RT Journal Article
SR Electronic
T1 Three genomes of Osteoglossidae shed light on ancient teleost evolution
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.01.19.911958
DO 10.1101/2020.01.19.911958
A1 Shijie Hao
A1 Kai Han
A1 Lingfeng Meng
A1 Xiaoyun Huang
A1 Chengcheng Shi
A1 Mengqi Zhang
A1 Yilin Wang
A1 Qun Liu
A1 Yaolei Zhang
A1 Inge Seim
A1 Xun Xu
A1 Xin Liu
A1 Guangyi Fan
YR 2020
UL http://biorxiv.org/content/early/2020/01/20/2020.01.19.911958.abstract
AB Osteoglossiformes is a basal clade of teleost, originated from late Jurassic and had seen the process of continental drift. The genomic differences amongst Osteoglossiformes species should reflect the unique evolve history of that time. Here, we presented the chromosome-level genome of Heterotis niloticus which is the only omnivore species of Osteoglossidae spreading in Africa. Together with other two Osteoglossidae species genomes of Arapaima gigas and Scleropages formosus which spread in South America and Australia respectively, we found great evolutionary differences in gene families and transposable elements. Phylogenetic analysis showed that the ancestor of H. niloticus and A. gigas diverged with S. formosus at ∼106.1Mya, consistent with the time of Afro-South American drift and A. gigas speciated from the ancestor of H. niloticus and A. gigas at ∼59.2 Mya, consistent with the separation of Eurasia and North American continents. And we proposed the evolutionary traces of Osteoglossidae species based on comparative genomics analysis and their living geographic habitats. We identified loss of LINEs and LTRs, fast evolutionary rate in parallel to fast pseudogenization rate in H. niloticus and A. gigas comparing to S. formosus during the evolutionary process. We also found notable OR genes contraction in H. niloticus, which might be related to the diet transition. Taken together, we reconstructed the evolutionary process of Osteoglossidae using three representative genomes, providing a possible clue for biogeographic and evolution study of ancient teleost clade.