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Projects / Programmes source: ARIS

Genomic and transcriptomic insights into the exceptional biology of proteus (Proteus anguinus)

Research activity

Code Science Field Subfield
1.03.01  Natural sciences and mathematics  Biology  Zoology and zoophysiology 

Code Science Field
1.06  Natural Sciences  Biological sciences 
Keywords
olm, proteus, large genome, genome assembly, transcriptome, non-coding DNA, pigment loss, troglomorphisms, longevity
Evaluation (rules)
source: COBISS
Researchers (9)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  11957  PhD Lilijana Bizjak Mali  Biology  Researcher  2020 - 2023 
2.  25974  PhD Cene Gostinčar  Biotechnology  Researcher  2020 - 2023 
3.  39092  PhD Tajda Gredar  Biology  Researcher  2021 - 2023 
4.  05935  PhD Nina Gunde-Cimerman  Biotechnology  Researcher  2020 - 2023  49 
5.  07673  PhD Dušan Kordiš  Biochemistry and molecular biology  Researcher  2020 - 2023  84 
6.  18749  PhD Rok Kostanjšek  Biology  Head  2020 - 2023 
7.  55612  Luka Močivnik  Biology  Researcher  2021 - 2023 
8.  55611  Nina Srečnik Lapanja    Technical associate  2021 
9.  14835  PhD Peter Trontelj  Biology  Researcher  2020 - 2023 
Organisations (2)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  3,930 
2.  0106  Jožef Stefan Institute  Ljubljana  5051606000  6,024 
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. As the top predator in its underground environment, this neotenic amphibian has an immense ecological role. Species is also endangered by the loss of its habitat. Due to its historical and conservation importance, proteus is considered the Slovenian national symbol, a flagship species of conservation of the karstic underground environment and a symbol of the world's natural heritage. 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. Besides assembly of the largest genome so far, the data encrypted in proteus genome will contribute to better understanding of the evolutionary role of repetitive sequences and processes leading to enormous size of genomes. By providing the first genome information of strictly cave organism, the project will deliver new insights into evolution processes in caves and open new chapter in research on cave organisms. Results will also provide essential information for more focused conservation efforts of proteus and establishment of sustainable breeding program of this endangered species. The genome of this charismatic creature might provide new clues about proteus longevity and other features of potential biomedical relevance and how these may be relevant for the human health and wellbeing.
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