Novel Lineage Specific Genes Expressed in Cattle Placenta: Discovery, Functional Annotation and Evolution
Kumar, Charu Gupta
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Permalink
https://hdl.handle.net/2142/83622
Description
Title
Novel Lineage Specific Genes Expressed in Cattle Placenta: Discovery, Functional Annotation and Evolution
Author(s)
Kumar, Charu Gupta
Issue Date
2008
Doctoral Committee Chair(s)
Lewin, Harris A.
Department of Study
Animal Sciences
Discipline
Animal Sciences
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biology, Virology
Language
eng
Abstract
To answer our original question as to the origin of these genes and whether they represent genes that have undergone lineage-specific changes, comparative genomics tools were used to generate phylogenetic profiles to determine the presence/absence of novel lineage-specific genes (LSGs) in various clades. The detailed analysis of gene sequence alignments allowed us to propose genetic mechanisms that may have resulted in the lineage-specificity of these genes. The approach relied on generating multi-species alignments of genomic regions spanning syntenic genes flanking the LSGs in 10 mammalian species. These anchored alignments along with the position of the LSG locus in cattle provided approximate coordinates of the LSG locus in other genomes, and allowed us to identify transcripts in the putative LSG locus in each genome using sensitive DNA sequence similarity search methods. The phylogenetic profiles of these LSGs suggest that many have evolved as a result of undergoing large SINE, LINE and LTR repeat insertions. The LSGs were shown to have undergone lineage-specific splice-site changes resulting in de novo formation of exons or exonization. Some of the LSGs may have originated by duplication from regions already diverging rapidly, such as regions containing pregnancy associated glycoproteins (PAGs), trophoblast Kunitz domain proteins (TKDPs) and sub-telomeric imprinted genes. The phylogenetic profiles of the LSGs indicate that a majority of the LSGs we identified as expressed in cattle placenta are present in cetartiodactyl species. On the basis of homology searches using current (April 2008) sequence databases, the LSGs were shown to be absent in non-cetartiodactyl clades. The LSGs may play important roles in the morphological and functional adaptations of the ruminant placenta.
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