Proteogenomics‐Guided Evaluation of RNA‐Seq Assembly and Protein Database Construction for Emergent Model Organisms

Cogne, Yannick; Gouveia, Duarte; Chaumot, Arnaud; Degli-Esposti, Davide; Geffard, Olivier; Pible, Olivier; Almunia, Christine; Armengaud, Jean

doi:10.1002/pmic.201900261

Cited by 8 publications

(4 citation statements)

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“…However, at least in our set-up, an optimum should be considered to select the entries used to create the sub-database. Indeed, a proteomics approach was recently used to assess the quality of transcriptomics data and their assembly [ 14 ], and metaproteomics data could be used in a similar way to assess the quality of metagenomics data assemblies.…”

Section: Discussionmentioning

confidence: 99%

Increasing the power of interpretation for soil metaproteomics data

et al. 2021

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Background Soil and sediment microorganisms are highly phylogenetically diverse but are currently largely under-represented in public molecular databases. Their functional characterization by means of metaproteomics is usually performed using metagenomic sequences acquired for the same sample. However, such hugely diverse metagenomic datasets are difficult to assemble; in parallel, theoretical proteomes from isolates available in generic databases are of high quality. Both these factors advocate for the use of theoretical proteomes in metaproteomics interpretation pipelines. Here, we examined a number of database construction strategies with a view to increasing the outputs of metaproteomics studies performed on soil samples. Results The number of peptide-spectrum matches was found to be of comparable magnitude when using public or sample-specific metagenomics-derived databases. However, numbers were significantly increased when a combination of both types of information was used in a two-step cascaded search. Our data also indicate that the functional annotation of the metaproteomics dataset can be maximized by using a combination of both types of databases. Conclusions A two-step strategy combining sample-specific metagenome database and public databases such as the non-redundant NCBI database and a massive soil gene catalog allows maximizing the metaproteomic interpretation both in terms of ratio of assigned spectra and retrieval of function-derived information.

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Section: Discussionmentioning

confidence: 99%

Increasing the power of interpretation for soil metaproteomics data

et al. 2021

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“…The appropriate environmental parameters and the improved diet applied to the paralarvae cultured in this study have favored good development and proper settlement of the early-life stage of the octopus in the benthic media, which has allowed us to analyze the paralarvae at a more advanced stage of growth than in our previous studies. This has been reflected in the transcriptomic and proteomic results obtained, and highlighted the benefits of combining both analyses, particularly in a non-model organism (Cogne et al, 2020).…”

Section: Discussionmentioning

confidence: 81%

Proteogenomic Study of the Effect of an Improved Mixed Diet of Live Preys on the Aquaculture of Octopus vulgaris Paralarvae

et al. 2022

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The common octopus is the most demanded cephalopod species for human consumption. Despite important advances realized recently, the main bottleneck for commercial production of the common octopus, Octopus vulgaris, is the mass mortality of paralarvae in the first 15–20 days post-hatching (dph), with the main responsible factors still unknown. Thus, the identification of the limiting culture factors is, therefore, crucial for their aquaculture. This study investigates proteomic and transcriptomic responses of octopus paralarvae fed on an improved live preys-mixed diet (M) compared to an Artemia-based (A) reference diet. M diet resulted in the highest paralarvae specific growth rate obtained to date under culture conditions. This is supported by most of the proteins and genes over-expressed in the M group being linked to the cell cycle and replication, production of structural components, and development of the nervous system. Furthermore, the differential nutritional regulation of several genes and proteins seems to indicate that, instead of fatty acids, the preferred fuels for cephalopods would be proteins and carbohydrates. Also, M diet provides a better nutrient balance, which has allowed carrying out this comparative study in paralarvae under optimal conditions at a more advanced stage of growth (20 dph) than in previous studies. Moreover, the paralarvae culture extended up to 40 dph showed for the first time a proper pre-settlement behavior.

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“…Proteogenomics integrates transcriptomics and proteomics to create an annotated protein database that can be used to interpret tandem mass spectrometry (MS/MS) spectra of enzymatic proteins. This strategy has been successfully applied to protein database construction and molecular phenotyping of emerging model organisms [ 22 ]. Moreover, international public archival resources, such as the Sequence Read Archive (SRA), preserve public-domain sequencing data that are free, unrestricted, and permanently accessible.…”

Section: Introductionmentioning

confidence: 99%