SNP Identification through Transcriptome Analysis of the European Brown Hare (Lepus europaeus): Cellular Energetics and Mother’s Curse

Abstract

The European brown hare (Lepus europaeus, Pallas 1778) is an important small game species in Europe. Due to its size and position in the food chain, as well as its life history, phenotypic variation and the relatively recent speciation events, brown hare plays an important role in the structure of various ecosystems and has emerged as an important species for population management and evolutionary studies. In order to identify informative SNPs for such studies, heart and liver tissues of three samples from the European lineage and a three-sample pool from the Anatolian lineage were subjected to RNA-Sequencing analysis. This effort resulted in 9496 well-assembled protein-coding sequences with close homology to human. After applying very stringent filtering criteria, 66185 polymorphic sites were identified in 7665 genes/cds and 2050 of those polymorphic sites are potentially capable of distinguishing the European from the Anatolian lineage. From these distinguishing mutations we focused on those in genes that are involved in cellular energy production, namely the glycolysis, Krebs cycle and the OXPHOS machinery. A selected set of SNPs was also validated by Sanger sequencing. By simulating the three European individuals as one pool, no substantial informative-SNP identification was lost, making it a cost-efficient approach. To our knowledge this is the first attempt to correlate the differentiation in both nuclear and mitochondrial genome between the two different lineages of L. europaeus with the observed spatial partitioning of the lineages of the species, proposing a possible mechanism that is maintaining the reproductive isolation of the lineages.

Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares

“…SNP calling was performed separately for mountain hares (Data Citation 1) and European hares (Data Citation 3, from Amoutzias et al 18 ). The three European hare specimens represent the European lineage of the species 18 .…”

“…SNP calling was performed separately for mountain hares (Data Citation 1) and European hares (Data Citation 3, from Amoutzias et al 18 ). The three European hare specimens represent the European lineage of the species 18 . First, reads from all the individuals were mapped to the filtered mountain hare de novo transcriptome with bwa-mem v0.7.15 34 with default parameters and read group information added to each sequencing lane-sample pair.…”

“…Therefore, permanent genomic resources provide fundamental information to develop monitoring tools to evaluate population status and implement protective policies. In this work, we use high-throughput RNA sequencing to: i) generate genomic resources for the mountain hare; and, ii) use published data on the European hare 18 to pinpoint candidate fixed differences between the species that can be used to build genotyping tools to monitor gene exchange in the contact zones. We here present the first mountain hare transcriptome, and the most complete among the currently available European Lepus transcriptomes.…”

“…The European hare data used here (Data Citation 3) was previously published by Amoutzias et al 18 ( NCBI Sequence Read Archive , accession number SRP055741, samples SRR1823098, SRR1863103 and SRR1863605).…”

The association between mitochondrial genetic variation and reduced colony fitness in an invasive wasp

“…Simultaneously, examining nuclear and mitochondrial genetic variation could be an important line of future research. Coadapted nuclear-encoded mitochondrial genes can restore deleterious effects caused by mtDNA polymorphisms (Dowling et al, 2008;Meiklejohn, Montooth, & Rand, 2007) so that a disruption of the two genomes can lead to mtDNA haplotypes becoming deleterious after being introduced into a new range (Amoutzias et al, 2016;Smith et al, 2010). In addition, functional differences of mtDNA are sensitive to variation in climate, which may differ in a new environment (Lamb et al, 2018).…”