Comparaison génomique et transcriptomique in silico entre tuniciers (chordata) à régénération élevée et à régénération limitée // In silico genomic and transcriptomic comparison among highly-regenerating and regeneration-limited tunicates (chordata)

Tunicates, the sister group of vertebrates, are a diverse group of marine chordates that display a remarkable range of regenerative abilities, from limited tissue and organ regeneration to whole body starting from somatic cells (1, 2). This diversity in regenerative capacity is observed even among closely related species. In fact, while solitary tunicates reproduce strictly sexually and possess limited regenerative abilities, several species of colonial tunicates can regenerate their entire body, either in response to injury or as part of their asexual life cycle through various budding mechanisms. The proposed PhD project study aims to leverage in silico genomic and transcriptomic comparisons to explore the genetic and molecular basis underlying these divergent regenerative capabilities, helping to better understand the evolutionary dynamics of regeneration within this pivotal chordate group.
Solitary and colonial species are scattered throughout the tunicate phylogenetic tree, suggesting that the various forms of budding have evolved convergently (1, 2). This is evidenced by the fact that each budding process involves non-homologous cells and tissues, such as epithelia or blood-like cells. However, one might hypothesize that the repeated acquisition of budding was facilitated by recurrent co-option of homologous genetic, developmental modules. To test this hypothesis of deep homology, the candidate will compare transcriptomic datasets from three distinct types of budding: peribranchial budding in Botryllus schlosseri, vasal budding in Polyandrocarpa zorritensis, and stolonial budding in Thalia democratica (2). The first step will involve contributing to the assembly and annotation of the genomes of P. zorritensis and T. democratica, using the existing chromosome-level genome of B. schlosseri as a reference (3). Following this, the candidate will analyze bulk and single-cell RNAseq data from budding tissues of the three species. They will develop a pipeline to identify orthologous genes and compare expression profiles across the different budding modes.
In order to further identify genomic features associated with budding capacity, the candidate will also compare the genomes of three tunicate species from the same family: the two colonial species B. schlosseri and P. zorritensis, and one solitary, non-budding species, Styela clava. While the genomes of B. schlosseri and S. clava are already assembled and annotated, the P. zorritensis genome will first be scaffolded and annotated. Various comparative genomic approaches will be used, to analyze gene family expansions or contractions, presence/absence of orphan genes, gene gains and losses, and synteny block structures. Additionally, the project may provide insights into how asexual propagation affects genome evolution, particularly in relation to heritable mutations in somatic pluripotent stem cells.
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Tunicates, the sister group of vertebrates, are a diverse group of marine chordates that display a remarkable range of regenerative abilities, from limited tissue and organ regeneration to whole body starting from somatic cells (1, 2). This diversity in regenerative capacity is observed even among closely related species. In fact, while solitary tunicates reproduce strictly sexually and possess limited regenerative abilities, several species of colonial tunicates can regenerate their entire body, either in response to injury or as part of their asexual life cycle through various budding mechanisms. The proposed PhD project study aims to leverage in silico genomic and transcriptomic comparisons to explore the genetic and molecular basis underlying these divergent regenerative capabilities, helping to better understand the evolutionary dynamics of regeneration within this pivotal chordate group.
Solitary and colonial species are scattered throughout the tunicate phylogenetic tree, suggesting that the various forms of budding have evolved convergently (1, 2). This is evidenced by the fact that each budding process involves non-homologous cells and tissues, such as epithelia or blood-like cells. However, one might hypothesize that the repeated acquisition of budding was facilitated by recurrent co-option of homologous genetic, developmental modules. To test this hypothesis of deep homology, the candidate will compare transcriptomic datasets from three distinct types of budding: peribranchial budding in Botryllus schlosseri, vasal budding in Polyandrocarpa zorritensis, and stolonial budding in Thalia democratica (2). The first step will involve contributing to the assembly and annotation of the genomes of P. zorritensis and T. democratica, using the existing chromosome-level genome of B. schlosseri as a reference (3). Following this, the candidate will analyze bulk and single-cell RNAseq data from budding tissues of the three species. They will develop a pipeline to identify orthologous genes and compare expression profiles across the different budding modes.
In order to further identify genomic features associated with budding capacity, the candidate will also compare the genomes of three tunicate species from the same family: the two colonial species B. schlosseri and P. zorritensis, and one solitary, non-budding species, Styela clava. While the genomes of B. schlosseri and S. clava are already assembled and annotated, the P. zorritensis genome will first be scaffolded and annotated. Various comparative genomic approaches will be used, to analyze gene family expansions or contractions, presence/absence of orphan genes, gene gains and losses, and synteny block structures. Additionally, the project may provide insights into how asexual propagation affects genome evolution, particularly in relation to heritable mutations in somatic pluripotent stem cells.
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Début de la thèse : 01/10/2025
WEB : http://www.tiozzolab.org

Contrat doctoral

Concours pour un contrat doctoral - SU

Sorbonne Université SIM (Sciences, Ingénierie, Médecine)

515 Complexité du vivant

We are seeking a passionate and skilled bioinformatician with a strong academic background in both programming and biology with proficiency in widely used programming languages such as Python, R, and others. The ideal candidate will have expertise (or willing to get one) in genome assembly, comparative genomics, and comparative transcriptomics. We're looking for someone who is not just technically capable, but also a true 'geek' who thrives on solving complex biological problems.
We are seeking a passionate and skilled bioinformatician with a strong academic background in both programming and biology with proficiency in widely used programming languages such as Python, R, and others. The ideal candidate will have expertise (or willing to get one) in genome assembly, comparative genomics, and comparative transcriptomics. We're looking for someone who is not just technically capable, but also a true 'geek' who thrives on solving complex biological problems.