|2021-02-18 ||Traces of transposable element in genome dark matter co-opted by flowering gene regulation networks|
Agnes Baud, Mariene Wan, Danielle Nouaud, Nicolas Francillonne, Dominique Anxolabehere, Hadi Quesneville
Recommended by Francois Sabot based on reviews by Josep Casacuberta and 1 anonymous reviewer
Using small fragments to discover old TE remnants: the Duster approach empowers the TE detection
Transposable elements are the raw material of the dark matter of the genome, the foundation of the next generation of genes and regulation networks". This sentence could be the essence of the paper of Baud et al. (2021). Transposable elements (TEs) are endogenous mobile genetic elements found in almost all genomes, which were discovered in 1948 by Barbara McClintock (awarded in 1983 the only unshared Medicine Nobel Prize so far). TEs are present everywhere, from a single isolated copy for some e...
|2020-10-09 ||An evaluation of pool-sequencing transcriptome-based exon capture for population genomics in non-model species|
Emeline Deleury, Thomas Guillemaud, Aurélie Blin & Eric Lombaert
Recommended by Thomas Derrien and Sebastian Ramos-Onsins based on reviews by Valentin Wucher and 1 anonymous reviewer
Assessing a novel sequencing-based approach for population genomics in non-model species
Developing new sequencing and bioinformatic strategies for non-model species is of great interest in many applications, such as phylogenetic studies of diverse related species, but also for studies in population genomics, where a relatively large number of individuals is necessary. Different approaches have been developed and used in these last two decades, such as RAD-Seq (e.g., Miller et al. 2007), exome sequencing (e.g., Teer and Mullikin 2010) and other genome reduced representation methods ...
|2020-09-24 ||A rapid and simple method for assessing and representing genome sequence relatedness|
M Briand, M Bouzid, G Hunault, M Legeay, M Fischer-Le Saux, M Barret
Recommended by B. Jesse Shapiro based on reviews by Gavin Douglas and 1 anonymous reviewer
A quick alternative method for resolving bacterial taxonomy using short identical DNA sequences in genomes or metagenomes
The bacterial species problem can be summarized as follows: bacteria recombine too little, and yet too much (Shapiro 2019).
Too little in the sense that recombination is not obligately coupled with reproduction, as in sexual eukaryotes. So the Biological Species Concept (BSC) of reproductive isolation does not strictly apply to clonally reproducing organisms like bacteria. Too much in the sense that genetic exchange can occur promiscuously across species (or even Domains), potentially obscur...