Introgressions lead to reference bias in wheat RNA-seq analysis DOI Creative Commons
Benedict Coombes, Thomas Lux, Eduard Akhunov

и другие.

BMC Biology, Год журнала: 2024, Номер 22(1)

Опубликована: Март 7, 2024

Abstract Background RNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of quantification and thus conclusions made downstream. Reference bias analysis has to be explored complex polyploid genomes despite evidence that they often mosaic wild relative introgressions, which introduce blocks highly divergent genes. Results Here we use hexaploid wheat as model polyploid, using both simulated experimental data show alignment suffers widespread largely driven by introgressed This leads underestimation gene expression incorrect assessment homoeologue balance. By incorporating models ten genome assemblies into pantranscriptome reference, present novel method reduce readily scaled capture more variation new transcriptome becomes available. Conclusions study shows presence introgressions lead analysis. Caution should exercised researchers non-sample for methods, such one presented here, considered.

Язык: Английский

EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023 DOI Creative Commons
Matthew Thakur, Annalisa Buniello, Cath Brooksbank

и другие.

Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D10 - D17

Опубликована: Ноя. 28, 2023

Abstract The European Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources public biomolecular data. Based at Wellcome Genome Campus in Hinxton, UK, EMBL-EBI six sites Laboratory (EMBL), Europe's only intergovernmental life sciences organisation. This overview summarises latest developments services provided by data resources to scientific communities globally. These aim ensure meet current and future needs these communities, accelerating impact open biological for all.

Язык: Английский

Процитировано

21
Genome-Wide Identification and Expression Analysis of the Xyloglucan Endotransglucosylase/Hydrolase Gene Family in Sweet Potato [Ipomoea batatas (L.) Lam] DOI Open Access

Jingzhen Zhang,

Pei-Wen He,

Ximing Xu

и другие.

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(1), С. 775 - 775

Опубликована: Янв. 1, 2023

The xyloglucan endotransglucosylase/hydrolase (XET/XEH, also named XTH) family is a multigene family, the function of which plays significant role in cell-wall rebuilding and stress tolerance plants. However, specific traits XTH gene members their expression pattern different tissues under have not been carried out sweet potato. Thirty-six genes were identified I. batatas, all had conserved structures (Glyco_hydro_16). Based on Neighbor-Joining phylogenetic analysis IbXTHs can be divided into three subfamilies-the I/II, IIIA, IIIB subfamilies, unevenly distributed 13 chromosomes, with exception Chr9 Chr15. Multiple cis-acting regions related to growth development, as well responses, may found IbXTH promoters. segmental duplication occurrences greatly aided evolution IbXTHs. results collinearity showed that potato shared evolutionary history additional species, including A. thaliana, G. max, O. sativa. Additionally, based transcriptome sequencing data, revealed patterns leaves, stems, root body (RB), distal end (DE), stock (RS), proximal (PE), initiative storage (ISR), fibrous (FR), many them are expressed roots. Differentially (DEG) FRs after hormone treatment roots indicated IbXTH28 IbXTH30 up-regulated salicylic acid (SA) but down-regulated methyl jasmonate (MeJA) treatment. Attentionally, there only two showing down-regulation cold drought Collectively, findings suggested from crucial for specificity. This study could provide theoretical basis further research molecular genes.

Язык: Английский

Процитировано

17
Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms DOI Creative Commons
Fabricio Almeida‐Silva, Yves Van de Peer

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(7)

Опубликована: Июль 1, 2023

Angiosperms have a complex history of whole-genome duplications (WGDs), with varying numbers and ages WGD events across clades. These WGDs greatly affected the composition plant genomes due to biased retention genes belonging certain functional categories following their duplication. In particular, regulatory encoding proteins that act in multiprotein complexes been retained excess WGD. Here, we inferred protein-protein interaction (PPI) networks gene (GRNs) for seven well-characterized angiosperm species explored impact both small-scale (SSDs) network topology by analyzing changes frequency motifs. We found PPI are enriched WGD-derived associated dosage-sensitive intricate systems, strong selection pressures constrain divergence at sequence levels. motifs mostly processes, such as regulation transcription cell cycle, translation, photosynthesis, carbon metabolism, whereas SSD-derived response biotic abiotic stress. Recent polyploids higher motif frequencies than ancient polyploids, tend be disrupted on longer term. Our findings demonstrate SSD contributed evolution GRNs, but different ways, likely having more significant short-term polyploids.

Язык: Английский

Процитировано

17
Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites DOI Creative Commons
Zheng Sun, Jiang Liu, Meng Zhang

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 1, 2023

Abstract Accurate species identification and abundance estimation are critical for the interpretation of whole metagenome sequencing (WMS) data. Yet, existing metagenomic profilers suffer from false-positive identifications, which can account more than 90% total identified species. Here, by leveraging species-specific Type IIB restriction endonuclease digestion sites as reference instead universal markers or microbial genomes, we present a profiler, MAP2B ( M et A genomic P rofiler based on type sites), to resolve those issues. We first illustrate pitfalls using relative only feature in determining false positives. then propose set distinguish positives true positives, simulated metagenomes CAMI2, establish recognition model. By benchmarking performance profiling simulation dataset with varying depth richness, superior over identification. further test real WMS data an ATCC mock community, confirming its precision against depth. Finally, IBD cohort, demonstrate taxonomic features generated better discriminate predict metabolomic profiles.

Язык: Английский

Процитировано

17
Introgressions lead to reference bias in wheat RNA-seq analysis DOI Creative Commons
Benedict Coombes, Thomas Lux, Eduard Akhunov

и другие.

BMC Biology, Год журнала: 2024, Номер 22(1)

Опубликована: Март 7, 2024

Abstract Background RNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of quantification and thus conclusions made downstream. Reference bias analysis has to be explored complex polyploid genomes despite evidence that they often mosaic wild relative introgressions, which introduce blocks highly divergent genes. Results Here we use hexaploid wheat as model polyploid, using both simulated experimental data show alignment suffers widespread largely driven by introgressed This leads underestimation gene expression incorrect assessment homoeologue balance. By incorporating models ten genome assemblies into pantranscriptome reference, present novel method reduce readily scaled capture more variation new transcriptome becomes available. Conclusions study shows presence introgressions lead analysis. Caution should exercised researchers non-sample for methods, such one presented here, considered.

Язык: Английский

Процитировано

7