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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.

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Repeat elements that flank the 3' end of MPRE61. The repeat content of 62 BAC-end sequences flanking the 3' end of MPRE61. The origin on the horizontal axis is the last position that matches the 3' end (minimum position within the repeat of 1000 out of the full 1059 bp length) of MPRE61. The 62 flanking sequences are ordered with the longest at the top and the shortest at the bottom. The horizontal position is the distance from the 3' end of the hit to MPRE61. Colored arrows are superimposed on the dotted outline of the flanking sequence to indicate the repeat elements that RepeatMasker found.
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Figure 5: Repeat elements that flank the 3' end of MPRE61. The repeat content of 62 BAC-end sequences flanking the 3' end of MPRE61. The origin on the horizontal axis is the last position that matches the 3' end (minimum position within the repeat of 1000 out of the full 1059 bp length) of MPRE61. The 62 flanking sequences are ordered with the longest at the top and the shortest at the bottom. The horizontal position is the distance from the 3' end of the hit to MPRE61. Colored arrows are superimposed on the dotted outline of the flanking sequence to indicate the repeat elements that RepeatMasker found.

Mentions: MPRE61 was further characterized by plotting BLAST hits of it to the 275,595 sequences in the trace archive of BAC-ends submitted by Sanger. These were plotted along with the repeat elements recognized by RepeatMasker. The most interesting observations included the fact that three times among the 140 hits a PRE1 was incorporated into MPRE61. PRE1 is a porcine specific SINE that is included in the RepeatMasker library. Several other examples existed of PRE1 next to a section of MPRE61, but the trace end occurred next to the PRE1, so that it may or may not have had the continuing section of MPRE61 on its other side. No other REs were found to be incorporated into MPRE61, suggesting that MPRE61 replicated relatively recently. Another interesting observation was that the density of REs on the 3' side of MPRE61 was much higher than on the 5' side. To take a closer look at this, we collected the trace sequence 3' of the 62 hits that ended near (within 60 bp of) the 3' end of MPRE61 (length of 1059 bp). This flanking sequence, ranging in length from 12 to 1368 nucleotides, was analyzed for repeat content and distance of that content from the end of MPRE61 (Figure 5). Running RepeatMasker on the entire collection (275,595 sequences) of Sanger BAC-ends shows that the number of SINE elements is 75% greater than the number of LINE elements (203,206 vs. 116,107). The LINEs tend to be longer than the SINEs, so the total percentage of sequence occupied by the LINEs is actually larger (13.29% vs. 10.29%). The most obvious feature of Figure 5 is that LINEs are significantly over represented on the 3 prime side of MPRE61, particularly in the region closest to the end of MPRE61. For the 22 LINEs that occur within 80 bp of the end of MPRE61, 15 are oriented on the opposite strand and 7 on the same strand. At this point, there is no way to know which strand of MPRE61 might be transcribed. We arbitrarily chose one of the strands and used it consistently. Because the LINEs have a particular internal structure, the 5' and 3' ends are well defined. So another way of looking at the result would be to say that the LINEs occur on the 5' end of MPRE61 (or rather, its reverse complement) with 15 on the same strand and 7 on the opposite strand. Either way, there is less strand conservation than would be expected if MPRE61 used LINEs as a vehicle for either replication or integration.


Novel porcine repetitive elements.

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

Repeat elements that flank the 3' end of MPRE61. The repeat content of 62 BAC-end sequences flanking the 3' end of MPRE61. The origin on the horizontal axis is the last position that matches the 3' end (minimum position within the repeat of 1000 out of the full 1059 bp length) of MPRE61. The 62 flanking sequences are ordered with the longest at the top and the shortest at the bottom. The horizontal position is the distance from the 3' end of the hit to MPRE61. Colored arrows are superimposed on the dotted outline of the flanking sequence to indicate the repeat elements that RepeatMasker found.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Repeat elements that flank the 3' end of MPRE61. The repeat content of 62 BAC-end sequences flanking the 3' end of MPRE61. The origin on the horizontal axis is the last position that matches the 3' end (minimum position within the repeat of 1000 out of the full 1059 bp length) of MPRE61. The 62 flanking sequences are ordered with the longest at the top and the shortest at the bottom. The horizontal position is the distance from the 3' end of the hit to MPRE61. Colored arrows are superimposed on the dotted outline of the flanking sequence to indicate the repeat elements that RepeatMasker found.
Mentions: MPRE61 was further characterized by plotting BLAST hits of it to the 275,595 sequences in the trace archive of BAC-ends submitted by Sanger. These were plotted along with the repeat elements recognized by RepeatMasker. The most interesting observations included the fact that three times among the 140 hits a PRE1 was incorporated into MPRE61. PRE1 is a porcine specific SINE that is included in the RepeatMasker library. Several other examples existed of PRE1 next to a section of MPRE61, but the trace end occurred next to the PRE1, so that it may or may not have had the continuing section of MPRE61 on its other side. No other REs were found to be incorporated into MPRE61, suggesting that MPRE61 replicated relatively recently. Another interesting observation was that the density of REs on the 3' side of MPRE61 was much higher than on the 5' side. To take a closer look at this, we collected the trace sequence 3' of the 62 hits that ended near (within 60 bp of) the 3' end of MPRE61 (length of 1059 bp). This flanking sequence, ranging in length from 12 to 1368 nucleotides, was analyzed for repeat content and distance of that content from the end of MPRE61 (Figure 5). Running RepeatMasker on the entire collection (275,595 sequences) of Sanger BAC-ends shows that the number of SINE elements is 75% greater than the number of LINE elements (203,206 vs. 116,107). The LINEs tend to be longer than the SINEs, so the total percentage of sequence occupied by the LINEs is actually larger (13.29% vs. 10.29%). The most obvious feature of Figure 5 is that LINEs are significantly over represented on the 3 prime side of MPRE61, particularly in the region closest to the end of MPRE61. For the 22 LINEs that occur within 80 bp of the end of MPRE61, 15 are oriented on the opposite strand and 7 on the same strand. At this point, there is no way to know which strand of MPRE61 might be transcribed. We arbitrarily chose one of the strands and used it consistently. Because the LINEs have a particular internal structure, the 5' and 3' ends are well defined. So another way of looking at the result would be to say that the LINEs occur on the 5' end of MPRE61 (or rather, its reverse complement) with 15 on the same strand and 7 on the opposite strand. Either way, there is less strand conservation than would be expected if MPRE61 used LINEs as a vehicle for either replication or integration.

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