triggers of asexual reproduction: on the crosslink between hybridization, asexuality, polyploidy and speciation on example of Cobitidae loaches

• Název práce v češtině: spouštěcí mechanismy asexuálního rozmnožování: propojení mezi hybridizací, asexualitou, polyploidií a speciací na příkladu sekavců čeledi Cobitidae
• Název v anglickém jazyce: triggers of asexual reproduction: on the crosslink between hybridization, asexuality, polyploidy and speciation on example of Cobitidae loaches
• Klíčová slova: speciace, asexualita, hybridizace, polyploidie, ontogeneze, genove editace
• Klíčová slova anglicky: speciation, asexuality, hybridisation, polyploidy, ontogeny, gene editing
• Akademický rok vypsání: 2017/2018
• Typ práce: disertační práce
• Jazyk práce: angličtina
• Ústav: Katedra zoologie (31-170)
• Vedoucí / školitel: Mgr. Karel Janko, Ph.D.
• Řešitel: skrytý - zadáno vedoucím/školitelem
• Datum přihlášení: 05.12.2017
• Datum zadání: 05.12.2017
• Datum odevzdání elektronické podoby: 11.01.2023
• Datum proběhlé obhajoby: 31.03.2023
• Oponenti: prof. Katsutoshi Arai

Předběžná náplň práce

The project aims at understanding crucial aspects of the evolution of asexual organisms. It is based on extensive knowledge regarding the evolutionary history of an emerging model organism for studies of hybridization, asexuality and polyploidy - spined loaches (Cobitis). The student will focus on several complementary approaches, with a potential to represent major leap in the knowledge about the evolution of asexuality and polyploidy. The strategy of the PhD project combines several overlapping proximate topics, some of which are guaranteed to achieve first-author publication during the PhD, some are more delicate but with considerably higher interest for the general biological societies. The project aimsfor the following tasks:
Identification of past hotspots of clonal emergence: for long time it has been considered that clonal loaches originate at hybrid zones of which the best studied is the central-European one. Nonetheless, due to repeated glaciations, the central European clones could have not evolve independent in that timeframe. Due to the fact that Anatol Marta has access to refugial regions, where parental species were in historical contact and might have survived inter/glacials for long periods (Romania, Moldova, Ukraine). Sampling at that localities with subsequent sequencing of suitable markers will thus greatly increase our understanding of long-term processes and identify ancient clonal lineages.
There are numerous theories predicting that clonal lineages will deteriorate in time either due to detrimental changes in their genomes or inability to adapt to changes fast enough. On the other hand, we found convincing evidence that genomes of asexual loaches aren’t strictly clonal as they undergo locus-restricted conversions/deletions, which may have both adaptive as well as detrimental effects. The student will be involved in studying the exome of ancient clones, identify loci with rearrangements and determine their topological positions on available genome.
Polyploidy is a common attribute of asexual organisms bringing along various pros&cons. One widely debated aspect of polyploidy is the dosage compensation, where researchers compare gene expression of di- and polyploids to understand the results in the expression of genes after one or more round of whole-genome duplication (WGD). An unstated assumption is that WGD affects entire genome. However, we found already that after the WGD in loaches, numerous deletions occurred in specific loci, whose number accumulates with the age of given clonal lineage. Therefore, most of loci of Cobitis diploids occur in 3n state but non-negligible part of genes occurs in 2n state.
The student will therefore complement exome sequencing with RNAseq to understand the dosage-compensation and aneuploidy of particular loci.
As a most advanced part of the project, the student will develop allele-specific probes targeting exones, which suffered deletions at some clones and will optimize the CRISPR-Cas9 methodics to simulate their deletion on artificially produced triploid hybrids.
Sex Determination


The project will be supported by ongoing projects GACR No. 17-09807S and OP VVV 0460.

Supervisor, Mgr. Karel Janko Ph.D.
Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Liběchov, Rumburská 89

Předběžná náplň práce v anglickém jazyce

The project aims at understanding crucial aspects of the evolution of asexual organisms. It is based on extensive knowledge regarding the evolutionary history of an emerging model organism for studies of hybridization, asexuality and polyploidy - spined loaches (Cobitis). The student will focus on several complementary approaches, with a potential to represent major leap in the knowledge about the evolution of asexuality and polyploidy. The strategy of the PhD project combines several overlapping proximate topics, some of which are guaranteed to achieve first-author publication during the PhD, some are more delicate but with considerably higher interest for the general biological societies. The project aimsfor the following tasks:
Identification of past hotspots of clonal emergence: for long time it has been considered that clonal loaches originate at hybrid zones of which the best studied is the central-European one. Nonetheless, due to repeated glaciations, the central European clones could have not evolve independent in that timeframe. Due to the fact that Anatol Marta has access to refugial regions, where parental species were in historical contact and might have survived inter/glacials for long periods (Romania, Moldova, Ukraine). Sampling at that localities with subsequent sequencing of suitable markers will thus greatly increase our understanding of long-term processes and identify ancient clonal lineages.
There are numerous theories predicting that clonal lineages will deteriorate in time either due to detrimental changes in their genomes or inability to adapt to changes fast enough. On the other hand, we found convincing evidence that genomes of asexual loaches aren’t strictly clonal as they undergo locus-restricted conversions/deletions, which may have both adaptive as well as detrimental effects. The student will be involved in studying the exome of ancient clones, identify loci with rearrangements and determine their topological positions on available genome.
Polyploidy is a common attribute of asexual organisms bringing along various pros&cons. One widely debated aspect of polyploidy is the dosage compensation, where researchers compare gene expression of di- and polyploids to understand the results in the expression of genes after one or more round of whole-genome duplication (WGD). An unstated assumption is that WGD affects entire genome. However, we found already that after the WGD in loaches, numerous deletions occurred in specific loci, whose number accumulates with the age of given clonal lineage. Therefore, most of loci of Cobitis diploids occur in 3n state but non-negligible part of genes occurs in 2n state.
The student will therefore complement exome sequencing with RNAseq to understand the dosage-compensation and aneuploidy of particular loci.
As a most advanced part of the project, the student will develop allele-specific probes targeting exones, which suffered deletions at some clones and will optimize the CRISPR-Cas9 methodics to simulate their deletion on artificially produced triploid hybrids.
Sex Determination


The project will be supported by ongoing projects GACR No. 17-09807S and OP VVV 0460.

Supervisor, Mgr. Karel Janko Ph.D.
Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Liběchov, Rumburská 89