Developmental genetics of amphioxus: an insight into the evolution of vertebrate body plan

• Název práce v češtině: Vývojová genetika kopinatce: vhled do evoluce tělního plánu obratlovců
• Název v anglickém jazyce: Developmental genetics of amphioxus: an insight into the evolution of vertebrate body plan
• Klíčová slova: evoluce, strunatci, kopinatec, mezoderm, gen, regulace
• Klíčová slova anglicky: evolution, chordates, amphioxus, mesoderm, gene, regulatory
• Akademický rok vypsání: 2024/2025
• Typ práce: disertační práce
• Jazyk práce: angličtina
• Ústav: Katedra buněčné biologie (31-151)
• Vedoucí / školitel: RNDr. Zbyněk Kozmik, CSc.
• Konzultanti: Iryna Kozmikova, Ph.D.

Seznam odborné literatury

Amphioxus as a model to study the evolution of development in chordates. D'Aniello S, Bertrand S, Escriva H. Elife. 2023 Sep 18;12:e87028. doi: 10.7554/eLife.87028.
Amphioxus functional genomics and the origins of vertebrate gene regulation. Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M. Nature. 2018 Dec;564(7734):64-70. doi: 10.1038/s41586-018-0734-6. Epub 2018 Nov 21.

Předběžná náplň práce

Projekt se zaměří na evoluci buněčných typů, znaků předků chordátů a inovací specifických pro obratlovce, a to na základě srovnávací analýzy mezi kopinatci a obratlovci. Použité metody budou zahrnovat základní bioinformatiku, studium genové exprese (single cell RNA-seq, whole-mount in situ hybridizace a imunohistochemie), analýzu genových knockoutů vytvořených v laboratoři pomocí systému CRISPR/Cas9 a transgenezi reportérových genů.

Předběžná náplň práce v anglickém jazyce

Project will focus on evolution of cell types, ancestral chordate features and vertebrate-specific innovations, using comparative analysis between amphioxus and vertebrates. The methods used will include basic bioinformatics, gene expression studies (single cell RNA-seq, whole-mount in situ hybridization, and immunohistochemistry), analysis of gene knockouts established in the lab using CRISPR/Cas9 system, and reporter gene transgenesis.

Background:
Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. The genome of invertebrate chordate amphioxus has not undergone whole-genome duplication and serves as a proxy to ancestral chordates. Although amphioxus lacks the specializations and innovations of vertebrates, it shares with them a basic body plan and has multiple organs and structures homologous to those of vertebrates. For these reasons, amphioxus has widely been used as a reference outgroup to infer ancestral versus novel features during vertebrate evolution. Over the past few years amphioxus has become an established laboratory model and its cultures can be maintained throughout the year at the Institute of Molecular Genetics. This allows for an implementation of plethora of molecular and genetics approaches common to classical vertebrate models such as mouse, chick or fish. Moreover, recent publication on Amphioxus functional genomics and the origins of vertebrate gene regulation (Marletaz et al., Nature 564(7734):64-70) provides a huge genomic resource for future studies focused on gene regulatory mechanisms underlying evolution of vertebrate body plan.