Leveraging multiple transcriptome assembly methods for improved gene structure annotation

Venturini, Luca; Caim, Shabhonam; Kaithakottil, Gemy; Mapleson, Daniel; Swarbreck, David

doi:10.1101/216994

Cited by 16 publications

(16 citation statements)

References 40 publications

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“…ORFs were predicted using TransDecoder 3.0.0 [ 10 ]. Scoring parameters for each species can be found in Mikado v1.0.1 [ 48 ], with a name scheme of species_name _scoring.yaml (e.g., “athaliana_scoring.yaml” for A. thaliana ). The same scoring files were used for all runs, both with simulated and real data.…”

Section: Methodsmentioning

confidence: 99%

“… Project name: Mikado Project home page: [ 1 ] Operating system(s): Linux Programming language: Python3 Other requirements: SnakeMake, BioPython, NumPY, SciPY, Scikit-learn, BLAST+ or DIAMOND, Prodigal or TransDecoder, Portcullis Available through: PyPI, bioconda, SciCruch (RRID: SCR_016159) License: GNU LGPL3 …”

Section: Availability Of Source Code and Requirementsmentioning

confidence: 99%

“…The human sequencing data of our parallel Illumina and PacBio experiment can be found under the accession code PRJEB22606. Mikado is present on GitHub [ 1 ]. Many of the scripts used to control the pipeline executions, together with the scripts used to create the charts presented in the article, can be found in the complementary repository [ 55 ].…”

Section: Availability Of Supporting Datamentioning

confidence: 99%

“…Many of the scripts used to control the pipeline executions, together with the scripts used to create the charts presented in the article, can be found in the complementary repository [ 55 ]. Extensive documentation for the program is available in the “docs” folder in the GitHub repository [ 1 ] and is published on the “Read The Docs” website [ 26 ]. All sequencing runs and reference sequence datasets used for this study are publicly available.…”

Section: Availability Of Supporting Datamentioning

confidence: 99%

“…In such cases, it is not uncommon to produce at least one set of transcript assemblies for each of the different sources of data, assemblies that then need to be reconciled. To address these challenges, we developed MIKADO [ 1 ], an approach to integrate transcript assemblies. The tool defines loci, scores transcripts, determines a representative transcript for each locus, and finally returns a set of gene models filtered to individual requirements, e.g., removing transcripts that are chimeric, fragmented, or with short or disrupted coding sequences.…”

Section: Introductionmentioning

confidence: 99%

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Leveraging multiple transcriptome assembly methods for improved gene structure annotation

et al. 2018

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BackgroundThe performance of RNA sequencing (RNA-seq) aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand.ResultsHere, we show that the accuracy of transcript reconstruction can be boosted by combining multiple methods, and we present a novel algorithm to integrate multiple RNA-seq assemblies into a coherent transcript annotation. Our algorithm can remove redundancies and select the best transcript models according to user-specified metrics, while solving common artifacts such as erroneous transcript chimerisms.ConclusionsWe have implemented this method in an open-source Python3 and Cython program, Mikado, available on GitHub.

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Section: Methodsmentioning

confidence: 99%

Section: Availability Of Source Code and Requirementsmentioning

confidence: 99%

Section: Availability Of Supporting Datamentioning

confidence: 99%

Section: Availability Of Supporting Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Leveraging multiple transcriptome assembly methods for improved gene structure annotation

et al. 2018

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Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups

Stroehlein

Young

Gasser

2018

Sci Rep

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Despite the substantial amount of genomic and transcriptomic data available for a wide range of eukaryotic organisms, most genomes are still in a draft state and can have inaccurate gene predictions. To gain a sound understanding of the biology of an organism, it is crucial that inferred protein sequences are accurately identified and annotated. However, this can be challenging to achieve, particularly for organisms such as parasitic worms (helminths), as most gene prediction approaches do not account for substantial phylogenetic divergence from model organisms, such as Caenorhabditis elegans and Drosophila melanogaster, whose genomes are well-curated. In this paper, we describe a bioinformatic strategy for the curation of gene families and subsequent annotation of encoded proteins. This strategy relies on pairwise gene curation between at least two closely related species using genomic and transcriptomic data sets, and is built on recent work on kinase complements of parasitic worms. Here, we discuss salient technical aspects of this strategy and its implications for the curation of protein families more generally.

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Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome

Alonge

Ramakrishnan

et al. 2022

The Plant Cell

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The highly diverse Solanaceae family contains several widely studied model and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative P. pruinosa and use these resources to study natural and engineered variation in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9 targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system, and establish a paradigm in the search for factors driving ICS.

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Leveraging multiple transcriptome assembly methods for improved gene structure annotation

Cited by 16 publications

References 40 publications

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups

Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome

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