Diversity, function and evolution of aquatic vertebrate genomes

Aquatic vertebrates consist of jawed fish (cartilaginous fish and bony fish), aquatic mammals, reptiles and amphibians. Here, we present a comprehensive analysis of 630 aquatic vertebrate genomes to generate a standardized compendium of genomic data. We demonstrate its value by assessing their genome features as well as illuminating gene families related to the transition from water to land, such as Hox genes and olfactory receptor genes. We found that LINEs are the major transposable element (TE) type in cartilaginous fish and aquatic mammals, while DNA transposons are the dominate type in bony fish. To our surprise, TE types are not fixed in amphibians, the first group that transitioned to living on land. These results illustrate the value of a unified resource for comparative genomic analyses of aquatic vertebrates. Our data and strategy are likely to support all evolutionary and ecological research on vertebrates.

First occurrence of brachyopid temnospondyls in Southeast Asia and review of the Mesozoic amphibians from Thailand

The non-marine Mesozoic sedimentary rocks of Thailand, which consist of the Indochina block and the Sibumasu block, have yielded several terrestrial and aquatic vertebrate fossils, but only few amphibian remains have been reported. Here, we present an overview on the Thai amphibian palaeo-diversity based on the literature, re-examination of published material, new findings, and unpublished material. Thai amphibian fossil remains are assigned to Stereospondyli (Cyclotosauridae, Plagiosauridae, and Brachyopoidea) and Anura and were discovered from four formations, ranging from the Upper Triassic to Lower Cretaceous of Thailand. The occurrence of Brachyopidae in Thailand, which are related to Chinese forms, supports the previous hypothesis of physical connections between the Indochina blocks and the Sibumasu block during the Mesozoic era.

Reproductive Toxicity of 3,4-dichloroaniline (3,4-DCA) on Javanese Medaka (Oryziasjavanicus, Bleeker 1854)

Compound 3,4-dichloroaniline (3,4-DCA) is a metabolite of several urea herbicides and intermediate chemical of several industrial products. Moreover, 3,4-DCA has been frequently detected in aquatic ecosystems around the world. This aniline is more toxic than the parent chemicals, and it affects non-target organisms. This study evaluated a 21-day reproductive response of an emerging aquatic vertebrate model, Javanese medaka (Oryzias javanicus), exposed to 3,4-DCA. Fecundity and gonads histopathology were observed. The spawning rate and fertilisation reduced significantly in the highest exposed-group (250 µg/L). Gonadosomatic index (GSI) was significantly low in females exposed to 250 µg/L. No substantial structural alteration of male gonads. However, oocyte development and ovarian cell structure were disrupted in 250 µg/L exposed females. The gonadal developmental was not affected in the males; however, a significant reduction in the developmental of female gonads was observed at 250 µg/L. These results show that 3,4-DCA interfere with the reproduction of Javanese medaka through fecundity and alteration of gonadal tissues.

How to increase precision in Xenopus gene editing and base editing experiments

A review focussed on improvements in genome editing methods for developmental biology research using aquatic vertebrate embryos from Xenopus frog species. It is aimed as an introduction for students learning the differences between CRISPR/Cas9-mediated gene mutation versus base editing strategies. The benefits, limitations and efficiencies achieved by the different methods are discussed.

Genotoxicity evaluation of Chlorfenapyr in exposed freshwater African catfish Clarias gariepinus using micronucleus test

Chlorfenapyr is a new formulated insecticide targeted against insecticide resistant species. Its application in targeting harmful aquatic insects may potentially contaminate aquatic environment. This study is to evaluate its genotoxic effects on non-targeted aquatic biota. The study assessed the genotoxic potentials of chlorfenapyr in African catfish (Clarias gariepinus) using the micronucleus (MN) test. Juvenile stage of C. gariepinus were exposed to different concentrations; 5.00 – 15.00 mgL-1 of chlorfenapyr for 96 hours, peripheral blood was collected through the caudal vein and examined for micronucleus induction in the erythrocytes. The tested concentrations of chlorfenapyr did not elicit significant [F (5, 18) = 0.167, p 0.971] increase in MN formation and other nuclear abnormalities in the peripheral erythrocytes of C. gariepinus. The outcome of this study gives credence to the view that chlorfenapyr is not clastogenic and or aneugenic to non-targeted aquatic vertebrate with reference to fish (C. gariepinus).