Conservation Track Settings
 
Nematode Multiz Alignment & Conservation (26 Species)   (All Comparative Genomics tracks)

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Multiz Alignments ▾       Basewise Conservation (phyloP) ▾       Element Conservation (phastCons) ▾       Conserved Elements ▾      
 
Multiz Alignments Configuration

Species selection:  + -

  Caenorhabditis  + -

c. sp. 5 ju800
c. brenneri
c. remanei
c. briggsae
c. tropicalis
c. japonica
c. angaria

  Others  + -

p. exspectatus
p. pacificus
pine wood nematode
a. ceylanicum
barber pole worm
n. americanus
microworm
h. bacteriophora/m31e
pig roundworm
threadworm
trichinella
whipworm
m. incognita
m. hapla
filarial worm
o. volvulus
eye worm
dog heartworm

Multiple alignment base-level:
Display bases identical to reference as dots
Display chains between alignments

Codon Translation:
Default species to establish reading frame:
No codon translation
Use default species reading frames for translation
Use reading frames for species if available, otherwise no translation
Use reading frames for species if available, otherwise use default species
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 26 nematodes Cons  26 nematodes Basewise Conservation by PhyloP   Schema 
 
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 26-way Cons  26 nematodes conservation by PhastCons   Schema 
 
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 26-way El  26 nematodes Conserved Elements   Schema 
 
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 Multiz Align  Multiz Alignments of 26 nematode assemblies   Schema 

Downloads for data in this track are available:

Description

This track shows multiple alignments of 26 nematode species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 26 species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.

PhastCons is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).

Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1.

Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data, and both were run with the same parameters.

UCSC has repeatmasked and aligned all genome assemblies, and provides all the sequences for download. For genome assemblies not available in the genome browser, there are alternative browser views in the preview genome browser. The species aligned for this track include 26 nematode genome sequences. Compared to the previous 6-nematode alignment (ce11), this track includes 4 new nematode genomes and 2 nematode genomes with updated sequence assemblies (Table 1). The four new species are the assemblies: H. contortus (haeCon1) at an unknown coverage, M. Hapla (melHap1) at 10.4X coverage, M. incognita (melInc1) at 5X coverage, and B. Malayi (bruMal1) at 9X coverage. The C. Japonica (22X, caeJap3) and P. pacificus (8.92X, priPac2) assemblies have been updated from those used in the previous 6-species nematode alignment.

OrganismSpeciesRelease dateUCSC/WormBase
version
alignment type
C. elegansCaenorhabditis elegans Aug. 2014ce11/WBcel235/GCA_000002985.3reference species
C. brenneriCaenorhabditis brenneri Nov. 2010caePb3/WS227_C. brenneri 6.0.1bMAF Net
C. remaneiCaenorhabditis remanei Jul. 2007caeRem4/WS220MAF Net
C. briggsaeCaenorhabditis briggsae Apr. 2011cb4/WS225MAF Net
C. japonicaCaenorhabditis japonica Aug. 2010caeJap4/WS227_WUSTL 7.0.1/GCA_000147155.1MAF Net
C. tropicalisCaenorhabditis tropicalis Nov. 2010caeSp111/WS226_WUSTL 3.0.1MAF Net
C. angariaCaenorhabditis angaria Apr. 2012caeAng2/WS232/ps1010rel8MAF Net
C. sp. 5 ju800Caenorhabditis sp5 ju800 Jan. 2012caeSp51/WS230_Caenorhabditis_sp_5-JU800-1.0MAF Net
H. bacteriophora/m31eHeterorhabditis bacteriophora Aug. 2011hetBac1/WS229_H. bacteriophora 7.0/GCA_000223415.1MAF Net
ThreadwormStrongyloides ratti Sep. 2014strRat2/S. ratti ED321/GCA_001040885.1MAF Net
MicrowormPanagrellus redivivus Feb. 2013panRed1/WS240_Pred3/GCA_000341325.1MAF Net
A. ceylanicumAncylostoma ceylanicum Mar. 2014ancCey1/WS243_Acey_2013.11.30.genDNA/GCA_000688135.1MAF Net
N. americanusNecator americanus Dec. 2013necAme1/WS242_N_americanus_v1/GCA_000507365.1MAF Net
Barber pole wormHaemonchus contortus Jul. 2013haeCon2/WS239_Haemonchus_contortus_MHco3-2.0MAF Net
Pig roundwormAscaris suum Sep. 2012ascSuu1/GCA_000298755.1MAF Net
P. exspectatusPristionchus exspectatus Mar. 2014priExs1/WS243_P_exspectatus_v1MAF Net
P. pacificusPristionchus pacificus Aug. 2014priPac3/WS221_P_pacificus-v2MAF Net
M. haplaMeloidogyne hapla Sep. 2008melHap1/WS210_M. hapla VW9MAF Net
M. incognitaMeloidogyne incognita Feb. 2008melInc2/WS245_M. incognita PRJEA28837MAF Net
Pine wood nematodeBursaphelenchus xylophilus Nov. 2011burXyl1/WS229_B. xylophilus Ka4C1MAF Net
Dog heartwormDirofilaria immitis Sep. 2013dirImm1/WS240_D. immitis v2.2MAF Net
Eye wormLoa loa Jul. 2012loaLoa1/WS235_L_loa_Cameroon_isolate/GCA_000183805.3MAF Net
O. volvulusOnchocerca volvulus Nov. 2013oncVol1/WS241_O_volvulus_Cameroon_v3/GCA_000499405.1MAF Net
Filarial wormBrugia malayi May. 2014bruMal2/WS244_B_malayi-3.1MAF Net
TrichinellaTrichinella spiralis Jan. 2011triSpi1/WS225_Trichinella_spiralis-3.7.1/GCA_000181795.2MAF Net
WhipwormTrichuris suis Jul. 2014triSui1/WS243_T. suis DCEP-RM93M male/GCA_000701005.1MAF Net

Table 1. Genome assemblies included in the 26-way Conservation track.

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Pairwise alignments of each species to the C. elegans genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.

Gap Annotation

The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:

  • Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the C. elegans genome or a lineage-specific deletion between the aligned blocks in the aligning species.
  • Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
  • Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Genomic Breaks

Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:

  • Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement.
  • Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the C. elegans genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence.

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the C. elegans sequence at those alignment positions relative to the longest non-C. elegans sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

  • No codon translation: The gene annotation is not used; the bases are displayed without translation.
  • Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment.
  • Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding.
  • Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation.

Gene TrackSpecies
WS245 Worm Base Genes A. ceylanicum, Barber pole worm/H. contortus, C. angaria, C. brenneri, C. briggsae, C. elegans, C. japonica, C. remanei, C. sp. 5 ju800, C. tropicalis, Dog heartworm/D. immitis, Eye worm/L. loa, Filarial worm/B. malayi, H. bacteriophora/m31e, Microworm/P. redivivus, M. hapla, M. incognita, N. americanus, O. volvulus, P. exspectatus, P. pacificus, Pine wood nematode/B. xylophilus, Trichinella/T. spiralis, Whipworm/T. suis
NCBI gene annotationsThreadworm/S. ratti
no annotationPig roundworm/A. suum
Table 2. Gene tracks used for codon translation.

Methods

Pairwise alignments with the C. elegans genome were generated for each species using lastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. All pairwise alignment and chaining parameters are the same for all pairs. See also: nematode 26-way alignment parameters. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.

The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.

Phylogenetic Tree Model

Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The nematode tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 26-way alignment (msa_view). The 4d sites were derived from the WormBase/Sanger gene set of C. elegans, filtered to select single-coverage long transcripts.

PhastCons Conservation

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005.

The phastCons parameters were tuned to produce approximately 70% conserved elements in the C. elegans WormBase/Sanger gene coding regions. This parameter set (expected-length=15, target-coverage=0.3, rho=0.3) was then used to generate the nematode and caenorhabditis conservation scoring.

PhyloP Conservation

The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).

Conserved Elements

The conserved elements were predicted by running phastCons with the --most-conserved (aka --viterbi) option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".

Credits

This track was created using the following programs:

  • Alignment tools: lastz (formerly blastz) and multiz by Bob Harris, Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
  • Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
  • Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
  • MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
  • Tree image generator: phyloPng by Galt Barber, UCSC
  • Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC

The phylogenetic tree is based on Kiontke et al. (2007).

References

Phylo-HMMs, phastCons, and phyloP:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396

Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Multiz:

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

Blastz:

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961

Phylogenetic Tree:

Kiontke K, Barrière A, Kolotuev I, Podbilewicz B, Sommer R, Fitch DH, Félix MA. Trends, stasis, and drift in the evolution of nematode vulva development. Curr Biol. 2007 Nov 20;17(22):1925-37. PMID: 18024125