Each year, migratory birds undergo behavioral changes associated with reproduction (Costa et al., 2021; Kimmitt, 2020; Lifjeld et al., 2022; Sharma et al., 2020; Yoshimura, 2013), and wintering, pre-migration and migration (Sharma & Kumar, 2019; Sharma, Singh, Malik, et al., 2018; Trivedi, Kumar, Rani, & Kumar, 2014), which are accompanied by molecular (Frias-Soler, Kelsey, Villarín Pildaín, Wink, & Bairlein, 2022; Frias-Soler, Pildaín, Pârâu, Wink, & Bairlein, 2020), cellular (Carvalho-Paulo et al., 2017; de Almeida Miranda et al., 2021; DeMoranville et al., 2019; Henrique et al., 2020), and systemic changes (Catry, Granadeiro, Gutiérrez, & Correia, 2022; Elowe & Gerson, 2022; Guglielmo, 2018; Schmaljohann, Eikenaar, & Sapir, 2022). Indeed, to promote adaptive responses for spring and autumnal migrations, migrating birds change between two life story states (LHS) (Malik, Singh, Rani, & Kumar, 2014) with contrasting seasonal phenotypic profiles emerging before and after breeding, respectively (Trivedi et al., 2014). These states are connected to significant brain molecular changes including differential hypothalamic gene expressions leading to distinct regulatory strategies at the transcriptional level in the autumn and in the spring (Sharma et al., 2020; Sharma, Singh, Das, & Kumar, 2018). For example in the Black-headed Bunting songbird, (Emberiza melanocephala) after photoperiodical induced seasonal LHS, it has been described contrasting differences in the activity-rest pattern, body fattening and weight gain, testis size, heart and intestine weights, blood glucose and triglyceride levels between spring premigratory and post-migratory phenotypes (Trivedi et al., 2014).
Spring migration requires preparation for prolonged migratory flights by fuelling at wintering sites, when fat accumulation, metabolic enzymatic changes, and lipogenesis in the liver with subsequent transport to skeletal muscle indicate readiness for departure (Sharma et al., 2021).
Low latitude climate zones around the equator are chosen for wintering by many species of shorebirds to escape harsh northern winter weather and lack of food. This tropical region remains stable between years, is a rich food resource area, and show warmer temperatures with little variation in the annual range, enabling migrant birds to prepare for (in spring) and recover from (in fall) long migratory flights. (Albert et al., 2020; Gratto-Trevor et al., 2012; PW Hicklin, 1987; Peter Hicklin & Gratto-Trevor, 2010). Because the environment on winter grounds is annually stable, endogenous rhythms imposed by internal clocks in association with weather at the wintering and stopover grounds, temperature rise and more favorable wind conditions, may determine the individual’s timing of vernal migration (Gwinner, 1996; Haest, Hüppop, & Bairlein, 2018, 2020; Horton et al., 2019; Hüppop & Hüppop, 2003; Marra, Francis, Mulvihill, & Moore, 2005).
The semipalmated sandpiper C. pusilla, performs a remarkable five to six days nonstop flight across the Atlantic Ocean from James Bay (Ontario, Canada) or from Bay of Fundy (between New Brunswick and Nova Scotia, Canada) to coastal South America, Caribbean and Central America, before moving on to his wintering area in Brazil (Brown, 2014; PW Hicklin, 1987). This species arrives on the coast of Venezuela (Mata, Marin, Rodriguez, Yurai Guerrero, & Cardillo, 2009) and in the Brazilian Coast (Larrazábal, AZEVEDO-JÚNIOR, & Pena, 2002) between the middle of August and early September and stay at resources-rich locations until April/May when birds start vernal migration (Mata et al., 2009). In these areas, these migratory shorebirds spend a large portion of the non-breeding season (Linhart et al., 2022), where they exchange feathers, increase body mass (Fedrizzi, Azevedo Júnior, & Larrazábal, 2004) and decreased corticosterone levels (Mata et al., 2009) maximizing fitness in preparation for the next long flight of spring migration.
There is not a single report related to brain molecular changes associated with the wintering period following the long uninterrupted migratory flight across the Atlantic Ocean (in fall) or preparation for the multiple stopover migratory flight for breeding (in spring) in this species. Similarly, brain transcriptome before and after reproduction in this species remain to be investigated. Because the ribonucleic acids represent the genomic expression, linking the genotype to the phenotype (Buccitelli & Selbach, 2020), we compared two snapshots of transcripts in the brain of recently arrived and pre-migratory semipalmated sandpiper (Calidris pusilla) captured respectively at two-time windows of wintering period: August/September (fall) and April/May (spring). In the absence of a sequenced genome to guide the reconstruction process, the transcriptome was assembled De novo based on RNA-sequencing reads (RNA-Seq) and annotation (Raghavan, Kraft, Mesny, & Rigerte, 2022). Using RNA-Seq we searched for differential gene expression in the brain of this latitudinal migrant species, and the results were used to interpret the functional implications of the genomic expression (Wang, Gerstein, & Snyder, 2009).