COMPARATIVE ANALYSIS OF TELEOST FISHGENOMES REVEALS NOVEL PATTERNS OF INTRON SIZE DISTRIBUTION ...
OVERVIEW• Introduction• Research• Results• Summary• The Future Photo by Jer Thorp (www.blprnt.com)
INTRODUCTION• Data• Laborious• Single locus investigations• Technology improvements• Compare whole genomes• Pipelines• Int...
INTRODUCTION• Comparative genomics• 1000 genomes• Genome architecture• Evolution• Phylogeny• Orthology• Why?
RESEARCH• Introns Danio rerio• Teleost Fish Gasterosteus ...
Gasterosteus Takifugu Tetraodon Danio rerio Oryzias latipes ...
Gasterosteus Oryzias Takifugu Tetraodon Danio rerio aculeatus lati...
Gasterosteus Oryzias Takifugu Tetraodon Danio rerio aculeatus ...
Gasterosteus Oryzias Takifugu Tetraodon Danio rerio aculeatus...
SUMMARY• Software pipeline• Introns test case• Familiar results• Danio rerio• Exciting subtle difference• Further investig...
THE FUTURE…• Test case• Introns• Comparative genomics• Decreasing costs• More published genomes• Increasing amounts of dat...
THANK YOU!ANY QUESTIONS?• Steve Moss• S.P.Moss@2007.hull.ac.uk• Twitter: @gawbul
Gasterosteus Oryzias Takifugu Tetraodon Danio rerio aculeatus...
Chen and Mayden, 2010
Comparative Analysis of Teleost Fish Genomes Reveals Novel Patterns of Intron Size Distribution
Comparative Analysis of Teleost Fish Genomes Reveals Novel Patterns of Intron Size Distribution
Comparative Analysis of Teleost Fish Genomes Reveals Novel Patterns of Intron Size Distribution
Comparative Analysis of Teleost Fish Genomes Reveals Novel Patterns of Intron Size Distribution
Comparative Analysis of Teleost Fish Genomes Reveals Novel Patterns of Intron Size Distribution
Comparative Analysis of Teleost Fish Genomes Reveals Novel Patterns of Intron Size Distribution
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Comparative Analysis of Teleost Fish Genomes Reveals Novel Patterns of Intron Size Distribution

My first conference presentation to the 44th Population Genetics Group meeting at The University of Hull.
Published on: Mar 4, 2016
Published in: Education      Technology      
Source: www.slideshare.net


Transcripts - Comparative Analysis of Teleost Fish Genomes Reveals Novel Patterns of Intron Size Distribution

  • 1. COMPARATIVE ANALYSIS OF TELEOST FISHGENOMES REVEALS NOVEL PATTERNS OF INTRON SIZE DISTRIBUTION Steve Moss PhD Student, Evolutionary Biology Group Dr Dave Lunt, Dr Domino Joyce and Dr Stuart Humphries
  • 2. OVERVIEW• Introduction• Research• Results• Summary• The Future Photo by Jer Thorp (www.blprnt.com)
  • 3. INTRODUCTION• Data• Laborious• Single locus investigations• Technology improvements• Compare whole genomes• Pipelines• Introns
  • 4. INTRODUCTION• Comparative genomics• 1000 genomes• Genome architecture• Evolution• Phylogeny• Orthology• Why?
  • 5. RESEARCH• Introns Danio rerio• Teleost Fish Gasterosteus aculeatus• EnsEMBL Oryzias• Size and Number latipes• First introns Takifugu rubripes• Ordinal position Tetraodon nigroviridis• Interesting patterns in distribution
  • 6. Gasterosteus Takifugu Tetraodon Danio rerio Oryzias latipes aculeatus rubripes nigroviridisGene number 28,509 22,456 20,422 19,388 20,562Intron number 195,273 198,500 184,946 186,317 187,991 Introns per 6.85 8.84 9.06 9.61 9.14 gene Total intron 515,220,234 151,334,388 219,607,334 107,109,300 90,258,622 length (bps)Mean length 15,941 6,981 9,463 5,505 5,123Median length 8,457 4,367 5,468 3,675 3,245Mode length 84 85 77 78 76
  • 7. Gasterosteus Oryzias Takifugu Tetraodon Danio rerio aculeatus latipes rubripes nigroviridisIntron number 195,273 198,500 184,946 186,317 187,991 Standard 180,390 169,939 156,438 160,374 155,002intron number Standard intron 92.38% 85.61% 84.59% 86.08% 82.45% percentage
  • 8. Gasterosteus Oryzias Takifugu Tetraodon Danio rerio aculeatus latipes rubripes nigroviridisRepeat element 523,465 81,087 81,780 47,247 59,001 numberRepeat element 36,355,102 3,866,576 4,321,148 2,546,951 2,727,306 lengthRepeat element 7.06% 2.55% 1.97% 2.38% 3.02% percentage
  • 9. Gasterosteus Oryzias Takifugu Tetraodon Danio rerio aculeatus latipes rubripes nigroviridisIntron number 195,273 198,500 184,946 186,317 187,991Intron length 515,220,234 151,334,388 219,607,334 107,109,300 90,258,622 GC content 35.55% 43.45% 39.41% 44.01% 45.38%Repeat bases 36,355,102 3,866,576 4,321,148 2,546,951 2,727,306Simple repeats 43.38% 60.25% 25.86% 71.56% 70.15% Low complexity 29.82% 26.92% 38.44% 21.01% 24.34% repeats Interspersed and Other 26.80% 12.83% 64.30% 7.43% 5.51% repeats
  • 10. SUMMARY• Software pipeline• Introns test case• Familiar results• Danio rerio• Exciting subtle difference• Further investigation required…
  • 11. THE FUTURE…• Test case• Introns• Comparative genomics• Decreasing costs• More published genomes• Increasing amounts of data• Advancing technologies• Software pipeline• Further evolutionary analyses
  • 12. THANK YOU!ANY QUESTIONS?• Steve Moss• S.P.Moss@2007.hull.ac.uk• Twitter: @gawbul
  • 13. Gasterosteus Oryzias Takifugu Tetraodon Danio rerio aculeatus latipes rubripes nigroviridisIntron number 195,273 198,500 184,946 186,317 187,991Intron length 515,220,234 151,334,388 219,607,334 107,109,300 90,258,622 GC content 35.55% 43.45% 39.41% 44.01% 45.38%Repeat length 36,355,102 3,866,576 4,321,148 2,546,951 2,727,306 SINEs 1,629,250 18,034 84,964 766 977 LINEs 1,044,210 219,064 244,435 98,599 17,848 LTRs 103,093 22,406 17,767 8,904 5,109DNA elements 6,727,879 199,588 1,128,935 68,312 111,074 Unclassified 480 183 214 168 282 Small RNA 251,282 38,210 66,562 13,118 15,908 Satellites 2,799 668 743 393 40Simple repeats 15,771,113 2,329,567 1,117,648 1,822,672 1,913,267 Low 10,841,712 1,040,957 1,661,147 535,107 663,798 complexity
  • 14. Chen and Mayden, 2010