title: Discovery and characterization of 91 novel transcripts expressed in cattle placenta.
abstract: BACKGROUND
  Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong Darwinian selection. Thus, the ruminant placenta may be a rich source of genes to explore adaptive evolutionary responses in mammals. The aim of our study was to identify novel transcripts expressed in ruminant placenta, and to characterize them with respect to their expression patterns, organization of coding sequences in the genome, and potential functions.
  
  
  RESULTS
  A combination of bioinformatics, comparative genomics and transcript profiling was used to identify and characterize 91 novel transcripts (NTs) represented in a cattle placenta cDNA library. These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence. Proteins longer than 100 aa were predicted for 29 NTs, and 21 are candidate non-coding RNAs. Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome. The authenticity of the NTs was confirmed by their alignment to cattle genome sequence, 42 of which showed evidence of mRNA splicing. Analysis of the genomic context where NT genes reside revealed 61 to be in intergenic regions, whereas 30 are within introns of known genes. The genes encoding the NTs were found to be significantly associated with subtelomeric regions.
  
  
  CONCLUSIONS
  The 91 lineage-specific transcripts are a useful resource for studying adaptive evolutionary responses of the ruminant placenta. The presence of so many genes encoding NTs in cattle but not primates or rodents suggests that gene loss and gain are important mechanisms of genome evolution in mammals. Furthermore, the clustering of NT genes within subtelomeric regions suggests that such regions are highly dynamic and may foster the birth of novel genes. The sequencing of additional vertebrate genomes with defined phylogenetic relationships will permit the search for lineage-specific genes to take on a more evolutionary context that is required to understand their origins and functions.
authors.affiliation: Laboratory of Mammalian Genome Biology, Department of Animal Sciences, University of Illinois at Urbana-Champaign, 210 Edward R. Madigan Laboratory, Urbana, IL 61801, USA. cgkumar@uiuc.edu <cgkumar@uiuc.edu>
authors.forename: Charu G
authors.initials: CG
authors.lastname: Kumar
authors.forename: Joshua H
authors.initials: JH
authors.lastname: Larson
authors.forename: Mark R
authors.initials: MR
authors.lastname: Band
authors.forename: Harris A
authors.initials: HA
authors.lastname: Lewin
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D002417:Cattle / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D005260:Female; D020869:Gene Expression Profiling; D015723:Gene Library; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics; D010920:Placenta / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D017422:Sequence Analysis, DNA
chemical_list: D012333:RNA, Messenger