A simple guide to de novo transcriptome assembly and annotation

Briefings in Bioinformatics, Journal Year: 2021, Volume and Issue: 23(2)

Published: Dec. 10, 2021

A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome assembly unnecessary, expensive or difficult. In the absence a sequenced to guide reconstruction process, must be assembled de novo using only information available in RNA-seq reads. Subsequently, sequences annotated order identify sequence-intrinsic and evolutionary features them (for example, regions). Although straightforward at first glance, annotation can quickly prove challenging undertakings. addition familiarizing themselves with conceptual technical intricacies tasks hand numerous pre- post-processing steps involved, those interested also grapple overwhelmingly large choice tools. The lack standardized workflows, fast pace development new tools techniques paucity authoritative literature have served exacerbate difficulty task even further. Here, we present comprehensive overview annotation. We discuss procedures including steps, compendium corresponding

Language: Английский

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ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 11

Published: Sept. 4, 2020

Hybridization and its relevance is a hot topic in ecology evolutionary biology. Interspecific gene flow may play key role species adaptation to environmental change, as well the survival of endangered populations. Despite fact that hybridization quite common plants, many hybridizing species, such Quercus spp., maintain their integrity, while precise determination genomic boundaries between remains elusive. Novel high throughput sequencing techniques have opened up new perspectives comparative analysis genomes study historical current interspecific flow. In this work, we applied ddRADseq technique developed an ad hoc bioinformatics pipeline for ongoing two relevant Mediterranean oaks, Q. ilex suber. We adopted local scale approach, analyzing adult hybrids (sensu lato) identified mixed stand open-pollinated progenies. 9,435 markers across genome estimated individual introgression levels adults seedlings. Estimated contribution suber higher, on average, hybrid progenies than adults, suggesting preferential backcrossing with parental maybe followed by selection during juvenile stages against individuals higher contribution. Most discriminating seem be scattered throughout genome, large number small regions underlie these species. A noticeable proportion (26%) showed allelic frequencies very similar one different from other; finding seems understanding process occurrence adaptive introgression. Candidate marker databases constitute valuable resource design re-sequencing experiments sclerophyllous oak could provide insight ilex.

Language: Английский

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Transcriptional time-course analysis during ash dieback infection revealed different responses in tolerant and susceptible Fraxinus excelsior genotypes

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Jan. 25, 2025

Abstract Hymenoscyphus fraxineus , the causal agent of Ash Dieback (ADB), has been introduced to eastern Europe in 1990s from where it spread causing decline European ash populations. However, genetic basis molecular response tolerant and susceptible trees this disease is still largely unknown. We performed RNA-sequencing study transcriptomic four genotypes (ADB-tolerant FAR3 FS36, ADB-susceptible UW1 UW2), during a time-course 7, 14, 21, 28 days post-inoculation, including mock-inoculated as control samples for each sampling time point. The analysis yielded 395 500 Differentially Expressed Genes (DEGs) along ADB-tolerant respectively, while UW2 revealed 194 571 DEGs, with most DEGs found exclusively just one genotypes. shared between included genes involved production phytoalexins other secondary metabolites roles plant defense. Moreover, we identified an earlier expression both pattern- effector-triggered immunity (PTI ETI) genotypes, responses were delayed (late response). Overall, these results different patterns not only but also within two groups. This hints individual natural tolerance ADB, possibly revealing diversified strategies across

Language: Английский

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Physiological and Molecular Response to Drought in Somatic Plants from Pinus Radiata Embryonal Masses Induced at High Temperatures

Published: Jan. 1, 2025

Language: Английский

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gymnotoa-db: a database and application to optimize functional annotation in gymnosperms

Database, Journal Year: 2025, Volume and Issue: 2025

Published: Jan. 1, 2025

Abstract Gymnosperms are a clade of non-flowering plants that include about 1000 living species. Due to their complex genomes and lack genomic resources, functional annotation in genomics transcriptomics on gymnosperms suffers from limitations. Here we present gymnotoa-db, which is novel, publicly accessible relational database designed facilitate gymnosperms. This stores non-redundant records gymnosperm proteins, encompassing taxonomic information. The complementary software, gymnotoa-app, enables users download gymnotoa-db execute comprehensive pipeline for high-throughput sequencing-derived DNA or cDNA sequences. gymnotoa-app’s user-friendly interface efficient algorithms streamline the process, making it an invaluable tool researchers studying We compared performance against other tools utilizing disparate reference databases. Our results demonstrate superior ability accurately annotate transcripts, recovering greater number transcripts unique, Gene Ontology terms. gymnotoa-db’s distinctive features coverage with dataset protein sequences, robust information integrates data multiple ontology systems, including GO, KEGG, EC, MetaCYC, while keeping context, Arabidopsis homologs. Database URL: https://blogs.upm.es/gymnotoa-db/2024/09/19/gymnotoa-app/

Language: Английский

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Single specimen genome assembly of Culicoides stellifer shows evidence of a non-retroviral endogenous viral element

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 14, 2025

Abstract Background Advancing our knowledge of vector species genomes is a key step in battle against the spread diseases. Biting midges genus Culicoides are vectors arboviruses that significantly affect livestock worldwide. stellifer suspected with wide range distribution North America, for which cryptic diversity has been described. Results With just one specimen C. , we assembled and annotated nuclear mitochondrial genome using ultra-low input DNA PacBio protocol. The assembly 119 Mb length contig N50 value 479.3 kb, contains 11% repeat sequences 18,895 protein-coding genes. To further elucidate role this as vector, provide genomic evidence non-retroviral endogenous viral element integrated into corresponds to rhabdovirus nucleocapsid proteins, same family vesicular stomatitis virus. Conclusions This information will pave way future investigations species’s putative role. We also demonstrate practicability completing studies small dipterans single specimens preserved ethanol well introduce workflow data analysis considers challenges insect assembly.

Language: Английский

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Physiological and molecular response to drought in somatic plants from Pinus radiata embryonal masses induced at high temperatures

Plant Physiology and Biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 109886 - 109886

Published: April 1, 2025

Language: Английский

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Comparative Transcriptome Analyses of Different Rheum officinale Tissues Reveal Differentially Expressed Genes Associated with Anthraquinone, Catechin, and Gallic Acid Biosynthesis

Genes, Journal Year: 2022, Volume and Issue: 13(9), P. 1592 - 1592

Published: Sept. 5, 2022

Rheum officinale Baill. is an important traditional Chinese medicinal herb, its dried roots and rhizomes being widely utilized to cure diverse diseases. However, previous studies mainly focused on the active compounds their pharmacological effects, molecular mechanism underlying biosynthesis of these ingredients in R. still elusive. Here, we performed comparative transcriptome analyses elucidate differentially expressed genes (DEGs) root, stem, leaf officinale. A total 236,031 unigenes with N50 769 bp was generated, 136,329 (57.76%) which were annotated. 5884 DEGs identified after different tissues; 175 126 key enzyme tissue-specific expression found anthraquinone, catechin/gallic acid biosynthetic pathway, respectively, some verified by qRT-PCR. The phylogeny PKS III family Polygonaceae indicated that probably only PL_741 PKSIII1, PL_11549 PKSIII5, PL_101745 PKSIII6 encoded PKSIII polyketide pathway. These results will shed light basis accumulation regulation secondary metabolites officinale, lay a foundation for future genetic diversity, assisted breeding, germplasm resource improvement this essential plant.

Language: Английский

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FaPKc2.2 negatively modulates strawberry fruit ripening by reprograming the carbon metabolic pathway

Scientia Horticulturae, Journal Year: 2022, Volume and Issue: 301, P. 111114 - 111114

Published: April 9, 2022

Language: Английский

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Transcriptomic Complexity in Strawberry Fruit Development and Maturation Revealed by Nanopore Sequencing

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: July 13, 2022

The use of alternative transcription start or termination sites (aTSS aTTS) as well splicing (AS) produce diverse transcript isoforms, playing indispensable roles in the plant development and environmental adaptations. Despite advances finding genome-wide alternatively spliced genes strawberry, it remains unexplored how AS responds to developmental cues what relevance do these outcomes have gene function. In this study, we systematically investigated transcriptome complexity using long-read Oxford Nanopore Technologies along four successive stages. full-length cDNA sequencing results unraveled thousands previously isoforms raised from aTSS, aTTS, AS. relative contributions three processes strawberry fruit transcripts were compared. aTSS aTTS more abundant than Differentially expressed key transitional role white stage. Isoform switches 757 observed. They associated with protein-coding potential change domain gain loss main consequences. Those switched take part maturation late A case study yeast two hybrid analysis supported functional divergence B-box protein 22. Our provided a new comprehensive overview dynamic transcriptomic landscape during maturation.

Language: Английский

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