Illuminating the impact of diel vertical migration on visual gene expression in deep‐sea shrimp

DeLeo, Danielle M.; Bracken‐Grissom, Heather D.

doi:10.1111/mec.15570

Cited by 16 publications

(22 citation statements)

References 103 publications

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“…Colored dots indicate krill opsins: red, previously cloned opsins; green, novel identified opsins. The spectral sensitivities of rhabdomeric opsin clades were inferred from the curated invertebrate-only opsin dataset proposed by DeLeo & Bracken-Grissom, 2020. Represented opsin classes: LWS, long-wavelenght-sensitive; LSM, long/middle-wavelenght-sensitive; MWS, middle-wavelenght-sensitive; SWS/UV, short/UV-wavelenght-sensitive; ONY, onychopsins; MEL, melanopsins; PER, peropsin; ART, arthropsin.…”

Section: Resultsmentioning

confidence: 99%

“…A phylogenetic tree was generated using the MUSCLE alignment tool and the Maximum Likelihood method (Dayhof substitution matrix and Nearest-Neighbor-Interchange method) as implemented in MEGA X (version 10.2.6, https://www.megasoftware.net/). New opsins were aligned against a curated invertebrate-only opsin data set [40], the previously cloned krill opsins [41], and the full-length onychopsin and arthropsin sequences available on the NCBI Protein database (May 2021, ncbi.nlm.nih.gov/protein). The tree was rooted using the human G protein-coupled receptor VIPR1 as an outgroup.…”

Section: Opsin Phylogenymentioning

confidence: 99%

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The most comprehensive annotation of the Krill transcriptome provides new insights for the study of physiological processes and environmental adaptation

Urso

Biscontin

Corso

et al. 2021

Preprint

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The krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem, as the abundance of its biomass affects trophic levels both below it and above. Major changes in climate conditions observed in the Antarctic Peninsula region in the last decades have the potential to alter the distribution of the krill population and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species, and of the molecular mechanisms behind them, are urgently needed. The availability of a large body of RNA-seq assays gave us the opportunity to extend the current knowledge of the krill transcriptome, considerably reducing errors and redundancies. The study covered the entire developmental process, from larval stages to adult individuals, information which are of central relevance for ecological studies. We describe KrillDB2 database, which combines the latest annotation of the krill transcriptome with a series of analyses specifically targeting genes and molecular processes relevant to krill physiology. KrillDB2 provides in a single resource the most complete collection of experimental data and bioinformatic annotations: it includes an extended catalog of krill genes; an atlas of their expression profiles over all RNA-seq datasets publicly available; a study of differential expression across multiple conditions such as developmental stages, geographical regions, seasons, and sexes. Finally, it provides information about non-coding RNAs, a class of molecules whose contribute to krill physiology, which have never been reported before.

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Section: Resultsmentioning

confidence: 99%

Section: Opsin Phylogenymentioning

confidence: 99%

The most comprehensive annotation of the Krill transcriptome provides new insights for the study of physiological processes and environmental adaptation

Urso

Biscontin

Corso

et al. 2021

Preprint

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“…However, this reduction could potentially be an issue for differential gene expression studies where gene variants (i.e., isoforms) are removed from the samples via the reduction of transcripts. Nevertheless, performing a reduction step before a gene expression analysis is a common practice (DeLeo & Bracken‐Grissom, 2020; Devens et al, 2020; Guo et al, 2017; Kashyap et al, 2020; Perez et al, 2021). Therefore, the nonredundant transcriptome generated by TransPi could be utilized for gene expression studies (Deshpande et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Rivera‐Vicéns

Garcia-Escudero

Conci

et al. 2022

Molecular Ecology Resources

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The use of RNA sequencing (RNA‐Seq) data and the generation of de novo transcriptome assemblies have been pivotal for studies in ecology and evolution. This is especially true for nonmodel organisms, where no genome information is available. In such organisms, studies of differential gene expression, DNA enrichment bait design and phylogenetics can all be accomplished with de novo transcriptome assemblies. Multiple tools are available for transcriptome assembly, but no single tool can provide the best assembly for all data sets. Therefore, a multi‐assembler approach, followed by a reduction step, is often sought to generate an improved representation of the assembly. To reduce errors in these complex analyses while at the same time attaining reproducibility and scalability, automated workflows have been essential in the analysis of RNA‐Seq data. However, most of these tools are designed for species where genome data are used as reference for the assembly process, limiting their use in nonmodel organisms. We present TransPi, a comprehensive pipeline for de novo transcriptome assembly, with minimum user input but without losing the ability of a thorough analysis. A combination of different model organisms, k‐mer sets, read lengths and read quantities was used for assessing the tool. Furthermore, a total of 49 nonmodel organisms, spanning different phyla, were also analysed. Compared to approaches using single assemblers only, TransPi produces higher BUSCO completeness percentages, and a concurrent significant reduction in duplication rates. TransPi is easy to configure and can be deployed seamlessly using Conda, Docker and Singularity.

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“…A phylogenetic tree was generated using the MUSCLE alignment tool and the Maximum Likelihood method (Dayhof substitution matrix and Nearest-Neighbor-Interchange method) as implemented in MEGA X (version 10.2.6, https://www.megasoftware.net/ ). New opsins were aligned against a curated invertebrate-only opsin data set 54 , the previously cloned krill opsins 20 , and the full-length onychopsin and arthropsin sequences available on the NCBI Protein database (May 2021, ncbi.nlm.nih.gov/protein). The tree was rooted using the human G protein-coupled receptor VIPR1 as an outgroup.…”

Section: Methodsmentioning

confidence: 99%

A thorough annotation of the krill transcriptome offers new insights for the study of physiological processes

Urso

Biscontin

Corso

et al. 2022

Sci Rep

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The krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem. Significant changes in climate conditions observed in the Antarctic Peninsula region in the last decades have already altered the distribution of krill and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species is urgently needed. The availability of a large body of RNA-seq assays allowed us to extend the current knowledge of the krill transcriptome. Our study covered the entire developmental process providing information of central relevance for ecological studies. Here we identified a series of genes involved in different steps of the krill moulting cycle, in the reproductive process and in sexual maturation in accordance with what was already described in previous works. Furthermore, the new transcriptome highlighted the presence of differentially expressed genes previously unknown, playing important roles in cuticle development as well as in energy storage during the krill life cycle. The discovery of new opsin sequences, specifically rhabdomeric opsins, one onychopsin, and one non-visual arthropsin, expands our knowledge of the krill opsin repertoire. We have collected all these results into the KrillDB2 database, a resource combining the latest annotation of the krill transcriptome with a series of analyses targeting genes relevant to krill physiology. KrillDB2 provides in a single resource a comprehensive catalog of krill genes; an atlas of their expression profiles over all RNA-seq datasets publicly available; a study of differential expression across multiple conditions. Finally, it provides initial indications about the expression of microRNA precursors, whose contribution to krill physiology has never been reported before.

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Illuminating the impact of diel vertical migration on visual gene expression in deep‐sea shrimp

Cited by 16 publications

References 103 publications

The most comprehensive annotation of the Krill transcriptome provides new insights for the study of physiological processes and environmental adaptation

The most comprehensive annotation of the Krill transcriptome provides new insights for the study of physiological processes and environmental adaptation

TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

A thorough annotation of the krill transcriptome offers new insights for the study of physiological processes

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