Targeted decontamination of sequencing data with CLEAN DOI Creative Commons
Marie Lataretu, Sebastian Krautwurst, Adrian Viehweger

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 6, 2023

Abstract Background Many biological and medical questions are answered based on the analysis of sequence data. However, we can find contaminations, artificial spike-ins, overrepresented rRNA sequences in various read collections assemblies; complicating data making interpretation difficult. In particular, spike-ins used as controls, such those known from Illumina (PhiX phage) or Nanopore (DNA CS lambda phage, yeast enolase ENO2), often not considered contaminants also appropriately removed during bioinformatics analyses. Findings To address this, developed CLEAN, a pipeline to remove unwanted both long short sequencing techniques wide range use cases. While focusing removing their technology-specific control sequences, be for everyday tasks, host decontamination metagenomic reads assemblies, removal RNA-Seq The results purified identified contaminated with statistics summarized an HTML report. Conclusions decontaminated output files directly subsequent analyses, resulting faster computations improved results. Although is task that seems mundane, many routinely overlooked, cleaned by steps fully reproducible difficult trace user. CLEAN will facilitate reproducible, platform-independent genomics transcriptomics freely available at https://github.com/hoelzer/clean under BSD3 license.

Language: Английский

Detecting signatures of selection on gene expression DOI
Peter D. Price, Daniela H. Palmer Droguett, Jessica A. Taylor

et al.

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(7), P. 1035 - 1045

Published: May 12, 2022

Language: Английский

Citations

71
Dominance reversals: the resolution of genetic conflict and maintenance of genetic variation DOI Creative Commons
Karl Grieshop, Eddie K. H. Ho, Katja R. Kasimatis

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2018)

Published: March 13, 2024

Beneficial reversals of dominance reduce the costs genetic trade-offs and can enable selection to maintain variation for fitness. are characterized by beneficial allele a given context (e.g. habitat, developmental stage, trait or sex) being dominant in that but recessive where deleterious. This dependence at least partially mitigates fitness consequence heterozygotes carrying one non-beneficial their result balancing maintains alternative alleles. Dominance theoretically plausible supported mounting empirical evidence. Here, we highlight importance as mechanism mitigation conflict review theory evidence them. We identify some areas need further research development outline three methods could facilitate identification antagonistic (dominance ordination, allele-specific expression ATAC-Seq (assay transposase-accessible chromatin with sequencing)). There is ample scope new well reanalysis existing data through lens reversals. A greater focus on this topic will expand our understanding mechanisms resolve whether they variation.

Language: Английский

Citations

16
The role of alternative splicing in adaptation and evolution DOI
Jukka‐Pekka Verta, Arne Jacobs

Trends in Ecology & Evolution, Journal Year: 2021, Volume and Issue: 37(4), P. 299 - 308

Published: Dec. 14, 2021

Language: Английский

Citations

90
Gill histological and transcriptomic analysis provides insights into the response of spotted sea bass (Lateolabrax maculatus) to alkalinity stress DOI

Yonghang Zhang,

Haishen Wen, Yang Liu

et al.

Aquaculture, Journal Year: 2022, Volume and Issue: 563, P. 738945 - 738945

Published: Oct. 17, 2022

Language: Английский

Citations

33
Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis DOI Creative Commons
Hope M. Healey, Susan Bassham, William A. Cresko

et al.

Genetics, Journal Year: 2022, Volume and Issue: 220(3)

Published: Feb. 10, 2022

Abstract Single-cell RNA sequencing is a powerful technique that continues to expand across various biological applications. However, incomplete 3′-UTR annotations can impede single-cell analysis resulting in genes are partially or completely uncounted. Performing with hinder the identification of cell identities and gene expression patterns lead erroneous inferences. We demonstrate performing isoform tandem rapidly improve annotations. Using threespine stickleback fish (Gasterosteus aculeatus), we show models from minimal embryonic dataset retained 26.1% greater reads than Ensembl alone. Furthermore, pooling our isoforms previously published adult bulk Iso-Seq stickleback, merging annotation models, resulted marginal improvement (+0.8%) over only dataset. In addition, identified by included thousands new splicing variants. The improved obtained using led successful types increased many Our work illuminates as cost-effective efficient mechanism annotate genomes for sequencing.

Language: Английский

Citations

19
Alternative splicing patterns of hnrnp genes in gill tissues of rainbow trout (Oncorhynchus mykiss) during salinity changes DOI
Dazhi Liu, Han Yu, Na Xue

et al.

Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology, Journal Year: 2024, Volume and Issue: 271, P. 110948 - 110948

Published: Jan. 26, 2024

Language: Английский

Citations

4
Challenges in identifying mRNA transcript starts and ends from long-read sequencing data DOI
Ezequiel Calvo-Roitberg, Rachel F. Daniels, Athma A. Pai

et al.

Genome Research, Journal Year: 2024, Volume and Issue: 34(11), P. 1719 - 1734

Published: Nov. 1, 2024

Long-read sequencing (LRS) technologies have the potential to revolutionize scientific discoveries in RNA biology through comprehensive identification and quantification of full-length mRNA isoforms. Despite great promise, challenges remain widespread implementation LRS for RNA-based applications, including concerns about low coverage, high error, robust computational pipelines. Although much focus has been placed on defining exon composition structure with data, less careful characterization done ability assess terminal ends isoforms, specifically, transcription start end sites. Such is crucial completely delineating full molecules regulatory consequences. However, there are substantial inconsistencies both coordinates reads spanning a gene, such that often fail accurately recapitulate annotated or empirically derived molecules. Here, we describe specific identifying quantifying how these issues influence biological interpretations data. We then review recent experimental advances designed alleviate problems, ideal use cases each approach. Finally, outline anticipated developments necessary improvements from

Language: Английский

Citations

4
Sex-biased gene expression across tissues reveals unexpected differentiation in the gills of the threespine stickleback DOI Creative Commons
Florent Sylvestre, Nadia Aubin‐Horth, Louis Bernatchez

et al.

Peer Community Journal, Journal Year: 2025, Volume and Issue: 5

Published: Jan. 13, 2025

Sexual dimorphism can evolve through sex-specific regulation of the same gene set. However, sex chromosomes also facilitate this by directly linking expression to sex. Moreover, differences in content between heteromorphic contribute sexual dimorphism. Understanding patterns sex-biased across organisms is important for gaining insight into evolution and chromosomes. studying species with recently established help understand evolutionary dynamics loss dosage compensation. The three-spined stickleback known its strong dimorphism, especially during reproductive period. Sex determined a young XY chromosome pair non-recombining region divided three strata, which have started degenerate. Using high multiplexing capability 3′ QuantSeq sequence transcriptome liver, gills, brain, we provide first characterization transcriptomes from ~80 sticklebacks (40 males 40 females) collected natural population We find that liver extremely differentiated sexes (36% autosomal genes) reflects ongoing reproduction, while brain shows very low levels differentiation (0.78%) no functional enrichment. Finally, gills exhibit (5%), suggesting should be considered physiological ecotoxicological studies gill responses fishes. hemizygous genes mainly driven lack conserved copies on both likely degeneration Y allele down-regulation male-beneficial mutations X chromosome.

Language: Английский

Citations

0
Transcriptomic Analysis Reveals Patterns of Expression of Stage-Specific Genes in Early Apis cerana Embryos DOI Open Access
R.K.L. Su, Yuhui Chen,

Rui Zhu

et al.

Genes, Journal Year: 2025, Volume and Issue: 16(2), P. 187 - 187

Published: Feb. 3, 2025

Background/Objectives: Apis cerana development is described as comprising four stages: embryo, larva, pupa, and adult. There are significant differences between workers drones in terms of physiological functions social roles, the formation organ primordia occurs during embryonic stage. Therefore, objective this study to investigate differential expression alternative splicing genes worker drone embryos explain their unique developmental patterns. Methods: Long-read sequencing (PacBio Iso-Seq) short-read (Illumina RNA-Seq) were used embryo gene A. across five points (12, 24, 36, 48, 60 h). Results: The identified 59,254 common isoforms, with 5744 5106 isoforms specific embryos, respectively. Additionally, a new transcript csd was identified. number differentially expressed (3391) events (470 genes) peaked at 24-h Differential csd, dsx, Y-y observed embryos. Conclusions: results indicated that point critical period for related behavioral drones. findings provide theoretical basis future research on

Language: Английский

Citations

0
The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback DOI Creative Commons
Man Luo, Junjie Zhao, Juha Merilä

et al.

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: March 5, 2025

Populations colonizing contrasting environments are likely to undergo adaptive divergence and evolve ecotypes with locally adapted phenotypes. While diverse molecular mechanisms underlying ecotype have been identified, less is known about their interplay degree of divergence. Here we integrated epigenomic transcriptomic data explore the interactions among gene expression, alternative splicing, DNA methylation, microRNA expression gauge extent which patterns at four levels aligned in a case postglacial between marine freshwater nine-spined sticklebacks (Pungitius pungitius). Despite significant genome-wide associations variation, found largely non-parallel across levels, predominantly nonoverlapping (ranging from 43.40 87.98%) sets differentially expressed, spliced methylated genes, candidate genes targeted by expressed miRNA ecotypes. Furthermore, variation different mechanisms, differential methylation splicing showing highest lowest ecotypes, respectively. Finally, enrichment associated methylation. Our results suggest nuanced relationship processes, alignment level masking relatively independent effects on level.

Language: Английский

Citations

0