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When I was young naive aspiring scientist I did not comprehend all the aspects of publishing. To be honest, I did not think about it much, but for me it’s the same as the climate change, it’s harder and harder to turn a blind eye. The last drop for me was the announcement of Nature’s Open Access option, it’s shocking €9,500, (or $11,390 / £8,290)! How did we come to this? Are we really going to let a private company to drain the already poor scholarly funds by these obscure amounts? And the problem is not just Nature…
About a year and half ago an article by John Tregoning was published in Nature News. The short piece was openly defending the prevalent usage of journal impact factor for evaluation of junior scientists for their sake. As a junior scientist I felt bitter. The publishing system is a huge academic problem we should do something about it! And as far as I know, young scientists are the loudest in pointing out new ways for less morally corrupted sharing of knowledge and therefore I find unfair a senior academic takes us, as an argument for keeping the status quo.
This easter I have spent on thinking / writing / editing of an introduction to the paper about smudgeplot - a tool for predicting ploidy and visualization of genome structure. I collaborated on this tool for my own data, I have not really thought through how far it goes, so I started to wonder how many polyploid species are out there. So I asked on Twitter and guess what, so many people have responded to the tweet that I have decided to compile the answers in a blogpost.
About a month ago we have posted a preprint to bioRxiv about genomic features of asexual animals. We found plenty of cool things I will try to summarize here the main points and mostly do the speculations that were too bold for the manuscript.
I was on my way back from Arthropod Genomics Symposium (which was a great conference by the way). The plan was to change planes in Iceland and get home in one go, but my flight to Iceland got delayed and I missed my connection. Fortunately, Iceland is amazing country and even around Reykjavik there is plenty to see. I decided to go to Perlan, a museum of Iceland natural history. I was shocked to hear that the island did not exist more than couple of millions years ago. I did not manage to remember the numbers, so I will take them from this web, where they say that the oldest rock is ~15 ml. Alright, 15 millions is not that little from the perspective of population genetics, enough time to generate some variability. However, we should also consider that the land was fully covered by ice during 30 rounds of glacial periods and the last time whole Iceland was under ice is 13,000 to 10,000 years ago. That means that all (or at least the most of) the macro life have started back then either as:
- tiny population that survived glaciation period (bottleneck).
- or colonization (founder effect).
At the beginning of December 2017 we have decided to do a meta-study/review of several published genomes. I optimistically started to collect data for some supplementary analyses. But then I found that about one fifth of genomes were were available “on request” and about one third of genomes were missing sequencing reads. It was a shock for me, I thought that every paper needs to deposit data to DDBJ / EMBL-EBI / NCBI. This was also the case for genomes published in journals that actually claim that data need to be accessible as PloS Biology.
This beauty is Bacillus rossius a proud mum of the tiny green stick insect crawling over her. You are maybe asking, who is father? Well, it’s her brother.
The ultimate goal of my PhD project is to analyze genomic consequences of asexuality. The species we are working with (Californian stick insects) are real hardcore asexuals - they just clone, they do not recombine (or at least if they do they do very very rarely). This kind of “pure” asexuality should lead to independent evolution of both haplotypes. There are a lot of very very cool consequences (think of how a coalescence of haplotypes of couple of individuals should look like), one of them is the activity of transposons (TEs). All the transposons that were active in asexual genome will leave trace only in one haplotype only, and it sounds to be a great fun to track them.
One of the most basic questions of evolutionary biology remains unanswered - how do species evolve? And what makes species separated species? What is causing sexual reproduction barrier between sister taxa? One of very popular systems for study of speciation are hybrid zones.
How does asymmetry in inheritance affect expected feminisation of sex chromosomes?
How many transposonable elements can you fit in one asexual genome?
How does a normal multilocus hybrid zone look like?
How hard is to find a pattern in the chaos?
Published in Bioinformatics, 2013
A scalable method for prediction of candidates for horizontally transferred genes.
Recommended citation: Jaron, K.S., Moravec, J.C. and Martínková, N., 2013. "SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes." Bioinformatics, 30(8), pp.1081-1086. http://doi.org/10.1093/bioinformatics/btt727
Published in PLoS ONE, 2014
We have reported European bat species infected by White-nose syndrome, a disease devastating American population. We have also showed that the fungus is a generalist pathogen attacking bat species of very diverse ecological traits.
Recommended citation: Zukal, J., Bandouchova, H., Bartonicka, T., Berkova, H., Brack, V., Brichta, J., Dolinay, M., Jaron, K.S., Kovacova, V., Kovarik, M. and Martínková, N., 2014. "White-nose syndrome fungus: a generalist pathogen of hibernating bats." PLoS One, 9(5), p.e97224. http://doi.org/10.1371/journal.pone.0097224
White-nose syndrome without borders: Pseudogymnoascus destructans infection tolerated in Europe and Palearctic Asia but not in North America
Published in Scientific Reports, 2016
We have reported White-nose syndrome in Asia and quantified fungal loads of bat wings using qPCR. Surprisingly loads we observed were higher than loads detected in American bats that have way way worse response to the infection.
Recommended citation: Zukal, J., Bandouchova, H., Brichta, J., Cmokova, A., Jaron, K.S., Kolarik, M., Kovacova, V., Kubátová, A., Nováková, A., Orlov, O. and Pikula, J., 2016. "White-nose syndrome without borders: Pseudogymnoascus destructans infection tolerated in Europe and Palearctic Asia but not in North America." Scientific reports, 6. http://doi.org/10.1038/srep19829
Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography—A structure-retention study assisted by soft-modelling and molecular dynamics
Published in Journal of Chromatography A, 2016
We showed nearly-deterministic relation of retention times of trinucleotides with their nucleotide composition. We modeled properties of trinucleotide molecules that actually explained most of the variability of the original model. I was invited to this study to construct models.
Recommended citation: Mikulášek, K., Jaroň, K. S., Kulhánek, P., Bittová, M., & Havliš, J., 2016. "Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography—A structure-retention study assisted by soft-modelling and molecular dynamics." Journal of Chromatography A, (1469), 88-95. http://doi.org/10.1016/j.chroma.2016.09.060
Published in Molecular biology and evolution, 2018
Taken from the abstract: We find strong evidence for higher rates of deleterious mutation accumulation, lower levels of segregating polymorphisms and arrested GC-biased gene conversion in asexuals as compared with sexuals. Taken together, our study conclusively shows that predicted consequences of genome evolution under asexuality can indeed be found in natural populations.
Recommended citation: Bast, J., Parker, D.J., Dumas, Z., Jalvingh, K.M., Tran Van, P., Jaron, K.S., Figuet, E., Brandt, A., Galtier, N. and Schwander, T., 2018. "Consequences of asexuality in natural populations: insights from stick insects." Molecular biology and evolution, 35(7), pp.1668-1677. https://doi.org/10.1093/molbev/msy058
Published in bioRxiv, 2019
Are there any universal consequences of asexuality in animals? We have collected genomes of 26 asexual animals and found that indeed there is not any really universal.
Recommended citation: Jaron, K. S., Bast, J., Nowell R. W., Ranallo-Benavidez, T. R., Robinson-Rechavi, M., & Schwander, T., 2018. "Genomic features of asexual animals." bioRxiv, 497495. https://doi.org/10.1101/497495
Published in Nature Communication, 2020
Genome sequencing can be messy and genome assembly is complicated and non-transparent process. Here we provide tools that allow some elementary characterisation of genomes using directly short read data. Now also aiming to provide help for polyploid genomes.
Recommended citation: Ranallo-Benavidez, T. R., Jaron, K. S., Schatz, M. C., 2020. "GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes" Nature Communication, In press. https://doi.org/10.1101/s41467-020-14998-3
Published in University of Lausanne, Department of Ecology & Evolution, 2015
Students are sequencing a genome of bacteria using latest sequencing technologies, assemble genome, map sequencing reads and build a gene annotation.
Published in University of Lausanne, Department of Ecology & Evolution, 2016
This class is a genomics project and therefore it’s a different every year. I have participated in this class in years 2016 and 2017.
Published in Swiss Institute of Bioinformatics, 2016
This is course I have co-developed with Amina Echchiki, Walid Gharib and Julien Roux. The full description can be found at the webpage of SIB and the teaching materials are available at GitHub. The goals of this workshop was to get hands-on experience with :
Published in Swiss Institute of Bioinformatics, 2017
Published in University of Lausanne, Department of Ecology & Evolution, 2018
I assisted students on individual basis, helping them to understand the practical exercises and getting them done. The practicals I have assisted to were covering concepts like Hardy Weinberg equilibrium, statistical testing of the departure from HW, calculation and interpretation of fst statistics between populations, effect of selection on genotype frequencies in case of heterozygosity advantage, and migration.