Dataset Information

MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms.

ABSTRACT: The symbiont-associated (SA) environmental package is a new extension to the minimum information about any (x) sequence (MIxS) standards, established by the Parasite Microbiome Project (PMP) consortium, in collaboration with the Genomics Standard Consortium. The SA was built upon the host-associated MIxS standard, but reflects the nestedness of symbiont-associated microbiota within and across host-symbiont-microbe interactions. This package is designed to facilitate the collection and reporting of a broad range of metadata information that apply to symbionts such as life history traits, association with one or multiple host organisms, or the nature of host-symbiont interactions along the mutualism-parasitism continuum. To better reflect the inherent nestedness of all biological systems, we present a novel feature that allows users to co-localize samples, to nest a package within another package, and to identify replicates. Adoption of the MIxS-SA and of the new terms will facilitate reports of complex sampling design from a myriad of environments.

SUBMITTER: Jorge F

PROVIDER: S-EPMC9723553 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms.

Jorge Fátima F Brealey Jaelle C JC Brindley Paul J PJ Buysse Marie M Cantacessi Cinzia C Duron Olivier O Fichorova Raina R Fitzpatrick Connor R CR Hahn Megan M Hunter Christopher C Hervé Vincent V Knoll Laura J LJ Kohl Kevin D KD Lalle Marco M Lukeš Julius J Martínez Joaquín Martínez JM Perkins Susan L SL Poulin Robert R Rosario Karyna K Schneider Adam C AC Schriml Lynn M LM Thompson Luke R LR Walls Ramona L RL Dheilly Nolwenn M NM

ISME communications 20220201 1

The symbiont-associated (SA) environmental package is a new extension to the minimum information about any (x) sequence (MIxS) standards, established by the Parasite Microbiome Project (PMP) consortium, in collaboration with the Genomics Standard Consortium. The SA was built upon the host-associated MIxS standard, but reflects the nestedness of symbiont-associated microbiota within and across host-symbiont-microbe interactions. This package is designed to facilitate the collection and reporting ...[more]

PMID: 37938691

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Project description:BACKGROUND: Expression microarrays are increasingly used to characterize environmental responses and host-parasite interactions for many different organisms. Probe selection for cDNA microarrays using expressed sequence tags (ESTs) is challenging due to high sequence redundancy and potential cross-hybridization between paralogous genes. In organisms with limited genomic information, like marine organisms, this challenge is even greater due to annotation uncertainty. No general tool is available for cDNA microarray probe selection for these organisms. Therefore, the goal of the design procedure described here is to select a subset of ESTs that will minimize sequence redundancy and characterize potential cross-hybridization while providing functionally representative probes. RESULTS: Sequence similarity between ESTs, quantified by the E-value of pair-wise alignment, was used as a surrogate for expected hybridization between corresponding sequences. Using this value as a measure of dissimilarity, sequence redundancy reduction was performed by hierarchical cluster analyses. The choice of how many microarray probes to retain was made based on an index developed for this research: a sequence diversity index (SDI) within a sequence diversity plot (SDP). This index tracked the decreasing within-cluster sequence diversity as the number of clusters increased. For a given stage in the agglomeration procedure, the EST having the highest similarity to all the other sequences within each cluster, the centroid EST, was selected as a microarray probe. A small dataset of ESTs from Atlantic white shrimp (Litopenaeus setiferus) was used to test this algorithm so that the detailed results could be examined. The functional representative level of the selected probes was quantified using Gene Ontology (GO) annotations. CONCLUSIONS: For organisms with limited genomic information, combining hierarchical clustering methods to analyze ESTs can yield an optimal cDNA microarray design. If biomarker discovery is the goal of the microarray experiments, the average linkage method is more effective, while single linkage is more suitable if identification of physiological mechanisms is more of interest. This general design procedure is not limited to designing single-species cDNA microarrays for marine organisms, and it can equally be applied to multiple-species microarrays of any organisms with limited genomic information.

Dataset Information

MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms.

Publications

MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms.

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