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

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

Meng Xu  1 , Ping Liu  1   2 , Qi Huang  1 , Shaolin Xu  1 , Henri J Dumont  1   3 , Bo-Ping Han  1
Affiliations

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

Meng Xu et al. iScience. .

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.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

None
Graphical abstract
Figure 1
Figure 1
The genome assembly of D. dubium (A) The genome-wide Hi-C heatmap of the assembly. (B) The genomic characteristics of D. dubium with siding windows of 100 kb. Track a, gene density, coordinate span, 1–40; Track b, repeat content, coordinate span, 0–90; Track c, GC content, coordinate span, 30–60.
Figure 2
Figure 2
Evolution landscapes of D. dubium (A) Phylogenetic tree, estimated divergence time, and estimated number of gene families with significant expansion/contraction evolution (CAFE, viterbi p<=0.05). (B) Venn map of shared and specific gene families among four water fleas. (C) KEGG function enrichment at level 2 category of specific genes in D. dubium, D. celebensis, D. magna, and D. pulex respectively. The path name is colored according to the level 1 category. The “RichFactor” = (number of specific genes in this pathway/number of all annotated specific genes)/(number of geneset genes in this pathway/number of all annotated genes of the whole geneset).
Figure 3
Figure 3
Annotation of anti-ROS genes and phylogenomic analysis of SOD genes (A) A photo of resting egg of D. dubium and D. magna respectively and schematic overview of the anti-ROS pathway. (B) The gene number of four mainly anti-ROS enzymes in seven species. Abbreviation: Diadu, D. dubium; Diace, D. celebensis; Dapma, D. magna; Dappu, D. pulex; Penva, P. vannamei; Euraf, E. affinis; Lsepa, L. salmonis. (C) The phylogeny tree of SOD family. The colored geometric shapes at the end-point of branches represent species.
Figure 4
Figure 4
Annotation of twelve main detoxification genes and phylogenomic analysis of CYP genes (A) An overview of the xenobiotics biodegradation pathway. (B) The gene number of twelve main xenobiotic-processing genes (XPGs) in seven species. Species abbreviation: Diadu, D. dubium; Diace, D. celebensis; Dapma, D. magna; Dappu, D. pulex; Penva, P. vannamei; Euraf, E. affinis; Lsepa, L. salmonis. Gene abbreviations: Ces, carboxylesterase; Ephx, epoxide hydrolase; Akr, aldo-keto reductase; Cbr, carbonyl reductase; Nqo, NADH:quinone oxidoreductase; Adh, alcohol dehydrogenase; Aldh, aldehyde dehydrogenase; GST, glutathione-S-transferase; UGT, UDP-glucuronosyltransferase; Sult, sulfotransferase; Abc, ATP-binding cassette transporter. (C) The phylogeny tree of CYP family. The track “i” represents sub-family classification, the track “ii” represents species.
Figure 5
Figure 5
The phylogenomic analysis of cathepsin C genes The colored branches and rectangles at the end-point of branches represent species. The colored outer tracks represent sub-family classification based on the best hit to MEROPS database. Abbreviations: CatB, cathepsin B; CatO, cathepsin O; CatL, cathepsin L; Nph, non peptidase homologues; DppI, dipeptidylpeptidase I; I26/29, insect 26/29 kDa peptidase.
Figure 6
Figure 6
The evolution of p53-like and SMS genes (A) The phylogeny tree of p53-likegenes. (B) Genome syntenic blocks of p53-like genes in water fleas. Triangles represent genes and are distinguished by color based on gene name. The red triangles represent p53-like genes which are at the same horizon line on the left phylogeny tree except the multiple p53-like genes shown in one block. The background color under p53-like genes is accordance with the background color in left phylogeny tree. The base to apex angle of triangle represents encoding direction. Five genes on upstream and downstream of p53-like are checked and the un-reappeared genes are not shown. Proportional scale, exon region: non-exon region = 10: 1. (C) The phylogeny tree of SMS gene. (D) Genome syntenic blocks of SMS genes in water fleas. The genes are colored independently with genes in panel B. The red triangles represent SMS genes.
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