Bioinformatics of 18 Fungal Genomes

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1 Bioinformatics of 18 Fungal Genomes Dave Ussery Comparative Microbial Genomics Workshop Pathumthani, Thailand 9 March, 2005

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4 Outline Comparison of 18 Fungal Genomes Introduction & disclaimer DNA (genome) comparisons RNA (transcriptome) comparisons Protein (proteome) comparisons

5 Organism Tax # Lengt %AT trna rrna CDS ref. Ashbya gossypii As 7 48% ,718 Dietrich et al (2004) Aspergillus nidulans As 8 30,095,91 50% ,342 FGI (2003) Candida albicans As 8 14,851,00 67% ,419 Odds et al (2004) Encephalitozoon cuniculi Mic 11 53% ,996 Katinka et al (2001) Gibberella zeae As 10 35,689,39 56% ,379 FGI (2003) Kluyveromyces waltii As 8 10,613,22 56% ,230 Kellis et al (2004) 5 Magnaporthe grisea As 7 38,760,32 48% ,856 FGI (2003) Neurospora crassa As 7 38,044,34 50% ,897 Katherine et al (2004) P h a n e r o c h a e t e Ba 10 29,965,58 49% 200? 11,777 Martinez et al (2004) Saccharomyces bayanus As 16 11,931,21 60% ,970 Kellis et al (2004) Saccharomyces castellii As ~9 11,354,15 63% ,681 Cliften et al (2003) Saccharomyces cerevisiae As 16 12,457,86 62% ,844 Goffeau et al (1997) Saccharomyces kluyveri As 8 11,028,82 58% ,975 Cliften et al (2003) Saccharomyces kudriavzevii As 16 11,178,41 60% ,788 Cliften et al (2003) Saccharomyces mikatae As 16 10,825,58 62% ,525 Kellis et al (2004) Schizosaccharomyces pombe As 3 12,515,11 64% ,043 Wood et al (2004) Trichoderma ressei As 20 34,485,77 46% 210? 8,620 JGI (2003) Ustilago maydis Ba 16 19,459,79 59% ,370 FGI (2003) Phyla: As = Ascomycota, Ba = Basidomycota and Mi = Microsporidia Class: Sac = Saccharomycotina, Schi = Schizosaccharomycetes, and Pez = Pezizomycotina

6 Neurospora crassa Trichoderma ressei Gebberella zeae Ashbya gossypii Kluyveromyces waltii 1.0 S.kluyveri Magnaporthe grisae Aspergillus nidulans Phanerochaete chrysosporium Schizosaccharomyces pombe Candida albicans Ustilago maydis 1 S.cerevisiae 1 1 S.castellii 1 1 S.paradoxus S.bayanus S.mikatae S.kudriavzevii Topics in Current Genetics, chapter 12 in Comparative Genomics Using Fungi as Models volume, to be published in 2005.

7 A) B) C) D) E) F) G) H) Schizosaccharomyces pombe strain 972, chromosome I SPAC23A1.07 0M 0.5M 1M 1.5M 2M 2.5M 3M 3.5M 4M 4.5M 5M 5.5M A) Intrinsic Curvature B) Stacking Energy dev dev 5,570,797 bp C) Position Preference dev D) Annotations: CDS + CDS - rrna trna E) Global Direct Repeats F) Global Inverted Repeats fix fix G) GC Skew H) Percent AT Resolution: 2229 fix fix Center for Biological Sequence Analysis DNA Conformation and Transcription, chapt14, (edited by Takashi Ohyama, 2004). GENOME ATLAS

8 Range: A) B) C) D) E) F) G) H) SPAC23A1.07 < cmk2 SPAC23A1.07 > < rpl34 A1.09 > ef1-b > 4052k k 4053k k 4054k k 4055k k 4056k k 4057 A) Intrinsic Curvature B) Stacking Energy Schizosaccharomyces pombe strain 972, chromosome I dev dev C) Position Preference dev 5,570,797 bp D) Annotations: CDS + CDS - rrna trna E) Global Direct Repeats F) Global Inverted Repeats fix fix G) GC Skew H) Percent AT Resolution: 2 fix fix Center for Biological Sequence Analysis DNA Conformation and Transcription, chapt14, (edited by Takashi Ohyama, 2004). GENOME ATLAS

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10 4!(,10-!"$#!"$% "$" "$% "$# Agossypii_ATCC10895_1: Structural Profile 56.,1+)-+) 71(')'1+.70-/-0-+,- 8)*,9'+:.;+-0:< " #""!"" &'()*+,-./012.)0*+(3*)'1+.()*0)

11 Z-score Z-score % coding, 73% AT 793,224 bp Mesoplasma florum stain L1 (Main) % coding, 49% AT 5,064,019 bp Distance from translation start Erwinia carotovora stain SCRI1043 (Main) AT content Position Preference Stacking Energy Intrinsic Curvature DNAase sensitivity AT content Position Preference Stacking Energy Intrinsic Curvature DNAase sensitivity Z-score Z-score % coding, 65% AT 5,237,682 bp % coding, 51% AT 2,303,261 bp Bacillus thuringiensis stain (Main) Distance from translation start Yarrowia lipolytica stain CLIB99 (1) AT content Position Preference Stacking Energy Intrinsic Curvature DNAase sensitivity AT content Position Preference Stacking Energy Intrinsic Curvature DNAase sensitivity Distance from translation start Distance from translation start Microbiology, 150: , (2004).

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13 CGG GAG GAC CGC GAU CCG CGU GUU GAA CCC GUA CGA GUG GUC CCU CUG CCA GCA GCC GCU CUC GCG CUU Codon Usage Agossypii_ATCC10895_1 GGA CUA CAG GGU GGC CAC GGG CAU AAA CAA AAU UGG AAC UGC UGU AAG AUA UGA AUU UCG AUC UCC UCU ACA UCA AUG ACU ACC AGA UUA UUU UUC UUG AGU ACG UAA AGC UAU UAC AGG UAG Frequency

14 3:U 3:C 3:A 3:G Position Bias Agossypii_ATCC10895_1 1:A 1:U 1:C 2:A 1:G Frequency 2:G 2:U 2:C

15 N E D Q R S Amino Acid Usage Agossypii_ATCC10895_1 T A V L I H G F P Frequency K W M C Y

16 N E D Q R S Amino Acid Usage Scerevisiae_S288C-AB972_1 T A V L I H G F P Frequency K W M C Y

17 Topics in Current Genetics, chapter 12 in Comparative Genomics Using Fungi as Models, to be published in 2005.

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20 Summary 1. Comparison of genes and rrna trees are in general agreement of the relationship between Fungal genomes. 2. Taxanomic groups exhibit specific patterns of codon and amino acid usage.

21 Comparative Microbial Genomics group Phatthanaphong Tom Wanchanthuek, M.Sci. student, comparison of 18 Fungal genomes Dave Ussery, group leader Anne Petersen, Ph.D., post-doctoral researcher, E. coli Tim Binnewies, Ph.D. student, bact. virulence Hanni Willenbrock, Ph.D. student, meta-analysis Peter Hallin, programmer and M.Sci. student, Campy Heng Wu, M.Sci. student, promoters Natascha Marteniz, M.Sci. student, highly exp. genes