Chapter 3 : Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era

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In light of the age of genomics, a compilation of small-subunit rRNA-encoding genes (16S rRNA genes) from is provided, with a phylogeny estimated from a subset of the sequences that spans the diversity of . Robust phylogeny estimation based on whole-genome sequences supports the close relationship of with another lineage of facultative intracellular bacteria, . The first genome sequence from the also reveals reductive genome evolution, with a genome size of 1.3 Mb and 1,195 predicted open reading frames (ORFs). Significant reclassification of the species within the was proposed based on data. Subsequent reevaluation of the trace file archives determined that the sequences discovered in were an artifact; however, 2,291 novel Wolbachia sequences were found in another fly genome, Drosophila willistoni. This work underscores the utility of eukaryotic genomes for discovering Rickettsiales endosymbionts and potentially assembling partial to complete bacterial genomes from the eukaryotic reads. A robust phylogeny based on whole-genome sequences supports the current taxonomic delineations within the and , with monophyly of each of the six genera strongly supported. The differences between RefSeq and Pathosystems Resource Integration Center (PATRIC) annotation undoubtedly result in discrepancies in protein family clustering between this work and previous studies. Two mitochondrial small-subunit rRNA gene sequences were included in the phylogeny estimation, and this lineage branched after the Holosporaceae, but basal to the derived Rickettsiales. The diversity of the highlighted in this chapter presents an exciting challenge for rickettsiology.

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 1

Compilation of genome statistics for 46 taxa. Taxon codes are described in Fig. 2 , with circles defining the monophyly of the major lineages: S, SAR11 clade; O, ; R, ; N, ; W, ; E, ; A, . Statistics for the outgroup taxa are not provided. Tree is a cladogram representation of the phylogram shown in Fig. 2 . RefSeq data were taken from GenBank, with statistics from PATRIC provided based on the RAST automated annotation technology ( ). Pl, plasmid; HP, hypothetical protein; FA, functional annotation. doi:10.1128/9781555817336.ch3.f1

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 2

Whole-genome-based phylogeny estimation for 46 taxa. Taxon codes used in Fig. 1 are shown in parentheses after each organism name. The following pipeline was implemented to estimate phylogeny. BLAT (refined BLAST algorithm) ( ) searches were performed to identify similar protein sequences between all genomes, including the two outgroup taxa. To predict initial homologous protein sets, MCL ( ) was used to cluster BLAT results, with subsequent refinement of these sets using in-house hidden Markov models ( ). These protein families were then filtered to include only those with membership in >80% of the analyzed genomes (39 or more taxa included per protein family). Multiple sequence alignment of each protein family was performed using MUSCLE (default parameters) ( ), with masking of regions of poor alignment (length heterogeneous regions) done using Gblocks (default parameters) ( ). All modified alignments were then concatenated into one dataset. Tree building was performed using FastTree ( ). Support for generated lineages was estimated using a modified bootstrapping procedure, with 100 pseudoreplications sampling only half of the aligned protein sets per replication. (Note: Standard bootstrapping tends to produce inflated support values for very large alignments.) All branches in the illustrated tree were supported by 100%. Local refinements to tree topology were attempted in instances where highly supported nodes have subnodes with low support. This refinement is executed by running the entire pipeline on only those genomes represented by the node being refined (with additional sister taxa for rooting purposes). The refined subtree was then spliced back into the full tree. More information pertaining to this phylogeny pipeline is available at PATRIC. doi:10.1128/9781555817336.ch3.f2

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 3a

Genus-level alignments of complete genome sequences. (A) Sixteen genomes: Br, RML369-C; Bo, OSU 85-389; Ca, McKiel; Ty, Wilmington; Pr, Madrid E; P2, Rp22; Fe, URRWXCal2; Ak, Hartford; Is, REIS; Ma, MTU5; Pe, Rustic; Ri, Sheila Smith; Rw, Iowa; Co, Malish 7; Si, 246; Af, ESF-5. (B) Two genomes: Bg, Boryong; Ik, Ikeda. (C) Two genomes: Rs, Illinois; Se, Miyayama. (D) Four genomes: Bm, endosymbiont strain TRS of ; Me, symbiont of . ; Wr, endosymbiont sp. Ri; Qp, symbiont of Pel. (E) Five genomes: Cj, Jake; Ha, Arkansas; Re, Welgevonden (Erwe); Ro, Welgevonden (Erum); Rg, Gardel. (F) Four genomes: Ce, Israel; Mf, Florida; Ms, St. Maries; Ph, HZ. Complete genome sequences were downloaded from PATRIC ( ). Alignments constructed with MAUVE (progressive) v. 2.3.1 ( ). Numbers above each alignment depict genome coordinates in Mb. doi:10.1128/9781555817336.ch3.f3

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 3b

Genus-level alignments of complete genome sequences. (A) Sixteen genomes: Br, RML369-C; Bo, OSU 85-389; Ca, McKiel; Ty, Wilmington; Pr, Madrid E; P2, Rp22; Fe, URRWXCal2; Ak, Hartford; Is, REIS; Ma, MTU5; Pe, Rustic; Ri, Sheila Smith; Rw, Iowa; Co, Malish 7; Si, 246; Af, ESF-5. (B) Two genomes: Bg, Boryong; Ik, Ikeda. (C) Two genomes: Rs, Illinois; Se, Miyayama. (D) Four genomes: Bm, endosymbiont strain TRS of ; Me, symbiont of . ; Wr, endosymbiont sp. Ri; Qp, symbiont of Pel. (E) Five genomes: Cj, Jake; Ha, Arkansas; Re, Welgevonden (Erwe); Ro, Welgevonden (Erum); Rg, Gardel. (F) Four genomes: Ce, Israel; Mf, Florida; Ms, St. Maries; Ph, HZ. Complete genome sequences were downloaded from PATRIC ( ). Alignments constructed with MAUVE (progressive) v. 2.3.1 ( ). Numbers above each alignment depict genome coordinates in Mb. doi:10.1128/9781555817336.ch3.f3

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 4

Comparative analysis of select genome sequences. (A) Heat map representation of the distribution of proteins across 12 selected genomes. (Note: For six genera, the two most divergent and complete genomes were selected.) O, genomes: Bg, Boryong; Ik, Ikeda. R, genomes: Br, RML369-C; Ty, Wilmington. N, genomes: Rs, Illinois; Se, Miyayama. W, genomes: Bm, endosymbiont strain TRS of ; Wr, endosymbiont sp. Ri. A, genomes: Ms, St. Maries; Ph, HZ. E, genomes: Cj, Jake; Rg, Gardel. Black depicts no representative proteins per genome, with shading spectrum (light to dark gray) illustrating one to multiple genes per genome. Heat map constructed using the Protein Family Sorter tool at PATRIC ( ). Protein families are based on curated subsystems (FIGFams), which form the core component of the RAST automated annotation technology ( ). (B) Schema depicting the protein families shared at the order, family, and genus levels. Unique proteins (singletons) are also listed for each genome. (C) Graphic representation of the membership of 1,858 protein families and 4,289 singletons. doi:0.1128/9781555817336.ch3.f4

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 5

Genomic analysis of genes involved PG synthesis, transport, degradation, and recycling in . (A) PG pathway: brown, aminosugar metabolism; green, early-stage muropeptide synthesis; blue, lipid I and lipid II synthesis and translocation; red, anhydromuropeptide transpeptidation and transglycosylation; purple, PG degradation and turnover. Dashed pathway lines depict enzymes not encoded in any genome. (B) Distribution of PG-associated genes across select genomes. taxon codes are described in the Fig. 3 legend, except for Pu (“ Pelagibacter ubique” HTCC1062). Letters over cladogram: P, “ Pelagibacter,” , ; , ; , ; , ; , ; , . Open circles depict gene absence; closed circles, gene presence; numbers, multiple gene copies; S, split ORF. doi:10.1128/9781555817336.ch3.f5

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 6

Phylogeny estimation of small-subunit rRNA gene sequences from 47 diverse taxa and 2 mitochondria. Sequences were aligned using MUSCLE v3.6 ( ) with default parameters, and subsequently analyzed under maximum likelihood using RAxML ( ). A gamma model of rate heterogeneity was used with estimation of the proportion of invariable sites. Brach support is from 1,000 bootstrap pseudoreplications. The term “” is used as originally suggested ( ). (Note: PATRIC accession numbers are given for rRNA gene sequences retrieved from completed genomes; all other numbers are NCBI nucleotide accession numbers.) Taxon information is as follows, moving from the top to the bottom of the tree. “ Pelagibacter ubique” HTCC1002 (VBICanPel113578_r025); alphaproteobacterium strain HIMB114 (VBIAlpPro140191_r032); uncultured bacterium clone PRTBB8516 (HM798949); “ Captivus acidiprotistae” (AF533508); uncultured “ Odyssella sp.” clone 5-F (EU305601); bacterium strain Serialkilleuse_9403403 (HM138368); “ Trojanella thessalonicensis” L13 (AF069496); endosymbiont of sp. KA/E23 (EF140636); 221 (X71837); “ Caedibacter acanthamoebae” (AF132138); “ Paraholospora nucleivisitans” (EU652696); uncultured bacterium clone Oh3123O11E (EU137369); (X58198); , mitochondria (NC_001660); , mitochondria (AF007261); “ Cryptoprodotis polytropus” isolate PSM1 (FM201293); “ Occidentia massiliensis” ( bacterium strain Os18; GU937608); Ikeda (VBIOriTsu129072_r006); secondary symbiont of clone Hefei (HM156647); uncultured bacterium clone SHFG464 (FJ203077); bacterial symbiont of (AJ630204); uncultured bacterium clone EV221H2111601SAH71 (DQ223223); endosymbiont of (AB066351); endosymbiont of (FM955311); RML369-C (VBIRicBel102610_r012); REIS (VBIRicEnd40569_r031); uncultured alphaproteobacterium clone SM1B06 (AF445655); “ Xenohaliotis californiensis” (AF069062); (U12457); Illinois (VBINeoRis104330_r001); uncultured sp. isolate 184 (EU780451); endosymbiont strain TRS of (VBIWolEnd7741_r015); endosymbiont of (M85267); “ Neoanaplasma japonica” ( bacterium strain IS136; AB190771); Gardel (VBIEhrRum72196_r011); “ Neoehrlichia mikurensis” (uncultured “ Neoehrlichia sp.” clone 2; GQ501090); St. Maries (VBIAnaMar46146_r010); (AY125087); uncultured bacterium clone Hv(lakePohlsee)_25 (EF667921); “ Cyrtobacter comes” (FN552697); uncultured bacterium “Montezuma” (AF493952); “ Anadelfobacter veles” (FN552695); uncultured alphaproteobacterium clone MD3.55 (FJ425643); uncultured proteobacterium clone PEACE2006/237_P3 (EU394580); uncultured bacterium clone Ho_lab_2_5 (EF667892); endosymbiont of sp. UWC36 (AF069962); uncultured bacterium clone ID25L (EU555284); “ Midichloria mitochondrii” (AJ566640); “ Nicolleia massiliensis” France (DQ788562). doi:10.1128/9781555817336.ch3.f6

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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