scholarly journals RNAseq-based transcriptome assembly ofClostridium acetobutylicumfor functional genome annotation and discovery

AIChE Journal ◽  
2018 ◽  
Vol 64 (12) ◽  
pp. 4271-4280 ◽  
Author(s):  
Matthew T. Ralston ◽  
Eleftherios T. Papoutsakis
Keyword(s):  
Genome Annotation ◽  
Transcriptome Assembly ◽  
Functional Genome Annotation ◽  
Functional Genome

scholarly journals Genomic Resources for Gene Discovery, Functional Genome Annotation, and Evolutionary Studies of Maize and Its Close Relatives

Genetics ◽  
2013 ◽  
Vol 195 (3) ◽  
pp. 723-737 ◽  
Author(s):  
Chao Wang ◽  
Xue Shi ◽  
Lin Liu ◽  
Haiyan Li ◽  
Jetty S.S. Ammiraju ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Gene Discovery ◽  
Genomic Resources ◽  
Evolutionary Studies ◽  
Close Relatives ◽  
Functional Genome Annotation ◽  
Functional Genome

Functional genome annotation depicts probiotic properties of Bacillus velezensis FTC01

Gene ◽  
2019 ◽  
Vol 713 ◽  
pp. 143971 ◽  
Author(s):  
Jamile Queiroz Pereira ◽  
Ana Carolina Ritter ◽  
Samuel Cibulski ◽  
Adriano Brandelli
Keyword(s):  
Genome Annotation ◽  
Probiotic Properties ◽  
Bacillus Velezensis ◽  
Functional Genome Annotation ◽  
Functional Genome

Functional genome annotation through phylogenomic mapping

2005 ◽  
Vol 23 (6) ◽  
pp. 691-698 ◽  
Author(s):  
Balaji S Srinivasan ◽  
Nora B Caberoy ◽  
Garret Suen ◽  
Rion G Taylor ◽  
Radhika Shah ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Functional Genome Annotation ◽  
Functional Genome

scholarly journals SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

2017 ◽  
Vol 34 (8) ◽  
pp. 1401-1403 ◽  
Author(s):  
Jasper J Koehorst ◽  
Jesse C J van Dam ◽  
Edoardo Saccenti ◽  
Vitor A P Martins dos Santos ◽  
Maria Suarez-Diez ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Semantic Framework ◽  
Fair Principles ◽  
Functional Genome Annotation ◽  
Functional Genome

scholarly journals PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes

2021 ◽  
Vol 12 ◽  
Author(s):  
Ali Ali ◽  
Gary H. Thorgaard ◽  
Mohamed Salem
Keyword(s):  
Rainbow Trout ◽  
Alternative Splicing ◽  
Single Molecule ◽  
Genome Annotation ◽  
Reference Genome ◽  
Cold Water ◽  
Intron Retention ◽  
Transcriptome Assembly ◽  
Model Organism ◽  
Fish Growth

Rainbow trout is an important model organism that has received concerted international efforts to study the transcriptome. For this purpose, short-read sequencing has been primarily used over the past decade. However, these sequences are too short of resolving the transcriptome complexity. This study reported a first full-length transcriptome assembly of the rainbow trout using single-molecule long-read isoform sequencing (Iso-Seq). Extensive computational approaches were used to refine and validate the reconstructed transcriptome. The study identified 10,640 high-confidence transcripts not previously annotated, in addition to 1,479 isoforms not mapped to the current Swanson reference genome. Most of the identified lncRNAs were non-coding variants of coding transcripts. The majority of genes had multiple transcript isoforms (average ∼3 isoforms/locus). Intron retention (IR) and exon skipping (ES) accounted for 56% of alternative splicing (AS) events. Iso-Seq improved the reference genome annotation, which allowed identification of characteristic AS associated with fish growth, muscle accretion, disease resistance, stress response, and fish migration. For instance, an ES in GVIN1 gene existed in fish susceptible to bacterial cold-water disease (BCWD). Besides, under five stress conditions, there was a commonly regulated exon in prolyl 4-hydroxylase subunit alpha-2 (P4HA2) gene. The reconstructed gene models and their posttranscriptional processing in rainbow trout provide invaluable resources that could be further used for future genetics and genomics studies. Additionally, the study identified characteristic transcription events associated with economically important phenotypes, which could be applied in selective breeding.

scholarly journals Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540

2019 ◽  
Vol 7 (11) ◽  
pp. 489 ◽  
Author(s):  
Ievgeniia A. Tiukova ◽  
Huifeng Jiang ◽  
Jacques Dainat ◽  
Marc P. Hoeppner ◽  
Henrik Lantz ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Biotechnological Applications ◽  
Genetic Determinants ◽  
Alcohol Content ◽  
Protein Coding ◽  
Biotechnological Potential ◽  
High Attenuation ◽  
Spoilage Yeast ◽  
Functional Genome Annotation ◽  
Low Alcohol

Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.

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