Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

Virag Sharma; Anas Elghafari; Michael Hiller

doi:10.1093/nar/gkw210

Coding Exon-Structure Aware Realigner (CESAR): Utilizing Genome Alignments for Comparative Gene Annotation

Methods in Molecular Biology - Gene Prediction ◽

10.1007/978-1-4939-9173-0_10 ◽

2019 ◽

pp. 179-191 ◽

Cited By ~ 1

Author(s):

Virag Sharma ◽

Michael Hiller

Keyword(s):

Gene Annotation ◽

Exon Structure

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Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression analysis

Human Genomics ◽

10.1186/s40246-021-00336-1 ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Zeeshan Ahmed ◽

Eduard Gibert Renart ◽

Saman Zeeshan ◽

XinQi Dong

Keyword(s):

Data Analysis ◽

Patient Care ◽

Expression Analysis ◽

High Throughput ◽

Gene Annotation ◽

Next Generation Sequencing Data ◽

Rna Seq ◽

Sequencing Data ◽

Complex Disorders ◽

Transcriptomics Data

Abstract Background Genetic disposition is considered critical for identifying subjects at high risk for disease development. Investigating disease-causing and high and low expressed genes can support finding the root causes of uncertainties in patient care. However, independent and timely high-throughput next-generation sequencing data analysis is still a challenge for non-computational biologists and geneticists. Results In this manuscript, we present a findable, accessible, interactive, and reusable (FAIR) bioinformatics platform, i.e., GVViZ (visualizing genes with disease-causing variants). GVViZ is a user-friendly, cross-platform, and database application for RNA-seq-driven variable and complex gene-disease data annotation and expression analysis with a dynamic heat map visualization. GVViZ has the potential to find patterns across millions of features and extract actionable information, which can support the early detection of complex disorders and the development of new therapies for personalized patient care. The execution of GVViZ is based on a set of simple instructions that users without a computational background can follow to design and perform customized data analysis. It can assimilate patients’ transcriptomics data with the public, proprietary, and our in-house developed gene-disease databases to query, easily explore, and access information on gene annotation and classified disease phenotypes with greater visibility and customization. To test its performance and understand the clinical and scientific impact of GVViZ, we present GVViZ analysis for different chronic diseases and conditions, including Alzheimer’s disease, arthritis, asthma, diabetes mellitus, heart failure, hypertension, obesity, osteoporosis, and multiple cancer disorders. The results are visualized using GVViZ and can be exported as image (PNF/TIFF) and text (CSV) files that include gene names, Ensembl (ENSG) IDs, quantified abundances, expressed transcript lengths, and annotated oncology and non-oncology diseases. Conclusions We emphasize that automated and interactive visualization should be an indispensable component of modern RNA-seq analysis, which is currently not the case. However, experts in clinics and researchers in life sciences can use GVViZ to visualize and interpret the transcriptomics data, making it a powerful tool to study the dynamics of gene expression and regulation. Furthermore, with successful deployment in clinical settings, GVViZ has the potential to enable high-throughput correlations between patient diagnoses based on clinical and transcriptomics data.

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Identification of Novel Toxin Genes from the Stinging Nettle Caterpillar Parasa lepida (Cramer, 1799): Insights into the Evolution of Lepidoptera Toxins

Insects ◽

10.3390/insects12050396 ◽

2021 ◽

Vol 12 (5) ◽

pp. 396

Author(s):

Natrada Mitpuangchon ◽

Kwan Nualcharoen ◽

Singtoe Boonrotpong ◽

Patamarerk Engsontia

Keyword(s):

Protease Inhibitors ◽

Proteolytic Enzymes ◽

Gene Annotation ◽

Sequence Similarity ◽

New Drugs ◽

Toxin Gene ◽

Cone Snail ◽

Stinging Nettle ◽

Toxin Genes ◽

Nettle Caterpillar

Many animal species can produce venom for defense, predation, and competition. The venom usually contains diverse peptide and protein toxins, including neurotoxins, proteolytic enzymes, protease inhibitors, and allergens. Some drugs for cancer, neurological disorders, and analgesics were developed based on animal toxin structures and functions. Several caterpillar species possess venoms that cause varying effects on humans both locally and systemically. However, toxins from only a few species have been investigated, limiting the full understanding of the Lepidoptera toxin diversity and evolution. We used the RNA-seq technique to identify toxin genes from the stinging nettle caterpillar, Parasa lepida (Cramer, 1799). We constructed a transcriptome from caterpillar urticating hairs and reported 34,968 unique transcripts. Using our toxin gene annotation pipeline, we identified 168 candidate toxin genes, including protease inhibitors, proteolytic enzymes, and allergens. The 21 P. lepida novel Knottin-like peptides, which do not show sequence similarity to any known peptide, have predicted 3D structures similar to tarantula, scorpion, and cone snail neurotoxins. We highlighted the importance of convergent evolution in the Lepidoptera toxin evolution and the possible mechanisms. This study opens a new path to understanding the hidden diversity of Lepidoptera toxins, which could be a fruitful source for developing new drugs.

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Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis

Nature Communications ◽

10.1038/s41467-021-22496-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Michael F. Z. Wang ◽

Madhav Mantri ◽

Shao-Pei Chou ◽

Gaetano J. Scuderi ◽

David W. McKellar ◽

...

Keyword(s):

Single Cell ◽

Genome Annotation ◽

Gene Annotation ◽

Active Regions ◽

Sequencing Analysis ◽

Biologically Relevant ◽

Mole Rat ◽

Genome Annotations ◽

Cell Expression ◽

High Quality Genome

AbstractConventional scRNA-seq expression analyses rely on the availability of a high quality genome annotation. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, genome annotations are often incomplete, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant transcriptional activity beyond the scope of the best available genome annotation by performing scRNA-seq analysis on any region in the genome for which transcriptional products are detected. Our tool generates a single-cell expression matrix for all transcriptionally active regions (TARs), performs single-cell TAR expression analysis to identify biologically significant TARs, and then annotates TARs using gene homology analysis. This procedure uses single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts and thereby uncovers biology to which scRNA-seq would otherwise be in the dark.

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A non-canonical Δ9-desaturase synthesizing palmitoleic acid identified in the thraustochytrid Aurantiochytrium sp. T66

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11425-5 ◽

2021 ◽

Author(s):

E-Ming Rau ◽

Inga Marie Aasen ◽

Helga Ertesvåg

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Fatty Acid Synthase ◽

Palmitoleic Acid ◽

Unsaturated Fatty Acids ◽

Gene Annotation ◽

Vaccenic Acid ◽

Strain Engineering ◽

Δ9 Desaturase ◽

Δ12 Desaturase

Abstract Thraustochytrids are oleaginous marine eukaryotic microbes currently used to produce the essential omega-3 fatty acid docosahexaenoic acid (DHA, C22:6 n-3). To improve the production of this essential fatty acid by strain engineering, it is important to deeply understand how thraustochytrids synthesize fatty acids. While DHA is synthesized by a dedicated enzyme complex, other fatty acids are probably synthesized by the fatty acid synthase, followed by desaturases and elongases. Which unsaturated fatty acids are produced differs between different thraustochytrid genera and species; for example, Aurantiochytrium sp. T66, but not Aurantiochytrium limacinum SR21, synthesizes palmitoleic acid (C16:1 n-7) and vaccenic acid (C18:1 n-7). How strain T66 can produce these fatty acids has not been known, because BLAST analyses suggest that strain T66 does not encode any Δ9-desaturase-like enzyme. However, it does encode one Δ12-desaturase-like enzyme. In this study, the latter enzyme was expressed in A. limacinum SR21, and both C16:1 n-7 and C18:1 n-7 could be detected in the transgenic cells. Our results show that this desaturase, annotated T66Des9, is a Δ9-desaturase accepting C16:0 as a substrate. Phylogenetic studies indicate that the corresponding gene probably has evolved from a Δ12-desaturase-encoding gene. This possibility has not been reported earlier and is important to consider when one tries to deduce the potential a given organism has for producing unsaturated fatty acids based on its genome sequence alone. Key points • In thraustochytrids, automatic gene annotation does not always explain the fatty acids produced. • T66Des9 is shown to synthesize palmitoleic acid (C16:1 n-7). • T66des9 has probably evolved from Δ12-desaturase-encoding genes.

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RcTGA1 and glucosinolate biosynthesis pathway involvement in the defence of rose against the necrotrophic fungus Botrytis cinerea

BMC Plant Biology ◽

10.1186/s12870-021-02973-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Penghua Gao ◽

Hao Zhang ◽

Huijun Yan ◽

Qigang Wang ◽

Bo Yan ◽

...

Keyword(s):

Disease Resistance ◽

Gene Annotation ◽

Infected Plant ◽

Grey Mould ◽

Cascade Reactions ◽

Postharvest Quality ◽

Rna Seq ◽

Protein Activity ◽

Phenylpropanoid Biosynthesis ◽

And Cluster Analysis

Abstract Background Rose is an important economic crop in horticulture. However, its field growth and postharvest quality are negatively affected by grey mould disease caused by Botrytis c. However, it is unclear how rose plants defend themselves against this fungal pathogen. Here, we used transcriptomic, metabolomic and VIGS analyses to explore the mechanism of resistance to Botrytis c. Result In this study, a protein activity analysis revealed a significant increase in defence enzyme activities in infected plants. RNA-Seq of plants infected for 0 h, 36 h, 60 h and 72 h produced a total of 54 GB of clean reads. Among these reads, 3990, 5995 and 8683 differentially expressed genes (DEGs) were found in CK vs. T36, CK vs. T60 and CK vs. T72, respectively. Gene annotation and cluster analysis of the DEGs revealed a variety of defence responses to Botrytis c. infection, including resistance (R) proteins, MAPK cascade reactions, plant hormone signal transduction pathways, plant-pathogen interaction pathways, Ca2+ and disease resistance-related genes. qPCR verification showed the reliability of the transcriptome data. The PTRV2-RcTGA1-infected plant material showed improved susceptibility of rose to Botrytis c. A total of 635 metabolites were detected in all samples, which could be divided into 29 groups. Metabonomic data showed that a total of 59, 78 and 74 DEMs were obtained for T36, T60 and T72 (T36: Botrytis c. inoculated rose flowers at 36 h; T60: Botrytis c. inoculated rose flowers at 60 h; T72: Botrytis c. inoculated rose flowers at 72 h) compared to CK, respectively. A variety of secondary metabolites are related to biological disease resistance, including tannins, amino acids and derivatives, and alkaloids, among others; they were significantly increased and enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways. This study provides a theoretical basis for breeding new cultivars that are resistant to Botrytis c. Conclusion Fifty-four GB of clean reads were generated through RNA-Seq. R proteins, ROS signalling, Ca2+ signalling, MAPK signalling, and SA signalling were activated in the Old Blush response to Botrytis c. RcTGA1 positively regulates rose resistance to Botrytis c. A total of 635 metabolites were detected in all samples. DEMs were enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways.

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A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula)

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03938-4 ◽

2021 ◽

Author(s):

Gangjun Zhao ◽

Caixia Luo ◽

Jianning Luo ◽

Junxing Li ◽

Hao Gong ◽

...

Keyword(s):

Gene Annotation ◽

Recessive Gene ◽

Genomic Region ◽

Dwarf Mutant ◽

Rna Seq ◽

Dwarf Phenotype ◽

Sponge Gourd ◽

Response To Stress ◽

Luffa Acutangula ◽

Generation Sequencing

Abstract Key message A dwarfism gene LacDWARF1 was mapped by combined BSA-Seq and comparative genomics analyses to a 65.4 kb physical genomic region on chromosome 05. Abstract Dwarf architecture is one of the most important traits utilized in Cucurbitaceae breeding because it saves labor and increases the harvest index. To our knowledge, there has been no prior research about dwarfism in the sponge gourd. This study reports the first dwarf mutant WJ209 with a decrease in cell size and internodes. A genetic analysis revealed that the mutant phenotype was controlled by a single recessive gene, which is designated Lacdwarf1 (Lacd1). Combined with bulked segregate analysis and next-generation sequencing, we quickly mapped a 65.4 kb region on chromosome 5 using F2 segregation population with InDel and SNP polymorphism markers. Gene annotation revealed that Lac05g019500 encodes a gibberellin 3β-hydroxylase (GA3ox) that functions as the most likely candidate gene for Lacd1. DNA sequence analysis showed that there is an approximately 4 kb insertion in the first intron of Lac05g019500 in WJ209. Lac05g019500 is transcribed incorrectly in the dwarf mutant owing to the presence of the insertion. Moreover, the bioactive GAs decreased significantly in WJ209, and the dwarf phenotype could be restored by exogenous GA3 treatment, indicating that WJ209 is a GA-deficient mutant. All these results support the conclusion that Lac05g019500 is the Lacd1 gene. In addition, RNA-Seq revealed that many genes, including those related to plant hormones, cellular process, cell wall, membrane and response to stress, were significantly altered in WJ209 compared with the wild type. This study will aid in the use of molecular marker-assisted breeding in the dwarf sponge gourd.

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PSVII-37 Late-Breaking Abstract: CNV analysis of indigenous sheep reveals genes linked to disease resistance and adaptation

Journal of Animal Science ◽

10.1093/jas/skaa278.602 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 339-339

Author(s):

Annelin Molotsi

Keyword(s):

Candidate Genes ◽

Copy Number ◽

Structural Changes ◽

Gene Annotation ◽

Smallholder Farmers ◽

Copy Number Variations ◽

Ovis Aries ◽

Matrix Composition ◽

Low Input ◽

Gene Group

Abstract Smallholder farmers often make use of low-input systems, suggesting that robust and adaptable individuals are needed in these systems that have good production and reproduction in these low-input systems. One of the reasons certain individuals may be more adaptable or have higher production outputs could be due to the presence of advantageous mutations or genetic structural variants. Genetic variants, namely copy number variations (CNVs), are structural changes to the DNA and are larger than a single nucleotide. In this study, 47 sheep were investigated for the presence of CNVs. A total of 206 CNVs passed quality control. These CNVs were compared to the NCBI RefSeq Ovis aries: Oar_v4.0 to identify candidate genes located within or overlapping the copy number variations identified. Gene annotation analysis was carried out on the identified candidate genes. Gene annotation assigned the candidate genes to two gene groups. The first gene group were protein coding genes responsible for interferons that are the natural defences individuals have against viral and bacterial infection. The second gene group was found to be responsible for a variety of biological functions including transport, metabolic precursors, neurogenesis, signalling as well as bone and cartilage matrix composition along with a number of other important functions. This indicates that CNVs could have various effects on important biological process which could possibly influence an individual’s survival or even production and reproduction. This highlights the need for CNV studies to determine the influence of these CNVs and how they can be utilised in breeding programmes to improve adaptation and production outputs.

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