Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon

Sahlin, Kristoffer; Tomaszkiewicz, Marta; Makova, Kateryna D.; Medvedev, Paul

doi:10.1038/s41467-018-06910-x

Cited by 60 publications

(57 citation statements)

References 69 publications

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“…This is a particularly useful approach in species that lack a reference genome, but it comes with disadvantages. ICE-Quiver has been known to merge together transcripts from highly similar genes and can smooth over real differences of interest such as sequence variants and RNA editing events 30 . In addition, the algorithm is stochastic by nature, and cluster assignments for individual reads can vary substantially across different runs.…”

Section: Introductionmentioning

confidence: 99%

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Wyman

Balderrama-Gutierrez

Reese

et al. 2019

Preprint

141

147

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Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short reads. Here we introduce TALON, the ENCODE4 pipeline for platform-independent analysis of long-read transcriptomes. We apply TALON to the GM12878 cell line and show that while both PacBio and ONT technologies perform well at full-transcript discovery and quantification, each displayed distinct technical artifacts. We further apply TALON to mouse hippocampus and cortex transcriptomes and find that 422 genes found in these regions have more reads associated with novel isoforms than with annotated ones. We demonstrate that TALON is a capable of tracking both known and novel transcript models as well as their expression levels across datasets for both simple studies and in larger projects. These properties will enable TALON users to move beyond the limitations of short-read data to perform isoform discovery and quantification in a uniform manner on existing and future long-read platforms.

show abstract

Section: Introductionmentioning

confidence: 99%

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Wyman

Balderrama-Gutierrez

Reese

et al. 2019

Preprint

141

147

View full text Add to dashboard Cite

show abstract

“…In this study we uncovered many principal features of ampliconic sequence and gene evolution, opening opportunities for new inquiries. Future investigations should focus on deciphering the sequences of different copies and isoforms of ampliconic genes (70) , which should allow one to examine natural selection operating at them in detail. Sequence amplification and increase in gene copy number (17) in orangutan should be examined further as well.…”

Section: Future Directionsmentioning

confidence: 99%

Dynamic evolution of great ape Y chromosomes

Čechová

Vegesna

Tomaszkiewicz

et al. 2020

Preprint

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The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee shared a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys, from short and long sequencing reads, and aligned them with the publicly available human, chimpanzee and gorilla Y assemblies. Analyzing this dataset, we found that the genus Pan , including chimpanzee and bonobo, experienced accelerated substitution rates. Additionally, Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan . Furthermore, we inferred that the great ape common ancestor already possessed multi-copy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Moreover, our ENCODE data analysis suggested that Y palindromes exist to promote gene conversion preventing degradation of not only genes, as is commonly believed, but also gene regulatory sites. Our results highlight the dynamic mode of Y chromosome evolution, and open avenues for studies of male-specific dispersal in endangered great ape species.

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“…Long-read sequencing of transcripts with Pacific Biosciences (PacBio) Iso-Seq and Oxford Nanopore Technologies (ONT) has proven to be central to the study of complex isoform landscapes in, e.g., humans [1][2][3][4], animals [5], plants [6], fungi [7] and viruses [8]. Long reads can reconstruct more complex regions than can short RNA-seq reads because the often complex assembly step is not required.…”

Section: Introductionmentioning

confidence: 99%

De novo clustering of long-read transcriptome data using a greedy, quality-value based algorithm

Sahlin

Medvedev

2018

Preprint

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Long-read sequencing of transcripts with PacBio Iso-Seq and Oxford Nanopore Technologies has proven to be central to the study of complex isoform landscapes in many organisms. However, current de novo transcript reconstruction algorithms from long-read data are limited, leaving the potential of these technologies unfulfilled. A common bottleneck is the dearth of scalable and accurate algorithms for clustering long reads according to their gene family of origin. To address this challenge, we develop isONclust, a clustering algorithm that is greedy (in order to scale) and makes use of quality values (in order to handle variable error rates). We test isONclust on three simulated and five biological datasets, across a breadth of organisms, technologies, and read depths. Our results demonstrate that isONclust is a substantial improvement over previous approaches, both in terms of overall accuracy and/or scalability to large datasets. Our tool is available at https://github.com/ksahlin/isONclust.

show abstract

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon

Cited by 60 publications

References 69 publications

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Dynamic evolution of great ape Y chromosomes

De novo clustering of long-read transcriptome data using a greedy, quality-value based algorithm

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