Ultrafast functional profiling of RNA-seq data for nonmodel organisms

Liu, Peng; Ewald, Jessica; Galvez, Jose Hector; Head, Jessica; Crump, Doug; Bourque, Guillaume; Basu, Niladri; Xia, Jianguo

doi:10.1101/gr.269894.120

Cited by 22 publications

(28 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Libraries were sequenced to produce paired‐end 101‐bp reads using the NovaSeq 6000 S4 PE100 system. Raw RNA‐seq fastq files were submitted to EcoOmicsAnalyst (2022) for primary data processing (Liu et al, 2021). Briefly, raw reads were preprocessed and filtered by Fastp with a minimum read quality score of 25 and minimum read length of 15 (S. Chen, Zhou, et al, 2018).…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic Points of Departure Calculated from Rainbow Trout Gill, Liver, and Gut Cell Lines Exposed to Methylmercury and Fluoxetine

Mittal

Ewald

Basu

2022

Enviro Toxic and Chemistry

Self Cite

View full text Add to dashboard Cite

Ethical and resource limitation concerns are pushing chemicals management to develop alternatives to animal testing strategies. The objective of our study was to determine whether transcriptomic point of departure (tPOD) values could be derived from studies that followed Organisation for Economic Co‐operation and Development (OECD) Test No. 249 (rainbow trout gill cell line), as well as from studies on trout liver and gut cells. Gill, liver, and gut cell lines were exposed to methylmercury and fluoxetine. Concentrations causing 50% cytotoxicity (LC50) were derived, the whole transcriptome was sequenced, and gene tPOD and pathway benchmark dose (BMD) values were derived from transcriptomic dose–response analysis. Differences in LC50 and transcriptomic responses across the cell lines were noted. For methylmercury, the tPODmode values were 14.5, 20.5, and 17.8 ppb for the gill, liver, and gut cells, respectively. The most sensitive pathway (pathway BMDs in parentheses) was ferroptosis in the gill (3.1 ppb) and liver (3.5 ppb), and glutathione metabolism in the gut (6.6 ppb). For fluoxetine, the tPODmode values were 109.4, 108.4, and 97.4 ppb for the gill, liver, and gut cells, respectively. The most sensitive pathway was neurotrophin signaling in the gill (147 ppb) and dopaminergic signaling in the gut (86.3 ppb). For both chemicals, the gene tPOD and pathway BMD values were lower than cytotoxic concentrations in vitro, and within 10‐fold below the in vivo LC50s. By bringing together transcriptomics and dose–response analysis with an OECD test method in three cell lines, the results help to establish an in vitro method yielding tPOD values that are hypothesized to be protective of in vivo concentrations associated with adverse outcomes, and also give insights into mechanisms of action. Environ Toxicol Chem 2022;41:1982–1992. © 2022 SETAC

show abstract

Section: Methodsmentioning

confidence: 99%

Transcriptomic Points of Departure Calculated from Rainbow Trout Gill, Liver, and Gut Cell Lines Exposed to Methylmercury and Fluoxetine

Mittal

Ewald

Basu

2022

Enviro Toxic and Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…An all‐in‐one and ultrafast tool for RNAseq data analysis for organisms without reference genomes, such as many endangered species is Seq. 2Fun (Liu et al, 2021). Raw FASTQ read files were submitted to Seq.…”

Section: Methodsmentioning

confidence: 99%

Exposure to Contaminated River Water is Associated with Early Hatching and Dysregulation of Gene Expression in Early Life Stages of the Endangered Copper Redhorse (Moxostoma hubbsi)

Marchand

Barst

Boulanger

et al. 2022

Enviro Toxic and Chemistry

View full text Add to dashboard Cite

The copper redhorse (Moxostoma hubbsi) is an endangered fish that spawns exclusively in the Richelieu River (Quebec, Canada). Tributaries of the Richelieu are contaminated with high levels of current‐use pesticides, which may impact early–life stage (ELS) copper redhorse and other native fishes. We assessed the effects of exposure to contaminated river water on ELS copper redhorse and river redhorse (Moxostoma carinatum), a related fish that shares the copper redhorse's spawning grounds and nursery habitat. A riverside flow‐through system was used to expose copper and river redhorse embryos (1000 each) to Richelieu River water or laboratory water as a control. Fish were maintained until 14 days posthatch, and water samples were taken daily for chemical analysis. Following a heavy rain event, concentrations of two neonicotinoid pesticides, clothianidin and thiamethoxam, exceeded water quality guidelines for aquatic life (20 ng/L). Using nontargeted screening, we tentatively identified an additional 24 pharmaceutical and personal care products and 23 pesticides in river water. Effects of river water on ELS fish were observed in both species, but the copper redhorse appeared to be more sensitive. Fish exposed to river water hatched 10.7 (copper redhorse) and 2.4 (river redhorse) cumulative degree days earlier than controls. Copper redhorse survival was significantly lower in river water (73 ± 16%) compared to laboratory water (93 ± 3%), whereas river redhorse survival was similar between treatments (84 ± 6% and 89 ± 4%, respectively). Sequencing of copper redhorse larvae RNA revealed 18 differentially expressed genes (DEGs) following 14 days of exposure to river water. Eight up‐regulated DEGs were linked to immune function and injury response, and seven down‐regulated DEGs were involved with digestion and nutrient absorption. The present study provided valuable data on the effects of ELS exposure to a real‐world mixture of contaminants in two fish species of concern. Environ Toxicol Chem 2022;41:1950–1966. © 2022 SETAC

show abstract

“…Reads obtained after trimming and quality estimating by FastQC and Seq2fun pipeline [5] were assembled using Trinity v2.1.1 [6] . Transcriptome assembly with Trinity can be divided into several parts: searching and calculating k-mers, assembling contigs from k-mers, clustering contigs into components.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

De novo transcriptome assembly and annotation of parthenogenetic lizard Darevskia unisexualis and its parental ancestors Darevskia valentini and Darevskia raddei nairensis

et al. 2021

View full text Add to dashboard Cite

Darevskia rock lizards include 29 sexual and seven parthenogenetic species of hybrid origin distributed in the Caucasus. All seven parthenogenetic species of the genus Darevskia were formed as a result of interspecific hybridization of only four sexual species. It remains unknown what are the main advantages of interspecific hybridization along with switching on parthenogenetic reproduction in evolution of reptiles. Data on whole transcriptome sequencing of parthenogens and their parental ancestors can provide value impact in solving this problem. Here we have sequenced ovary tissue transcriptomes from unisexual parthenogenetic lizard D. unisexualis and its parental bisexual ancestors to facilitate the subsequent annotation and to obtain the collinear characteristics for comparison with other lizard species. Here we report generated RNAseq data from total mRNA of ovary tissues of D. unisexualis, D. valentini and D. raddei with 58932755, 51634041 and 62788216 reads. Obtained RNA reads were assembled by Trinity assembler and 95141, 62123, 61836 contigs were identified with N50 values of 2409, 2801 and 2827 respectively. For further analysis top Gene Ontology terms were annotated for all species and transcript number was calculated. The raw data were deposited in the NCBI SRA database (BioProject PRJNA773939 ). The assemblies are available in Mendeley Data and can be accessed via doi: 10.17632/rtd8cx7zc3.1 .

show abstract

Ultrafast functional profiling of RNA-seq data for nonmodel organisms

Abstract: Service Email Alerting click here. top right corner of the article or Receive free email alerts when new articles cite this article-sign up in the box at the object identifier (DOIs) and date of initial publication.

Cited by 22 publications

References 46 publications

Transcriptomic Points of Departure Calculated from Rainbow Trout Gill, Liver, and Gut Cell Lines Exposed to Methylmercury and Fluoxetine

Transcriptomic Points of Departure Calculated from Rainbow Trout Gill, Liver, and Gut Cell Lines Exposed to Methylmercury and Fluoxetine

Exposure to Contaminated River Water is Associated with Early Hatching and Dysregulation of Gene Expression in Early Life Stages of the Endangered Copper Redhorse (Moxostoma hubbsi)

De novo transcriptome assembly and annotation of parthenogenetic lizard Darevskia unisexualis and its parental ancestors Darevskia valentini and Darevskia raddei nairensis

Contact Info

Product

Resources

About