the entirety of Ig7, respectively. We also identified two alternatively spliced exons in the cytoplasmic tail, with transmembrane domains in exon variants 32.1 and 32.2, and stop codons in exon variants 44.1 and 44.2. This means that alternative splicing is involved in the selection of the stop codon. There are also 7 non-constitutive cytoplasmic tail exons that can either be included or skipped. Alternative splicing and the non-constitutive exons together produce more than 21 million isoform combinations from one PmDscam locus in the P. monodon gene. A public-facing database that allows BLAST searches of all 175 exons in the PmDscam gene has been established at http://pmdscam.dbbs.ncku.edu.tw/.

scholarly journals IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

2019 ◽  
Vol 35 (21) ◽  
pp. 4469-4471 ◽  
Author(s):  
Kristoffer Vitting-Seerup ◽  
Albin Sandelin
Keyword(s):  
Alternative Splicing ◽  
The Cancer Genome Atlas ◽  
Supplementary Information ◽  
Rna Seq ◽  
Genome Wide ◽  
Functional Consequences ◽  
Cancer Genome Atlas ◽  
Health And Disease ◽  
Splicing Patterns

Abstract Summary Alternative splicing is an important mechanism involved in health and disease. Recent work highlights the importance of investigating genome-wide changes in splicing patterns and the subsequent functional consequences. Current computational methods only support such analysis on a gene-by-gene basis. Therefore, we extended IsoformSwitchAnalyzeR R library to enable analysis of genome-wide changes in specific types of alternative splicing and predicted functional consequences of the resulting isoform switches. As a case study, we analyzed RNA-seq data from The Cancer Genome Atlas and found systematic changes in alternative splicing and the consequences of the associated isoform switches. Availability and implementation Windows, Linux and Mac OS: http://bioconductor.org/packages/IsoformSwitchAnalyzeR. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

2015 ◽  
Vol 28 (3) ◽  
pp. 298-309 ◽  
Author(s):  
Alyssa Burkhardt ◽  
Alex Buchanan ◽  
Jason S. Cumbie ◽  
Elizabeth A. Savory ◽  
Jeff H. Chang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Intron Retention ◽  
Draft Genome ◽  
Pseudoperonospora Cubensis ◽  
Rna Seq ◽  
Transcriptome Regulation ◽  
Oomycete Pathogen ◽  
Alternatively Spliced ◽  
Genome Annotations ◽  
Obligate Pathogen

Pseudoperonospora cubensis is an obligate pathogen and causative agent of cucurbit downy mildew. To help advance our understanding of the pathogenicity of P. cubensis, we used RNA-Seq to improve the quality of its reference genome sequence. We also characterized the RNA-Seq dataset to inventory transcript isoforms and infer alternative splicing during different stages of its development. Almost half of the original gene annotations were improved and nearly 4,000 previously unannotated genes were identified. We also demonstrated that approximately 24% of the expressed genome and nearly 55% of the intron-containing genes from P. cubensis had evidence for alternative splicing. Our analyses revealed that intron retention is the predominant alternative splicing type in P. cubensis, with alternative 5′- and alternative 3′-splice sites occurring at lower frequencies. Representatives of the newly identified genes and predicted alternatively spliced transcripts were experimentally validated. The results presented herein highlight the utility of RNA-Seq for improving draft genome annotations and, through this approach, we demonstrate that alternative splicing occurs more frequently than previously predicted. In total, the current study provides evidence that alternative splicing plays a key role in transcriptome regulation and proteome diversification in plant-pathogenic oomycetes.

scholarly journals EmpiReS: Differential Analysis of Gene Expression and Alternative Splicing

2020 ◽  
Author(s):  
Gergely Csaba ◽  
Evi Berchtold ◽  
Armin Hadziahmetovic ◽  
Markus Gruber ◽  
Constantin Ammar ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
High Reliability ◽  
Simulated Data ◽  
Absolute Quantification ◽  
Differential Analysis ◽  
Rna Seq ◽  
Error Distributions ◽  
Alternatively Spliced ◽  
Replicate Measurements ◽  
Recall Level

ABSTRACTWhile absolute quantification is challenging in high-throughput measurements, changes of features between conditions can often be determined with high precision. Therefore, analysis of fold changes is the standard method, but often, a doubly differential analysis of changes of changes is required. Differential alternative splicing is an example of a doubly differential analysis, i.e. fold changes between conditions for different isoforms of a gene. EmpiRe is a quantitative approach for various kinds of omics data based on fold changes for appropriate features of biological objects. Empirical error distributions for these fold changes are estimated from Replicate measurements and used to quantify feature fold changes and their directions. We assess the performance of EmpiRe to detect differentially expressed genes applied to RNA-Seq using simulated data. It achieved higher precision than established tools at nearly the same recall level. Furthermore, we assess the detection of alternatively Spliced genes via changes of isoform fold changes (EmpiReS) on distribution-free simulations and experimentally validated splicing events. EmpiReS achieves the best precision-recall values for simulations based on different biological datasets. We propose EmpiRe(S) as a general, quantitative and fast approach with high reliability and an excellent trade-off between sensitivity and precision in (doubly) differential analyses.

scholarly journals Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis

2018 ◽  
Author(s):  
Jin Li ◽  
Peng Yu
Keyword(s):  
Alternative Splicing ◽  
Computational Analysis ◽  
Potential Role ◽  
Exon Skipping ◽  
Chronic Inflammatory Disease ◽  
Splicing Factors ◽  
The Novel ◽  
Rna Seq ◽  
Genome Wide

AbstractPsoriasis is a chronic inflammatory disease that affects the skin, nails, and joints. For understanding the mechanism of psoriasis, though, alternative splicing analysis has received relatively little attention in the field. Here, we developed and applied several computational analysis methods to study psoriasis. Using psoriasis mouse and human datasets, our differential alternative splicing analyses detected hundreds of differential alternative splicing changes. Our analysis of conservation revealed many exon-skipping events conserved between mice and humans. In addition, our splicing signature comparison analysis using the psoriasis datasets and our curated splicing factor perturbation RNA-Seq database, SFMetaDB, identified nine candidate splicing factors that may be important in regulating splicing in the psoriasis mouse model dataset. Three of the nine splicing factors were confirmed upon analyzing the human data. Our computational methods have generated predictions for the potential role of splicing in psoriasis. Future experiments on the novel candidates predicted by our computational analysis are expected to provide a better understanding of the molecular mechanism of psoriasis and to pave the way for new therapeutic treatments.

Profiling novel alternative splicing within multiple tissues puts insight into the porcine genome annotation

2019 ◽  
Author(s):  
Jian-Feng Liu ◽  
Wen Feng ◽  
Pengju Zhao ◽  
Xianrui Zheng
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
Genome Annotation ◽  
Donor Site ◽  
The Novel ◽  
Rna Seq ◽  
Novel Proteins ◽  
Genome Wide ◽  
Alternative Donor ◽  
Mrna Precursor

Abstract Background Alternative splicing (AS) is a process that mRNA precursor splices intron to form the mature mRNA. AS plays important roles in contributing to transcriptome and proteome divert. However, to date there is no research about pig AS in genome-wide level by RNA sequencing. Results To characterize the AS in pigs, herein we detected genome-wide transcripts and events by RNA sequencing technology (RNA-seq) 34 different tissues in Duroc pigs. In total, we identified 138, 403 AS events and 29, 270 expressed genes. We found alternative donor site was the most common AS form, which is accounted for 44% of the total AS events. The percentage of the other 3 AS forms are all around 19%. The results showed that the most common AS events (alternative donor site) can produce different transcripts or different proteins which affect the biological process. Among these AS events, 109, 483 were novel AS events, and the number of alternative donor splice site has increased the most (Accounting for 44% of the novel AS events).Conclusions The expression of gene with tissue specific AS events showed that the functions of these genes were consistent with the tissue function. AS increased proteome diversity and resulted in novel proteins that gained and lost important functional domains. In summary, these findings extend genome annotation and highlight roles that AS acts in tissue identity in pig.Key words: Alternative splicing; transcript; protein; SNP

scholarly journals Dynamic Insertion of Pot3 in AvrPib Prevailing in a Field Rice Blast Population in the Philippines Led to the High Virulence Frequency Against the Resistance Gene Pib in Rice

2019 ◽  
Vol 109 (5) ◽  
pp. 870-877 ◽  
Author(s):  
Toluwase Olukayode ◽  
Berlaine Quime ◽  
Yin-Chi Shen ◽  
Mary Jeannie Yanoria ◽  
Suobing Zhang ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Rice Blast ◽  
Indica Rice ◽  
The Philippines ◽  
Avirulence Gene ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Polymerase Chain

The Magnaporthe oryzae avirulence gene AvrPib is required for the resistance mediated by its cognate resistance gene Pib, which has been intensively used in indica rice breeding programs in many Asian countries. However, the sequence diversity of AvrPib among geographically distinct M. oryzae populations was recently shown to be increasing. Here, we selected a field population consisting of 248 rice blast isolates collected from a disease hotspot in Philippine for the analysis of AvrPib haplotypes and their pathogenicity against Pib. We found that all of the isolates were virulent to Pib and each of them contained an insertion of Pot3 transposon in AvrPib. Moreover, Pot3 insertion was detected in different genomic positions, resulting in three different AvrPib haplotypes, designated avrPib-H1 to H3. We further conducted a genome-wide Pot2 fingerprinting analysis by repetitive element palindromic polymerase chain reaction (PCR) and identified seven different lineages out of 47 representative isolates. The isolates belonging to the same lineage often had the same AvrPib haplotype. In contrast, the isolates having the same AvrPib haplotypes did not always belong to the same lineages. Both mating types MAT1-1 and MAT1-2 were identified in the population in Bohol and the latter appeared dominant. On the host side, we found that 32 of 52 released rice varieties in the Philippines contained Pib diagnosed by PCR gene-specific primers and DNA sequencing of gene amplicons, suggesting that it was widely incorporated in different rice varieties. Our study highlights the genetic dynamics of rice blast population at both the AvrPib locus and the genome-wide levels, providing insight into the mechanisms of the mutations in AvrPib leading to the breakdown of Pib-mediated resistance in rice.

scholarly journals Genome-wide Profiling of Histone Lysine Butyrylation Reveals its Role in the Positive Regulation of Gene Transcription in Rice

Rice ◽  
2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Shuai Liu ◽  
Guanqing Liu ◽  
Peifeng Cheng ◽  
Chao Xue ◽  
Yong Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Rice Genome ◽  
Enrichment Analysis ◽  
Carbon Chain ◽  
Main Body ◽  
Rice Varieties ◽  
Genome Wide ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Intergenic Regions

Abstract Background Histone modifications play important roles in growth and development of rice (Oryza sativa L.). Lysine butyrylation (Kbu) with a four-carbon chain is a newly-discovered histone acylation modification in rice. Main Body In this study, we performed chromatin immunoprecipitation sequencing (ChIP-seq) analyses, the result showed that major enrichment of histone Kbu located in genebody regions of rice genome, especially in exons. The enrichment level of Kbu histone modification is positively correlated with gene expression. Furthermore, we compared Kbu with DNase-seq and other histone modifications in rice. We found that 60.06% Kub enriched region co-located with DHSs in intergenic regions. The similar profiles were detected among Kbu and several acetylation modifications such as H3K4ac, H3K9ac, and H3K23ac, indicating that Kbu modification is an active signal of transcription. Genes with both histone Kbu and one other acetylation also had significantly increased expression compared with genes with only one acetylation. Gene Ontology (GO) enrichment analysis revealed that these genes with histone Kbu can regulate multiple metabolic process in different rice varieties. Conclusion Our study showed that the lysine butyrylation modificaiton may promote gene expression as histone acetylation and will provide resources for futher studies on histone Kbu and other epigenetic modifications in plants.

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