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. 2020 Oct 9;23(11):101662.
doi: 10.1016/j.isci.2020.101662. eCollection 2020 Nov 20.

African Arowana Genome Provides Insights on Ancient Teleost Evolution

Shijie Hao  1   2 , Kai Han  2 , Lingfeng Meng  1   2 , Xiaoyun Huang  2 , Wei Cao  3 , Chengcheng Shi  1   2 , Mengqi Zhang  2 , Yilin Wang  2 , Qun Liu  2 , Yaolei Zhang  2   4 , Haixi Sun  3 , Inge Seim  5   6 , Xun Xu  2   3   7 , Xin Liu  2   3   8 , Guangyi Fan  2   3   8
Affiliations

African Arowana Genome Provides Insights on Ancient Teleost Evolution

Shijie Hao et al. iScience. .

Abstract

Osteoglossiformes is a basal clade of teleost, evolving since the Jurassic period. The genomes of Osteoglossiformes species would shed light on the evolution and adaptation of teleost. Here, we established a chromosome-level genome of African arowana. Together with the genomes of pirarucu and Asian arowana, we found that they diverged at ∼106.1 million years ago (MYA) and ∼59.2 MYA, respectively, which are coincident with continental separation. Interestingly, we identified a dynamic genome evolution characterized by a fast evolutionary rate and a high pseudogenization rate in African arowana and pirarucu. Additionally, more transposable elements were found in Asian arowana which confer more gene duplications. Moreover, we found the contraction of olfactory receptor and the expansion of UGT in African arowana might be related to its transformation from carnivore to be omnivore. Taken together, we provided valuable genomic resource of Osteoglossidae and revealed the correlation of biogeography and teleost evolution.

Keywords: Evolutionary Biology; Paleobiology; Paleogenetics; Phylogenetics.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
The Evolution History of Asian arowana, African arowana and Pirarucu (A) The characteristics of the assembled H. niloticus genome. The tracks from outer to inner represent the gene density, TE density, tandem repeat density, GC content and non-coding RNA respectively. (B) The phylogenetic relationships of 10 teleost fishes with L. oculatus as outgroup. The numbers on clades represent the evolutionary rates (dN + dS). The numbers beside the inner nodes represent the support values of the nodes (The asterisk represents a support value of 100). (C) pirarucu and Asian arowana’ divergence pattern through the continents drift.
Figure 2
Figure 2
The Evolution Rate of Asian arowana, African arowana and Pirarucu (A) The dS and dN distribution of Asian arowana, African arowana, and pirarucu. The statistic significancy was calculated by Wilcoxon rank-sum test and three asterisks indicate a p value that less than 2.22∗e−16 and two asterisks indicate a p value that equal to 2.5 × 10−11 while one asterisks indicate a p value that equal to 0.9. (B) Syntenic pattern of African arowana and Asian arowana. (C) Syntenic pattern of intra-African arowana. (D) Syntenic pattern of intra-Asian arowana.
Figure 3
Figure 3
Transposable Element (TE) Dynamics of Pirarucu, African Arowana and Asian Arowana (A) The distribution of three Osteoglossidae fishes' TEs. (B) The phylogenetic trees of three Osteoglossidae fishes' Tc1 TEs. (C) The phylogenetic trees of three Osteoglossidae fishes' Tigger TEs. (D) The insertion timeline of LINE TEs of three Osteoglossidae fishes. (E) The insertion timeline of LTR TEs of three Osteoglossidae fishes. (F) An example of the positional relationship of Asian arowana's genes and TEs, in which the blue bars indicate the genes and the red bar indicate the TEs. In this case, all of the five genes are olfactory receptors.
Figure 4
Figure 4
Gene Family Dynamics of Three Osteoglossidae Fishes (A) The venn diagram represents the overlap relationship of three Osteoglossidae fishes' gene families. (B) The gene tree of three Osteoglossidae fishes' OR genes in which the bold clades indicated two gene expansions of pirarucu. (C) The insertion timeline of OR genes.
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