Contract number

J1-2469

Department:

Department of Biology

Type of project

ARRS projects

Type of project

Basic research project

Role

Lead

Duration

01.09.2020 - 31.08.2023

Total

1.4 FTE

Project manager at BF

Kostanjšek Rok

ABSTRACT

The European cave salamander Proteus anguinus, is the largest known obligate cave animal in the world. During its evolution in the underground waters of the Dinaric karst, proteus developed a variety of adaptations to subterranean environment including depigmentation, loss of sight, specialization of the sensory organs, slow metabolism and capability of extreme starvation for up to eight years. Other extraordinary features of this charismatic amphibian include lifespan of over 100 years, negligible sighs of aging and, like some other salamanders, capability of complete regeneration of damaged limbs.
Holding promise of information essential for illumination of profound biological questions related to evolution, adaptations to cave environment and processes related to human well-being, the genome of proteus has been eagerly awaited by the scientific community. However, the information encoded in the genome remains unknown due to its enormous size; with estimated size of 50 Gbp, proteus genome surpass the size of human genome by 15 times and represents one of the largest known genomes in the animal kingdom.

The challenges of sequencing such an enormous genome have recently been overcome by joined efforts of partners from Slovenia (University of Ljubljana), Denmark (Aarhus University) and China (“BGI Research”, “MGI Tech” and “Lars Bolund Institute of regenerative medicine”). Their expertise and technological capabilities led to the first successful reading of the largest genome red to date. Multiple readings of genetic information in proteus genome generated over 7 Tbp of information, which was accompanied by a multiple readings of transcriptomic data from fourteen different proteus tissues.

The aim of the proposed project is bioinformatic analysis and organization of this vast amount of sequencing data into an assembled genome, as well as identification of potential biological topics that can be addressed using information encoded in the genome and the transcriptome. The objectives of the proposed project include: i) description of the genome structure, annotation and assembly of the genomic data; ii) analysis of the non-coding part of the genome and illumination of the processes that generate its enormous size; iii) identification of the mechanisms behind the loss of pigmentation in proteus and iv) identification of the potential mechanisms associated with the longevity of proteus.


THE PHASES OF THE PROJECT AND THEIR REALIZATION

The project will build upon two stages. The objective of the first stage includes genome assembly and general descriptive analysis of genomic data (described in Work Packages 1 and 2 - WP1 and WP2), whereas in the second stage we will try to address specific aspects of information encoded in proteus genetic information (described in WP3 and WP4). WP5 will cover the aspects related to management of the project and dissemination of the results.

  • WP1 - Assembly and description of the genome and analysis of the transcriptome
  • WP2 - Analysis of non-coding part of the genome
  • WP3 - Analysis of potential genes and pathways related to depigmentation in underground environments
  • WP4 - Identification of genes related to longevity
  • WP5 - Project management and dissemination of results

SICRIS link