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Tuesday, July 28 • 13:10 - 13:15
First insights in transcriptome-derived SNPs of two cryptic species Lasiopodomys gregalis and L. raddei (Cricetidae, Rodentia)

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Recently described narrow-headed vole species complex consists of two cryptic species: widespread in the Palearctic realm Lasiopodomys gregalis and Lasiopodomys raddei, whose distribution range is confined to the South-Eastern Transbaikalia.
Next generation sequencing is a powerful tool that could provide a clue to cryptic speciation processes. In this study, we use 6 RNA-seq data sets (3 for each species) in order to find and annotate variants that possibly contribute to the speciation process of L. raddei and L. gregalis.
The raw reads were assessed and trimmed by FastQC and TRIMMOMATIC, correspondingly. The reference transcriptome was prepared on the basis of one L. raddei RNA-seq data set assembled by Trinity. For final reference, we choose contigs that match any mammalian genes (DIAMOND BLASTx against nr NCBI, E-value < 10-5). The alignment was created by the bwa-mem algorithm and resulted in a mean coverage of 96%. The .bam files were sorted and filtered in Picard, variant calling was held by GATK HaplotypeCaller.
The final list included 904 SNPs contrasting in L. gregalis and in L. raddei. The contigs having SNP were annotated by eggNOG mapper and Gene Ontology Resource (http://geneontology.org/).
Our search resulted in revealing at least 73 genes involved in reproduction, cell division, developmental and metabolic processes. For example, the list of identified genes included Bag6 involved in spermatogenesis, the replication protein RPA2, also playing role in reproductive processes, KLHL21 (Kelch-like protein) required for efficient chromosome alignment and cytokinesis, Dnm1l (dynamin-1-like protein gene) functions in the mitochondrial and peroxisomal division.
The study was supported by the Russian Fund for Basic Research grant No 18-34-20118 and Russian Academy of Science research program No АААА-А19-119020790106-0.

avatar for Maria Skazina

Maria Skazina

Researcher, Bioinformatics Institute; Saint-Petersburg State University, Department of Applied Ecology

Tuesday July 28, 2020 13:10 - 13:15 MSK
Zoom Conference https://zoom.us/j/94321101353?pwd=QlJBb09uM0NVVnVyK0FkbTJ3Nkcrdz09