Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus

Abstract

BackgroundAnimal migration requires adaptations in morphological, physiological and behavioural traits. Several of these traits have been shown to possess a strong heritable component in birds, but little is known about their genetic architecture. Here we used 454 sequencing of brain-derived transcriptomes from two differentially migrating subspecies of the willow warbler Phylloscopus trochilus to detect genes potentially underlying traits associated with migration.ResultsThe transcriptome sequencing resulted in 1.8 million reads following filtering steps. Most of the reads (84%) were successfully mapped to the genome of the zebra finch Taeniopygia gutatta. The mapped reads were situated within at least 12,101 predicted zebra finch genes, with the greatest sequencing depth in exons. Reads that were mapped to intergenic regions were generally located close to predicted genes and possibly located in uncharacterized untranslated regions (UTRs). Out of 85,000 single nucleotide polymorphisms (SNPs) with a minimum sequencing depth of eight reads from each of two subspecies-specific pools, only 55 showed high differentiation, confirming previous studies showing that most of the genetic variation is shared between the subspecies. Validation of a subset of the most highly differentiated SNPs using Sanger sequencing demonstrated that several of them also were differentiated between an independent set of individuals of each subspecies. These SNPs were clustered in two chromosome regions that are likely to be influenced by divergent selection between the subspecies and that could potentially be associated with adaptations to their different migratory strategies.ConclusionsOur study represents the first large-scale sequencing analysis aiming at detecting genes underlying migratory phenotypes in birds and provides new candidates for genes potentially involved in migration.

Avian transcriptomics: opportunities and challenges

“…One experimental difficulty is to obtain non-degraded RNA from wild birds (see "Preservation methods"). By comparing the genetic diversity of the transcriptomes of two differentially migrating subspecies of the Willow Warbler Phylloscopus trochilus Lundberg et al (2013) confirmed results from previous studies that showed that the majority of the genetic variation is shared between the subspecies. The authors, however, also found a small set of SNPs that was differentiated between the subspecies.…”

“…The authors, however, also found a small set of SNPs that was differentiated between the subspecies. These SNPs clustered on two chromosome regions, and the authors suggest that these regions might be influenced by divergent selection associated with the subspecies' migration strategies (Lundberg et al 2013). These results provide a starting point for further research to better understand the importance of these genome regions for bird migration.…”

“…SNPs are abundant in the genome and can be found especially in non-coding but also in coding regions, and are hence valuable markers for many types of research questions or to see whether genetic variants are associated with a certain trait or disease. SNPs have been discovered using transcriptomics in many avian species (Balakrishnan et al 2013;Ekblom and Wang 2017;Ekblom et al 2014;Hagen et al 2013;Kaiser et al 2017;Lundberg et al 2013;Ramstad et al 2016;Santure et al 2011;Srivastava 2011;Srivastava et al 2012;Vijayakumar et al 2014;Zhang et al 2014b) (Box 3). Whole body transcriptomics was used to find candidate loci explaining the divergence between two subspecies of songbirds with several phenotypically different characteristics inhabiting either the mainland or islands of Alaska (Srivastava 2011).…”

Disruptive selection without genome‐wide evolution across a migratory divide

“…; Lundberg et al . ). When populations differing in migratory behaviour come into secondary contact, hybrid zones with mixed and intermediate migratory phenotypes can form (Helbig ; Delmore & Irwin ).…”

Weak geographical structure in sperm morphology across the range of two willow warbler Phylloscopus trochilus subspecies in Scandinavia

“…On the other hand, there seems to be a lack of genetic diff erentiation at neutral loci (Bensch et al 1999(Bensch et al , 2002(Bensch et al , 2009, which might indicate a rather recent divergence and/or high levels of gene fl ow between the two subspecies. Th is was further elaborated by Lundberg et al (2013), who found that out of 85 000 SNPs obtained from brain-derived cDNA, only 55 were highly diff erentiated between trochilus and acredula , and they clustered in two chromosome regions.…”