Project Summary

Background: Genome and transcriptome analyses are powerful tools to shed light on the history, ecology, molecular and physiological characteristics of a species. The advent of next generation sequencing technologies within the last 10 years has opened up genome and transcriptome studies for non-model organisms. This study is part of the Lake Van Pearl Mullet Genom Project, which aims to sequence, analyze and publish the genome of one of Turkey’s most interesting and endemic species: the pearl mullet (Chalcalburnus tarichi, Pallas 1811). This fish is the only vertebrate dweller of Lake Van, the largest soda lake of the world. The pearl mullet, endemic to the lake, is of the Cyprinidae family. It is anandromous: it spends most of its life in the high soda (pH=9.8) and saline waters of Lake Van, but migrates to freshwater streams flowing into the lake for spawning. This exceptional adaptation is equaled by only two other species in the world. After the discovery of the adaptation, the fish attracted interest from physiologists and ecologist; however, the mechanisms undelying its adaptation have remained obscure. The pearl mullet, in addition to its ecological and evolutionary value, is also dear to the region’s socioeconomy as a protein source and source of income for thousands of people. But the fish population underwent a severe decrease in the 1990’s due to overfishing and habitat loss. The population started to recover in the 2000’s owing to new measures, but remains vulnerable. Investigating the population and physiological characteristics of this fish at the genome level can open up opportunities for new studies on its biological characterization, conservation and management.

Preliminary work: In the year 2013 a group of researchers from Ankara, Van, Gebze and İstanbul initiated the Pearl Mullet Genome Project. Deep Illumina sequencing (~200X coverage) was performed in 2014. However, for the genome sequence to be interpreted and yield insight into the fish’s biology, an annotation of protein coding and non-coding genes of the pearl mullet and their functional predictions are also needed. For this, transcriptome sequencing is required. In April 2016, RNA isolation from pearl mullet samples were performed. In this project, existing RNA samples will be used.

Goal and methods: In this 1001 project our main goal is to sequence mRNA and miRNA from 10 tissues from 10 pearl mullet individuals (male, female and adolescent) on the Illumina platform (20M reads from each library for mRNA). We will use computational analysis to construct a reference transcript list. Through comparative analysis, we will identify the genes’ homologs in other species, and predict the genes’ functional properties based on homology. We will thus create a comprehensive repertoire of the pearl mullet genes, which will be published along with the genome sequence. In addition, we will perform three analyses as part of the pearl mullet genome study: (1) The fish’s C-value will be measured. (2) Pearl mullet gene sequences and gene expression levels will be compared with published data from other fish species. In this way, we will search for genes and pathways specific to, or showing an excess of gene sequence or expression level changes in the pearl mullet. This approach will indicate possible positive selection events in the pearl mullet genome, and provide insight into the fish’s adaptation to Lake Van waters. (3) We will extract DNA polymorphism using the sequenced transcriptomes from the 10 individuals. This data will provide information on the genetic variation and differentiation within the pearl mullet population.

Expected outcome: The project will describe properties of the pearl mullet genome. This will be a first step towards better understanding the genetic characteristics of the species, which, in turn, will inform on its ecology, evolutionary history, population characteristics and physiology. The genome’s publication will facilitate future work on the pearl mullet and its relatives. To our knowledge, this will also be the first genome analysis of a species endemic to Turkey.