Limits...
Novel porcine repetitive elements.

Wiedmann RT, Nonneman DJ, Keele JW - BMC Genomics (2006)

Bottom Line: Once found, we characterized the prevalence of these repeats in other mammals.Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor.None of the repeat elements were found in primate, rodent or dog genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: USDA, ARS U, S, Meat Animal Research Center, Clay Center, NE, USA. wiedmann@email.marc.usda.gov

ABSTRACT

Background: Repetitive elements comprise approximately 45% of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression and by affecting genomic size, diversity and evolution. The ubiquity and increasingly understood importance of repetitive elements contribute to the need to identify and annotate them. We set out to identify previously uncharacterized repetitive DNA in the porcine genome. Once found, we characterized the prevalence of these repeats in other mammals.

Results: We discovered 27 repetitive elements in 220 BACs covering 1% of the porcine genome (Comparative Vertebrate Sequencing Initiative; CVSI). These repeats varied in length from 55 to 1059 nucleotides. To estimate copy numbers, we went to an independent source of data, the BAC-end sequences (Wellcome Trust Sanger Institute), covering approximately 15% of the porcine genome. Copy numbers in BAC-ends were less than one hundred for 6 repeat elements, between 100 and 1000 for 16 and between 1,000 and 10,000 for 5. Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor. None of the repeat elements were found in primate, rodent or dog genomes. We were unable to identify any of the replication machinery common to active transposable elements in these newly identified repeats.

Conclusion: The presence of both orthologous and non-orthologous sites indicates that some sites existed prior to speciation and some were generated later. The identification of low to moderate copy number repetitive DNA that is specific to artiodactyls will be critical in the assembly of livestock genomes and studies of comparative genomics.

Show MeSH

Related in: MedlinePlus

Distribution of BLAST hits to cow and pig DNA across selected MPREs. BLAST hits plotted across MPREs 12, 15, 17, 42, 51 and 58. Along the abscissa lies each MPRE sequence and stacked above are the corresponding hits to the cow genome in blue and to pig BAC-ends in red. The hits are ordered from the top down by length.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1713245&req=5

Figure 1: Distribution of BLAST hits to cow and pig DNA across selected MPREs. BLAST hits plotted across MPREs 12, 15, 17, 42, 51 and 58. Along the abscissa lies each MPRE sequence and stacked above are the corresponding hits to the cow genome in blue and to pig BAC-ends in red. The hits are ordered from the top down by length.

Mentions: Not surprisingly, the bovine hits tend to be shorter than the porcine hits because the MPREs were defined from pig sequence and as such would be expected to be more intact in porcine. What is interesting is that in both species the endpoints of the hits have a strong tendency to line up to particular spots in the MPRE, as shown in Figure 1 using MPRE12, 15, 17, 41, 51 and 58 as examples. Sometimes the common endpoints are the same in both species, sometimes not. This could be a result of the repeat elements being comprised of smaller repeat elements, not all of which have the same frequency of occurrence in either genome. The longer MPREs often had more than one sub-region with multiple extra hits. This, too, could be evidence of internal repeat structure.


Novel porcine repetitive elements.

Wiedmann RT, Nonneman DJ, Keele JW - BMC Genomics (2006)

Distribution of BLAST hits to cow and pig DNA across selected MPREs. BLAST hits plotted across MPREs 12, 15, 17, 42, 51 and 58. Along the abscissa lies each MPRE sequence and stacked above are the corresponding hits to the cow genome in blue and to pig BAC-ends in red. The hits are ordered from the top down by length.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1713245&req=5

Figure 1: Distribution of BLAST hits to cow and pig DNA across selected MPREs. BLAST hits plotted across MPREs 12, 15, 17, 42, 51 and 58. Along the abscissa lies each MPRE sequence and stacked above are the corresponding hits to the cow genome in blue and to pig BAC-ends in red. The hits are ordered from the top down by length.
Mentions: Not surprisingly, the bovine hits tend to be shorter than the porcine hits because the MPREs were defined from pig sequence and as such would be expected to be more intact in porcine. What is interesting is that in both species the endpoints of the hits have a strong tendency to line up to particular spots in the MPRE, as shown in Figure 1 using MPRE12, 15, 17, 41, 51 and 58 as examples. Sometimes the common endpoints are the same in both species, sometimes not. This could be a result of the repeat elements being comprised of smaller repeat elements, not all of which have the same frequency of occurrence in either genome. The longer MPREs often had more than one sub-region with multiple extra hits. This, too, could be evidence of internal repeat structure.

Bottom Line: Once found, we characterized the prevalence of these repeats in other mammals.Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor.None of the repeat elements were found in primate, rodent or dog genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: USDA, ARS U, S, Meat Animal Research Center, Clay Center, NE, USA. wiedmann@email.marc.usda.gov

ABSTRACT

Background: Repetitive elements comprise approximately 45% of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression and by affecting genomic size, diversity and evolution. The ubiquity and increasingly understood importance of repetitive elements contribute to the need to identify and annotate them. We set out to identify previously uncharacterized repetitive DNA in the porcine genome. Once found, we characterized the prevalence of these repeats in other mammals.

Results: We discovered 27 repetitive elements in 220 BACs covering 1% of the porcine genome (Comparative Vertebrate Sequencing Initiative; CVSI). These repeats varied in length from 55 to 1059 nucleotides. To estimate copy numbers, we went to an independent source of data, the BAC-end sequences (Wellcome Trust Sanger Institute), covering approximately 15% of the porcine genome. Copy numbers in BAC-ends were less than one hundred for 6 repeat elements, between 100 and 1000 for 16 and between 1,000 and 10,000 for 5. Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor. None of the repeat elements were found in primate, rodent or dog genomes. We were unable to identify any of the replication machinery common to active transposable elements in these newly identified repeats.

Conclusion: The presence of both orthologous and non-orthologous sites indicates that some sites existed prior to speciation and some were generated later. The identification of low to moderate copy number repetitive DNA that is specific to artiodactyls will be critical in the assembly of livestock genomes and studies of comparative genomics.

Show MeSH
Related in: MedlinePlus