Professor Xu Peng's research group and their collaborators recently published research article " Genomic basis of adaptive evolution: the survival of Amur ide (Leuciscus waleckii) in an extremely alkaline environment ", revealing the molecular mechanisms of genomic evolution and adaptation in the extreme alkaline environment in teleost.

Global climate change is changing environment and habitats of the living creature all the time. The change of genetic diversity and adaptive evolution under climate change is a popular scientific topic. In the eastern Inner Mongolia Plateau, Dali Nur Lake is a typical alkalized carbonate-brackish lake with a pH value up to 9.6. The geological evidence suggested that the lake has been developed from freshwater lake during the late Holocene. The L. waleckii population in Lake Dali Nur, unlike other freshwater species, is not only tolerant to high alkaline conditions, but also reproduces and grows, making it one of the only remaining fish species. Therefore, it is important model species to study adaptive evolution in teleost fish in responding to acid-base stress during the global climate change.

In order to dissect the potential genetic mechanisms underlying the adaptive evolution, Xu’s team had completely sequenced and annotated the whole genome of L. waleckii. Whole genome re-sequencing and population genomic studies were also performed on samples from the alkalized Lake Dali Nur and the freshwater environment of the Wusuli River. Comparative genomics analysis revealed that gene expansion related to extreme alkaline environment adaptation. Genome-scale diversity scan and selective pressure analysis also revealed a series of genes and regulatory pathways related to the adaptation and survivals in extreme alkaline environments. Further gene function analysis suggested that potential mechanisms were involved in acid-base regulation, ion transport, nitrogenous wastes excretion and stress response.

The study was published online in Molecular Biology and Evolution (doi:10.1093/molbev/msw230) on October 20, 2016. Professor Xu Peng is the correspondence author. The research work has been funded by the National Natural Science Foundation of China, Ministry of Science and Technology of China, and the Xiamen University Principal Fund.

Abstract:

The Amur ide (Leuciscus waleckii) is a cyprinid fish that is widely distributed in Northeast Asia. The Lake Dali Nur population inhabits one of the most extreme aquatic environments on Earth, with an alkalinity up to 50 mmol/L ( pH 9.6), thus providing an exceptional model with which to characterize the mechanisms of genomic evolution underlying adaptation to extreme environments. Here, we developed the reference genome assembly for L. waleckii from Lake Dali Nur. Intriguingly, we identified unusual expanded long terminal repeats (LTRs) with higher nucleotide substitution rates than in many other teleosts, suggesting their more recent insertion into the L. waleckii genome. We also identified expansions in genes encoding egg coat proteins and natriuretic peptide receptors, possibly underlying the adaptation to extreme environmental stress. We further sequenced the genomes of 10 additional individuals from freshwater and 18 from Lake Dali Nur populations, and we detected a total of 7.6 million SNPs from both populations. In a genome scan and comparison of these two populations, we identified a set of genomic regions under selective sweeps that harbour genes involved in ion homoeostasis, acid-base regulation, unfolded protein response, reactive oxygen species elimination, and urea excretion. Our findings provide comprehensive insight into the genomic mechanisms of teleost fish that underlie their adaptation to extreme alkaline environments.

Link for full article: doi:10.1093/molbev/msw230