DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Audoux, Jérôme; Naveilhan, Philippe; Chikhi, Rayan; Salson, Mikaël; Gallopin, Mélina; Gabriel, Marc; Coz, Jérémy Le; Drouineau, Emilie; Commes, Thérèse; Gautheret, Daniel

doi:10.1186/s13059-017-1372-2

Cited by 44 publications

(54 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The “dump” command was used to output the k-mers and their counts. The k-mer abundances were formatted into a matrix using joinCounts from the DE-kupl software ( Audoux et al. 2017 ).…”

Section: Methodsmentioning

confidence: 99%

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)

Fraser

Whiting

Paris

et al. 2020

Genome Biology and Evolution

101

View full text Add to dashboard Cite

Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male colour patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing (SMRT) and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.

show abstract

“…The “dump” command was used to output the k-mers and their counts. The k-mer abundances were formatted into a matrix using joinCounts from the DE-kupl software ( Audoux et al. 2017 ).…”

Section: Methodsmentioning

confidence: 99%

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)

Fraser

Whiting

Paris

et al. 2020

Genome Biology and Evolution

101

View full text Add to dashboard Cite

show abstract

“…Another possible application is to identify sequences that contribute to the difference between sequencing samples of different states, as a distribution of Nubeam numbers of a sample can be viewed as a mixture distribution with component distributions of different weights. Nubeam can be effective in some areas where the k-mer approach is useful, such as characterizing protein binding motif (Newburger and Bulyk 2009), CpG island by the flanking regions (Chae et al 2013), and sequence feature for haplotype grouping (Navarro-Gomez et al 2015), analyzing RNA-seq data to gain novel insights on new exons and splicing isoforms (Bray et al 2016;Audoux et al 2017), and even detecting genetic associations (Rahman et al 2018).…”

Section: Discussionmentioning

confidence: 99%

The Nubeam reference-free approach to analyze metagenomic sequencing reads

Dai

Guan

2020

Genome Res.

View full text Add to dashboard Cite

We present Nubeam (nucleotide be a matrix) as a novel reference-free approach to analyze short sequencing reads. Nubeam represents nucleotides by matrices, transforms a read into a product of matrices, and assigns numbers to reads based on the product matrix. Nubeam capitalizes on the noncommutative property of matrix multiplication, such that different reads are assigned different numbers and similar reads similar numbers. A sample, which is a collection of reads, becomes a collection of numbers that form an empirical distribution. We demonstrate that the genetic difference between samples can be quantified by the distance between empirical distributions. Nubeam includes the k-mer method as a special case, but unlike the k-mer method, it is convenient for Nubeam to account for GC bias and nucleotide quality. As a reference-free approach, Nubeam avoids reference bias and mapping bias, and can work with organisms without reference genomes. Thus, Nubeam is ideal to analyze data sets from metagenomics whole genome shotgun (WGS) sequencing, where the amount of unmapped reads is substantial. When applied to a WGS sequencing data set to quantify distances between metagenomics samples from various human body habitats, Nubeam recapitulates findings made by mapping-based methods and sheds light on contributions of unmapped reads. Nubeam is also useful in analyzing 16S rRNA sequencing data, which is a more prevalent type of data set in metagenomics studies. In our analysis, Nubeam recapitulated the findings that natural microbiota in mouse gut are resilient under challenges, and Nubeam detected differences in vaginal microbiota between cases of polycystic ovary syndrome and healthy controls.

show abstract

“…Because mRNA sequences preferred by an RNA-cleaving toxin [33] are expected to be depleted from RNA-seq reads, we also used DE-kupl [34] to look for differences in kmer frequencies between RNA-seq samples from cells with and without active toxin. No significant differences were found.…”

Section: Unopposed Toxin Does Not Cleave Competence-induced Mrnas Atmentioning

confidence: 99%

A competence-regulated toxin-antitoxin system in Haemophilus influenzae

et al. 2020

View full text Add to dashboard Cite

Natural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, thus gaining both nutrients and genetic information. In the Gram-negative bacterium Haemophilus influenzae, the genes needed for DNA uptake are induced by the CRP and Sxy transcription factors in response to lack of preferred carbon sources and nucleotide precursors. Here we show that one of these genes, HI0659, encodes the antitoxin of a competence-regulated toxin-antitoxin operon ('toxTA'), likely acquired by horizontal gene transfer from a Streptococcus species. Deletion of the putative toxin (HI0660) restores uptake to the antitoxin mutant. The full toxTA operon was present in only 17 of the 181 strains we examined; complete deletion was seen in 22 strains and deletions removing parts of the toxin gene in 142 others. In addition to the expected Sxy-and CRP-dependent-competence promoter, HI0659/660 transcript analysis using RNA-seq identified an internal antitoxin-repressed promoter whose transcription starts within toxT and will yield nonfunctional protein. We propose that the most likely effect of unopposed toxin expression is non-specific cleavage of mRNAs and arrest or death of competent cells in the culture. Although the high frequency of toxT and toxTA deletions suggests that this competence-regulated toxin-antitoxin system may be mildly deleterious, it could also facilitate downregulation of protein synthesis and recycling of nucleotides under starvation conditions. Although our analyses were focused on the effects of toxTA, the RNA-seq dataset will be a useful resource for further investigations into competence regulation.

show abstract

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Cited by 44 publications

References 55 publications

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)

The Nubeam reference-free approach to analyze metagenomic sequencing reads

A competence-regulated toxin-antitoxin system in Haemophilus influenzae

Contact Info

Product

Resources

About