<i>LDJump</i>: Estimating variable recombination rates from population genetic data

Hermann, Philipp; Heissl, Angelika; Tiemann‐Boege, Irene; Futschik, Andreas

doi:10.1111/1755-0998.12994

Cited by 24 publications

(14 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Population recombination rates ( ρ = 4 N e r ; where N e is the effective population size and r is the recombination rate per base pair and generation) were estimated using LDJump [ 89 ] (with a window of 1000 pb) from the ‘core’ genome MSAs. The distributions of recombination rates along MSAs were compared for the different reference genomes of each species and were represented graphically with the R package ggplot2 [ 90 ].…”

Section: Methodsmentioning

confidence: 99%

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads

et al. 2021

View full text Add to dashboard Cite

Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species were selected as reference sequences, and read alignment statistics, SNP calling, recombination rates, dN/dS ratios, and phylogenetic trees were evaluated depending on the mapping reference. The choice of different reference genomes proved to have an impact on almost all the parameters considered in the five species. In addition, these biases had potential epidemiological implications such as including/excluding isolates of particular clades and the estimation of genetic distances. These findings suggest that the single reference approach might introduce systematic errors during mapping that affect subsequent analyses, particularly for data sets with isolates from genetically diverse backgrounds. In any case, exploring the effects of different references on the final conclusions is highly recommended.

show abstract

Section: Methodsmentioning

confidence: 99%

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Only blocks where all isolates were present were retained; a window of 10 bp was slided by 1 bp, and windows containing at least two insertion and or deletion events were discarded and the containing blocks split; in addition, windows with a total of > 100 gap characters were discarded and the containing blocks were split; and all blocks were merged according to reference genome with empty positions filled by "N". Refined multiple sequence alignments were subjected to variable recombination rate analyses using LDJump (Hermann et al, 2019) with segment length of 5 kb interval, P value of 0.05. LDJump requires other recombination analyses tools including LDhat (Auton & McVean, 2007) and PhiPack to estimate variable recombination rate and generate a recombination map in a specific DNA segment.…”

Section: Whole Genome Sequence Based Recombination Analysismentioning

confidence: 99%

Species hybridisation and clonal expansion as a new fungicide resistance evolutionary mechanism in Pyrenophora teres spp

Turo

Mair

Martín

et al. 2021

Preprint

View full text Add to dashboard Cite

The barley net blotch diseases are caused by two fungal species of the Pyrenophora genus. Specifically, spot form net blotch is caused by P. teres f. sp. maculata (Ptm) whereas net form net blotch is caused by P. teres f. sp. teres (Ptt). Ptt and Ptm show high genetic diversity in the field due to intraspecific sexual recombination and hybridisation of the two species although the latter is considered rare. Here we present occurrence of a natural Ptt/Ptm hybrid with azole fungicides resistance and its implication to barley disease management in Australia. We collected and sequenced a hybrid, 3 Ptm and 10 Ptt isolates and performed recombination analyses in the intergenic and whole genome level. Eleven out of 12 chromosomes showed significant (P < 0.05) recombination events in the intergenic regions while variable recombination rate showed significant recombination across all the chromosomes. Locus specific analyses of Cyp51A1 gene showed at least four recombination breakpoints including a point mutation that alter target protein function. This point mutation did not found in Ptt and Ptm collected prior to 2013 and 2017, respectively. Further genotyping of fourteen Ptt, 48 HR Ptm, fifteen Ptm and two P. teres isolates from barley grass using Diversity Arrays Technology markers showed that all HR Ptm isolates were clonal and not clustered with Ptt or Ptm. The result confirms occurrence of natural recombination between Ptt and Ptm in Western Australia and the HR Ptm is likely acquired azole fungicide resistance through recombination and underwent recent rapid selective sweep likely within the last decade. The use of available fungicide resistance management tactics are essential to minimise and restrict further dissemination of these adaptive HR Ptm isolates.

show abstract

“…However, as noted in Smukowski Heil et al 2015, statistical LD based methods have their limitations due other factors that influence LD including sudden demographic changes, genetic drift, changing mutation rates, and selection (Smith and Fearnhead, 2005; Slatkin, 2008; Dapper and Payseur, 2018; van Eeden et al, 2021). Furthermore, LD-based methods are typically utilized to infer historical recombination rates over long timespans into the past (Hermann et al, 2019; van Eeden et al, 2021) which contrasts the relatively short experimental-evolution time frame of our populations.…”

Section: Resultsmentioning

confidence: 99%

Variation in fine scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection

Winbush

Singh

2022

Preprint

View full text Add to dashboard Cite

Meiotic recombination plays a critical evolutionary role in maintaining fitness in response to selective pressures due to changing environments. Variation in recombination rate has been observed amongst and between species and populations and within genomes across numerous taxa. Studies have demonstrated a link between changes in recombination rate and selection but the extent to which fine scale recombination rate varies between evolved populations during the evolutionary period in response to selection is under active research. Here we utilize a set of three temperature-evolved Drosophila melanogaster populations that were shown to have diverged in several phenotypes including recombination rate based on the temperature regime in which they evolved. Using whole genome sequencing data of these populations, we generated fine scale recombination maps of the three populations. We compare recombination rates and patterns among the three populations and show that they have diverged at fine scales but are conserved at broader scales. We further demonstrate a correlation between recombination rates and genomic variation in the three populations and observe variation in putative warm-spots between the populations with these enhanced areas and associated genes overlapping areas previously shown to have diverged in the three populations due to selection. These data support the existence of recombination modifiers in these populations which are subject to selection during evolutionary change.

show abstract

LDJump: Estimating variable recombination rates from population genetic data

Cited by 24 publications

References 72 publications

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads

Species hybridisation and clonal expansion as a new fungicide resistance evolutionary mechanism in Pyrenophora teres spp

Variation in fine scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection

Contact Info

Product

Resources

About