High-quality genome of Diaphanosoma dubium provides insights into molecular basis of its broad ecological adaptation

Meng Xu; Ping Liu; Qi Huang; Shaolin Xu; Henri J Dumont; Bo-Ping Han

doi:10.1016/j.isci.2023.106006

High-quality genome of Diaphanosoma dubium provides insights into molecular basis of its broad ecological adaptation

iScience. 2023 Jan 18;26(2):106006. doi: 10.1016/j.isci.2023.106006. eCollection 2023 Feb 17.

Authors

Meng Xu¹, Ping Liu^{1

2}, Qi Huang¹, Shaolin Xu¹, Henri J Dumont^{1

3}, Bo-Ping Han¹

Affiliations

¹ Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China.
² College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China.
³ Ghent University, Department of Biology, Ledeganckstraat 35, 9000 Ghent, Belgium.

Abstract

Diaphanosoma dubium Manuilova, 1964, is a widespread planktonic water flea in Asian freshwater. Although sharing similar ecological roles with species of Daphnia, studies on D. dubium and its congeners are still few and lacking a genome for the further studies. Here, we assembled a high quality and chromosome level genome of D. dubium by combining long reads sequencing and Hi-C technologies. The total length of assembled genome was 101.8 Mb, with 98.92 Mb (97.2%) anchored into 22 chromosomes. Through comparative genomic analysis, we found the genes, involved in anti-ROS, detoxification, protein digestion, germ cells regulation and protection, underwent expansion in D. dubium. These genes and their expansion helpfully explain its widespread geographical distribution and dominance in eutrophic waters. This study provides insight into the adaptive evolution of D. dubium at genomic perspectives, and the present high quality genomic resource will be a footstone for future omics studies of the species and its congeners.

Keywords: Biological sciences; Evolutionary biology; Genomics.