Bioinformatics: from Algorithms to Applications 2020

Dipteran insects characterized by the huge taxonomic diversity (more than 160 thousand species at the time of 2013 (Zhang, 2013)), the diversity of ecological niches, and adaptation to various extreme environmental conditions. At the same time, the mechanisms of these adaptations are poorly studied, especially at the genomics level. Now the NCBI Genome database contains only 165 dipteran genomes (for comparison, for 40 thousand vertebrates we have more than 1000 sequenced genomes). Different species of the large family Ephydridae (shore flies), about 2000 species, are adapted to the most adverse environmental conditions from saline and alkaline impoundment and hot springs to oil puddles (Kadavy et al., 2020), but the genomes of only two species of this curious family - Ephydra gracilis and E. hians (syn. Cirrula hians) - were sequenced. The genome of the third fly from family Ephydridae - E. riparia - were sequenced at the department of biological evolution at Lomonosov Moscow State University.
In this study we de novo assembled the E. riparia genome, assessed assemble quality and compared it with the assemblies of two related species.
Raw reads were filtered by Trimmomatic and cleaned of contamination by Kraken2. E. riparia genome was assembled by SPAdes, SOAPdenovo and Platanus programs, the best one was done by SPAdes. The quality was assessed by QUAST and BUSCO. We made structural genomes annotation and turned to the functional one. See more details on our GitHub repository: https://github.com/Terraslavonica/E_riparia.
E. riparia genome, about 600M bp, was assembled into scaffold with average coverage 11.2x, with N50 equal 3.5K. bp and L50 – 53K contigs. In assembly we detected 53% of genes typical for Diptera by BUSCO. Comparing with assembling of close relatives, E. gracilis (410M bp, cov. 9.4x, N50 2.1K, L50 46K, BUSCO 81%) and E. hians (399M bp, cov. 27.0x, N50 1.8K, L50 53K, BUSCO 37%), we can conclude that E. riparia assembling is good enough for further analyses.
Based on these three assemblies we carry out functional annotation of the genomes and search the genes that can contribute to adaptation to extreme habitats and stressful conditions, it might be genes encoding LEA-proteins, heat shock proteins, aquaporins, metal-transport proteins, proteins that are the part of the signalling cascades p38 and JNK MAPK, etc. (Craig et al., 2004; Xu et al., 2013; Davies et al., 2014; Benoit et al., 2014; Reidl et al., 2016; Huang et al., 2016; Muthusamy et al., 2017; Pawłowicz, Masajada, 2019; Das et al., 2020).