Subterranean Fishes of the World

6930

2024

Garra longipinnis is a cyprinid fish endemic to Northern Oman. This species has both troglomorphic cave populations found in two nearby underground locations in the Hajar mountains and surface populations that inhabit several wadis in Northern Oman. Our previous research compared the genetic diversity of these cave populations with their surface counterparts, revealing that the cave population of G. longipinnis is genetically isolated from surface populations. This isolation is relatively recent, dating back between 0.8 to 0.1 million years ago, and the cave population has experienced genetic bottlenecks in the past. These findings establish G. longipinnis as an excellent model for studying cave fish evolution. In our current project, we aim to address the following questions: 1) Is genetic differentiation among cave and surface populations the result of adaptation to the cave environment or due to random fixation from genetic drift? 2) Are adaptive genetic changes the result of de-novo mutations or due to shifts in standing genetic variation? 3) Are troglomorphic characters the result of changes in protein structure of genes and/or due to regulatory changes modifying expression patterns? To uncover the genomic basis of the troglomorphic phenotype, we will perform population genomic analyses using comprehensive genome-wide data generated through Whole Genome Resequencing (WGR). We will use large sample sizes from both cave and surface populations of G. longipinnis, as well as from a population of a closely related surface species. Initially, we constructed a draft genome of a surface specimen of G. longipinnis using sequence data from the MinION Nanopore sequencing platform (Oxford Nanopore Technologies, ONT). This yielded a draft genome approximately 1.2 GB in length, consisting of 8,888 scaffolds with an N50 of 650 kbp. We further assessed the completeness of the draft genome using the BUSCO pipeline v. 5.3.2, which indicated a high level of completeness with over 95% of vertebrate-specific benchmarking universal single-copy orthologous (BUSCO) genes detected as complete copies

1

26th International Conference on Subterranean Biology and 6th International Symposium on Anchialine Ecosystems: Cagliari 9-14 Sept 2024