Deep Insights into the Mudskipper genomes! -A species new to Whole Genome sequencing (WGS)

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The male mudskippers defend their territory with wild hissing and an impressive mohawk. Source: http://bit.ly/1ECo0LS
The male mudskippers defend their territory with wild hissing and an impressive mohawk. Source: http://bit.ly/1ECo0LS

Mudskippers are amphibious fishes that are an interesting group of vertebrates. These species made a successful transition from aquatic life to terrestrial living around 360 million years ago. Since they evolved independently, they serve as key models for understanding the genetic changes associated with water-to-land transition of vertebrates.

Scientists from China did whole-genome sequencing of four representative mudskippers. This study gave deep insights into the molecular mechanisms that underlie such transitions. Illumina HiSeq 2000 was used to generate the raw data and they were SOAPdenovo2 assembled. Out of the four assemblies, Blue-spotted Mudskipper’s assembly is of high quality and maybe used as a reference mudskipper genome. A standard annotation pipeline was used to predict the gene sets of all the four species. These involve the protein coding genes from the draft assemblies of the Giant and Blue Mudskipper also.

Phylogenetic evidence shows that they diverged from other teleosts ~ 140 million years ago. The immune and DNA metabolism of these fishes witnessed an expansion of innate immune system genes; also positive selection of certain genes of the ammonia excretion pathway shows them having remarkable tolerance level to the environmental ammonia compared to their counterparts. Differential loss of some vision related genes and olfactory receptor genes (α and γ group) illustrate their genomic changes associated with these systems.

Thus, the genomic and transcriptomic data obtained in this study is indeed a valuable resource to understand their genetic changes, adaptation and perform comparison analysis too. This study provides insights into the terrestrial adaptation of amphibious fishes.

Figure: Habitats of the four sequenced mudskippers - BP and SH are predominantly water dwelling, whereas PM and PS spend extended periods of time on land. Interestingly, the genome size decreases in the following order: BP>SH>PS>PM, which may be associated with their terrestrial affinity but unrelated to their body size (PS>BP>SH>PM).  Source: http://bit.ly/1FOk3pc
Figure: Habitats of the four sequenced mudskippers – BP and SH are predominantly water dwelling, whereas PM and PS spend extended periods of time on land. Interestingly, the genome size decreases in the following order: BP>SH>PS>PM, which may be associated with their terrestrial affinity but unrelated to their body size (PS>BP>SH>PM). Source: http://bit.ly/1FOk3pc

So, next time you happen to visit mangroves, don’t forget to keep your camera lenses ready so that you don’t miss capturing these fascinating creatures!

The original publication can be accessed here.