Computational tools and Interoperability in Comparative ... - CBS

More documents

Recommendations

Info

Figure 1 Phylogenetic tree of the 16S rRNA gene extracted from 32 sequenced Vibrio genomes listed in Table 1. Environmental V. cholerae lacking the cholera enterotoxin genes are highlighted in bright green, whilst pathogenic V. cholerae genomes are in dark green. Further colouring was used for species for which two genomes are represented number of gene families (as defined above) now recognised in total was plotted for the pan-genome. The number of gene families with at least one representative gene in both genomes was plotted for the core genome. A running total is plotted for the pan-genome which increases as more genomes are added, whilst the core genome representing conserved gene families slowly decreases with the addition of more genomes. Whole-Genome BLAST Analysis and Construction of a BLAST Matrix The predicted genes of every genome (annotated or found by Easygene) were translated and every gene was compared, by BLASTP against every other genome and its own genome. In the latter case, the hit to self was ignored. The 50/50 rule for BLAST hits as described above was used. If these requirements were met, genes were combined in a gene family. The BLAST results were visualised in a BLAST matrix [2], which summarises the results of genomic pairwise comparisons and reports, both as percentage and as absolute numbers, the number of reciprocal BLAST hits as a fraction of the total number of gene families found in the two genomes. For easier visual inspection, the cells in the matrix are coloured darker as 56 88 65 55 86 the fraction of similarity increases. Hits identified within a genome are differently coloured. BLAST Atlas BLAST results were also visualised in a BLAST atlas, this time visualising, for all genes in the reference genome V cholerae N16961, their best hit in all other genomes, again with a threshold of 50% identity over at least 50% of the length of the query protein. The atlas displays the hits as they are located in the reference strain [14]. The BLAST scores obtained for each queried gene is plotted, so that conserved and variable regions are located with respect to the reference genome. Note that genes absent in the reference genome are not shown in the lanes of the query genomes. Results Vibrio sp. MED222 A A Vibrio sp. Ex25 Ribosomal RNA Analysis A phylogenetic tree based on the 16S rRNA gene extracted from the 32 analysed Vibrionaceae genomes is shown in Fig. 1. The 18 V. cholerae genomes build a tight subcluster, 45 T. Vesth et al.
Origins of V. cholerae 68 68 93 64 64 95 100 Vibrio, stabilome 0.20 0.15 0.10 0.05 0.00 Relative manhattan distance quite distanced from the other species. Above this in the figure, another subcluster comprising eight genomes representing at least six species is recognised, and within this cluster the two V. parahaemolyticus genes are not found on the same branch. A third cluster, a bit further removed, includes Aliivibrio fischeri and A. almonidica as well as V. splendidus and Vibrio species MED 222; the gene of Photobacterium profundum is the most distant. Pan-Genome Family Trees 99 99 100 48 100 100 98 98 67 Vibrio harveyi ATCC BAA1116 Vibrio parahaemolyticus RIMD2210633 Vibrio vulnificus CMCP6 Vibrio vulnificus YJ016 Vibrio sp MED222 Vibrio splendidus LGP32 Vibrio shilonii AK1 Vibrio sp Ex25 Vibrio parahaemolyticus 16 Vibrio campbellii AND4 Aliivibrio fischeri Aliivibrio fischeri Aliivibrio salmonicida LFI1238 Photobacterium profundum SS9 Vibrio cholerae 1587 Vibrio cholerae AM 19226 Vibrio cholerae MO10 Vibrio cholerae B33VCE Vibrio cholerae MJ1236 Vibrio cholerae RC9 Vibrio cholerae BX330286 Vibrio cholerae M662 Vibrio cholerae O395 TEDA Vibrio cholerae N16961 Vibrio cholerae O395 TIGR Vibrio cholerae 12129 Vibrio cholerae TMA21 Vibrio cholerae V52 Vibrio cholerae TM1107980 Vibrio cholerae 2740 80 Vibrio cholerae VL426 Vibrio cholerae MZO 2 Starting with a database containing the total set of all Vibrio gene families, a profile of matching gene families was constructed for each individual genome. This was stored as a matrix, containing a column for each gene families, and a row for each genome. The rows contain a 0 or 1 representing the presence or absence of the gene family. This matrix was weighted to emphasise either the genes found in most genomes (the “stabilome”) or in only a few genomes (the “mobilome”); from these weighted matrices, clustering of gene families yielded the resulting trees shown in Fig. 2. Shorter distances represent genomes with many gene families in common, and larger distances reflect genomes with fewer gene families in common. As expected, in both trees, genomes from the same species cluster together, whereby the depth of resolution within a species is considerably better than can be seen in the 16S rRNA tree in Fig. 1. Similarity between the unspeciated 100 80 66 37 54 100 98 67 46 Figure 2 Pan-genome family clustering of the 32 Vibrio genome sequences. The two plots represent weighted values for genes present in at least 90% of the genomes (stabilome) or genes found in only a 40 100 100 58 82 91 59 59 100 100 71 48 Vibrio, mobilome 59 80 100 100 100 0.20 0.15 0.10 0.05 0.00 100 100 100 Relative manhattan distance Vibrio isolate MED222 and V. splendidus is suggested by their close clustering; this is a connection also suggested by others [21]. Note that the unspeciated Vibrio isolate Ex25 and V. parahaemolyticus 2210633 cluster together in the mobilome tree, but are more distant in the stabilome. This implies that the genes shared between these two genomes are less common genes within the Vibrio genomes examined here. As already indicated by the 16S rRNA tree, the two V. parahaemolyticus isolates are quite dissimilar, and appear on separate branches. The Aliivibrio cluster is placed within Vibrio genomes in both the stabilome and the mobilome, as was the case for their 16S rRNA gene. P. profundum is not such an outlier as in the 16S rRNA tree, and in the stabilome. It is even positioned close to the Aliivibrio genomes. Zooming in at the genomes of V. cholerae, a division into two subclusters can be seen; these clusters correspond to environmental vs. clinical isolates (with the exception of V52 in the stabilome). Pan- and Core Genome Plot 99 77 100 67 82 100 90 90 100 89 89 Vibrio sp Ex25 Vibrio parahaemolyticus RIMD2210633 Vibrio campbellii AND4 Vibrio cholerae 1587 Vibrio cholerae AM 19226 Vibrio cholerae MZO 2 Vibrio cholerae 2740 80 Vibrio cholerae V52 Vibrio cholerae MO10 Vibrio cholerae O395 TIGR Vibrio cholerae BX330286 Vibrio cholerae RC9 Vibrio cholerae B33VCE Vibrio cholerae MJ1236 Vibrio cholerae N16961 Vibrio cholerae M662 Vibrio cholerae O395 TEDA Vibrio cholerae TMA21 Vibrio cholerae 12129 Vibrio cholerae TM1107980 Vibrio cholerae VL426 Vibrio parahaemolyticus 16 Aliivibrio fischeri Aliivibrio fischeri Aliivibrio salmonicida LFI1238 Vibrio vulnificus CMCP6 Vibrio vulnificus YJ016 Vibrio sp MED222 Vibrio splendidus LGP32 Vibrio harveyi ATCC BAA1116 Vibrio shilonii AK1 Photobacterium profundum SS9 BLAST results were analysed to construct a pan-genome, which is a hypothetical collection of all the gene families that are found in the investigated genomes [28]. The core genome was constructed from all gene families that were represented at least once in every genome. Thus, the gene families conserved in all genomes represent their core genome; adding the remaining gene families produces the 65 82 100 100 100 100 few (two to four) genomes (mobilome). The colours highlighting the species are the same as in Fig. 1
Page 1 and 2:
Peter Fischer Hallin | 2009 Peter F
Page 4:
Preface This Ph.D. thesis is writte
Page 7 and 8:
thesis, the work is just being publ
Page 9 and 10:
ved at blive publiceret i Standards
Page 11 and 12:
viii
Page 13 and 14:
Paper VI [Lagesen K, Hallin P] 1 ,
Page 15 and 16:
xii
Page 17 and 18:
3.3.3 Refining E. coli and Shigella
Page 19 and 20:
xvi
Page 21 and 22:
xviii 2.17 Pan- and core-genome plo
Page 24 and 25:
Chapter 1 Introduction Introduction
Page 26 and 27:
Chapter 2 Comparative Genomics 2.1
Page 28 and 29:
Comparative Genomics the publicly a
Page 30 and 31:
Comparative Genomics source CDS tot
Page 32 and 33:
Comparative Genomics 1 mysql -N -B
Page 34 and 35:
Listing 2.8: R code to generate a 2
Page 36 and 37:
1st U C A G U 2nd position C A G 3r
Page 38 and 39:
1st U C A G U 2nd position C A G 3r
Page 40 and 41:
Escherichia coli strain K-12, subst
Page 42 and 43:
Comparative Genomics
Page 44 and 45:
3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B.
Page 46 and 47:
Streptococcus Escherichia Bacillus
Page 48 and 49:
2.4 Summary Comparative Genomics Th
Page 50 and 51:
Comparative Genomics 2.5 Instant in
Page 52 and 53: ‘ReSourCe is he best online submi
Page 54 and 55: up to a total of 41 different E. co
Page 56 and 57: Fig. 2 Genes (or segments) from eac
Page 58 and 59: Fig. 5 BLASTatlas of Clostridium bo
Page 60 and 61: different applications, such as ide
Page 62 and 63: 1 Comparative Genomics 2.7 Paper II
Page 64 and 65: 166 literally millions of bacterial
Page 66 and 67: 168
Page 68 and 69: 170 resistance genes on mobile gene
Page 70 and 71: 172 involved in generating diversit
Page 72 and 73: 174 recipient DNA. A feature observ
Page 74 and 75: 176 Fig. 5 Genome length distributi
Page 76 and 77: 178
Page 78 and 79: 180 reasons why organisms remain un
Page 80 and 81: 182 A final problem has to do with
Page 82 and 83: 184 Middendorf B, Hochhut B, Leipol
Page 84 and 85: 1 Comparative Genomics 2.8 Paper II
Page 86 and 87: 2 O. N. Reva et al. Fig. 1. Genome
Page 88 and 89: 4 O. N. Reva et al. decrease of the
Page 90 and 91: 6 O. N. Reva et al. of which are kn
Page 92 and 93: 8 O. N. Reva et al. compiled into a
Page 94 and 95: 10 O. N. Reva et al. encoded by a c
Page 96 and 97: 12 O. N. Reva et al. systems and ef
Page 98 and 99: 1 2.9 Paper IV: The origins of Vibr
Page 100 and 101: phylogenies based on alternative ho
Page 104 and 105: 25000 20000 15000 10000 5000 0 Pan
Page 106 and 107: Gap F 2M 2.5M Gap E 875k 750k 625k
Page 108 and 109: Table 2 A selection of genes locate
Page 110 and 111: Open Access This article is distrib
Page 112 and 113: 1 Comparative Genomics 2.10 Paper V
Page 114 and 115: 4314 74 Tools Abstract: Of the plet
Page 116 and 117: 4316 74 Tools Size distribution of
Page 118 and 119: 4318 74 Tools Genome atlas Intrinsi
Page 120 and 121: 4320 74 Tools Genome atlas Intrinsi
Page 122 and 123: 4322 74 Tools for Comparison of Bac
Page 124 and 125: 4324 74 Tools for Comparison of Bac
Page 126 and 127: 4326 74 Tools information, as genet
Page 128 and 129: Chapter 3 rRNA operons and promoter
Page 130 and 131: tuB murI Fis III Fis II Fis I UP -3
Page 132 and 133: Bits 2.0 1.5 1.0 0.5 0.0 Bits 2.0 1
Page 134 and 135: RNA operons and promoter analysis O
Page 136 and 137: Bits 2.0 1.5 1.0 0.5 0.0 Bits T A T
Page 138 and 139: Code Meaning Example C Coding CCCCC
Page 140 and 141: RNA operons and promoter analysis 3
Page 142 and 143: P2 -10 -35 UP P1 -10 -35 UP FIS FIS
Page 144 and 145: 1 rRNA operons and promoter analysi
Page 146 and 147: Using HMMs also simplifies the use
Page 148 and 149: Information content Information con
Page 150 and 151: of the annotation. Some of the majo
Page 152 and 153:
where match states stop around 10 c
Page 154 and 155:
1 rRNA operons and promoter analysi
Page 156 and 157:
synthesis in flow cells to simultan
Page 158 and 159:
Read absence. A boolean where ‘on
Page 160 and 161:
Hallin, et al. Figure 4 | The dataf
Page 162 and 163:
Genome homology: Comparing multiple
Page 164 and 165:
ing platform-‐independent Java
Page 166 and 167:
34. Wang H, Noordewier M, Benham CJ
Page 168 and 169:
Chapter 4 Web Services and Interope
Page 170 and 171:
Web Services and Interoperability i
Page 172 and 173:
Page 174 and 175:
Page 176 and 177:
Page 178 and 179:
Chapter 5 Conclusion and perspectiv
Page 180 and 181:
Appendix A Appendix: Workshops, tea
Page 182 and 183:
Appendix B Appendix: Ph.D. study pl
Page 184 and 185:
Danmarks Tekniske Universitet AFI,
Page 186 and 187:
Danmarks Tekniske Universitet AFI,
Page 188 and 189:
Appendix C Appendix: Courses C.1 Gl
Page 190 and 191:
D.2 Sample output from queryGenomes
Page 192 and 193:
Appendix: Software 13 w a r n " $ o
Page 194 and 195:
Appendix: Software 109 m y ( $ m i
Page 196 and 197:
Appendix: Software 25 [ ] A l t e r
Page 198 and 199:
BIBLIOGRAPHY J. Rogers, P. F. Stadl
Page 200 and 201:
BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
Page 202 and 203:
BIBLIOGRAPHY Velicer, F.-J. Vorholt
show all

Computational tools and Interoperability in Comparative ... - CBS

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?