Abstract
BackgroundThe diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage-specific genes. Previously, we identified 91 novel lineage-specific transcripts (LSTs) from a cow term-placenta cDNA library, which are excellent candidates for adaptive placental functions acquired by the ruminant lineage. The aim of the present study was to infer functions of previously uncharacterized lineage-specific genes (LSGs) using co-expression, promoter, pathway and network analysis.ResultsClusters of co-expressed genes preferentially expressed in liver, placenta and thymus were found using 49 previously uncharacterized LSTs as seeds. Over-represented composite transcription factor binding sites (TFBS) in promoters of clustered LSGs and known genes were then identified computationally. Functions were inferred for nine previously uncharacterized LSGs using co-expression analysis and pathway analysis tools. Our results predict that these LSGs may function in cell signaling, glycerophospholipid/fatty acid metabolism, protein trafficking, regulatory processes in the nucleus, and processes that initiate parturition and immune system development.ConclusionsThe placenta is a rich source of lineage-specific genes that function in the adaptive evolution of placental architecture and functions. We have shown that co-expression, promoter, and gene network analyses are useful methods to infer functions of LSGs with heretofore unknown functions. Our results indicate that many LSGs are involved in cellular recognition and developmental processes. Furthermore, they provide guidance for experimental approaches to validate the functions of LSGs and to study their evolution.
Highlights
The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution
Two large clusters were identified with average pairwise Pearson correlation r ≥ 0.75, and r ≥ 0.90 between any lineage-specific transcripts (LSTs) and transcripts encoded by known genes
As we and others have shown, the placenta is a rich source of expressed lineagespecific genes (LSGs) and rapidly diverging genes [2,3,57,58,59,60]
Summary
The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. We identified 91 novel lineage-specific transcripts (LSTs) from a cow term-placenta cDNA library, which are excellent candidates for adaptive placental functions acquired by the ruminant lineage. The diversity of placental architectures is thought to be the result of adaptive evolution arising from rapidly diverging and novel genes [2,3,4]. We previously identified and bioinformatically characterized novel transcripts in cattle using placenta as a source tissue [2]. These transcripts are lineage-specific (LSTs), and the genes that encode them have no detectable homology to genes outside of that lineage (LSGs). A complementary approach that would direct the genetic and biochemical characterization of LSGs and their products is functional inference using co-expression [11] and promoter analysis [12]
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