Lawrence, M. L. | bioRxiv Science

bioRxiv2022

A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination

Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechanism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.

genomics↗

bioRxiv2019

Effects of siRNA silencing on the susceptibility of the fish cell line CHSE-214 to Yersinia ruckeri

Bacterial pathogens are known to co-opt mechanisms of the host cells physiology to gain intracellular entrance. Among the facultative intracellular bacteria is Yersinia ruckeri, an enterobacterium mostly known as the causative agent of enteric redmouth disease in salmonid fish. In the present study, we applied RNA inhibition to silence twenty pre-selected genes on the genome of a fish cell line (CHSE-214) followed by a gentamycin assay to quantify the effect of this silencing on the susceptibility of the cells to infection. It was found that silencing of 16 out of 20 genes significantly reduced the number of Y. ruckeri recovered at the end of the gentamycin assay. Among the genes with the strongest impact were Rab1A, actin and Rac1, which is consistent with our previous findings that N-acetylcysteine, a chemical inhibitor of Rac1, completely prevented invasion of cells by Y. ruckeri. Conversely, silencing of the Rho GTPase activating protein had no statistically significant effect, possibly because Y. ruckeri, like some other members of the Yersinia genus is able to activate Rho GTPase directly. Similarly, the effect of silencing E-cadherin was not statistically significant, suggesting that this might not be a target for the adhesion molecules of Y. ruckeri. Taken together, these findings improve our understanding of the infection process by Y. ruckeri and of the interactions between this bacterial pathogen and host cells.\n\nImportanceIntracellular invasiveness is a mean for bacterial pathogen to gain shelter from the immune system as well as access nutrients. The enterobacterium Y. ruckeri is well characterised as a facultative intracellular pathogen. However, the mechanisms of invasion scrutiny. Investigations have mostly focused on the bacterial virulence rather than on the hosts mechanisms hicjacked during invasion. The present findings therefore allow us to better understand the interaction between this important potentially zoonotic pathogen of fish and host cells in vitro.

microbiology↗