Downloads for data in this track are available:
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.
Organism Species Release date UCSC/WormBase
versionalignment type C. elegans Caenorhabditis elegans Aug. 2014 ce11/WBcel235/GCA_000002985.3 reference species C. brenneri Caenorhabditis brenneri Nov. 2010 caePb3/WS227_C. brenneri 6.0.1b MAF Net C. remanei Caenorhabditis remanei Jul. 2007 caeRem4/WS220 MAF Net C. briggsae Caenorhabditis briggsae Apr. 2011 cb4/WS225 MAF Net C. japonica Caenorhabditis japonica Aug. 2010 caeJap4/WS227_WUSTL 7.0.1/GCA_000147155.1 MAF Net C. tropicalis Caenorhabditis tropicalis Nov. 2010 caeSp111/WS226_WUSTL 3.0.1 MAF Net C. angaria Caenorhabditis angaria Apr. 2012 caeAng2/WS232/ps1010rel8 MAF Net C. sp. 5 ju800 Caenorhabditis sp5 ju800 Jan. 2012 caeSp51/WS230_Caenorhabditis_sp_5-JU800-1.0 MAF Net H. bacteriophora/m31e Heterorhabditis bacteriophora Aug. 2011 hetBac1/WS229_H. bacteriophora 7.0/GCA_000223415.1 MAF Net Threadworm Strongyloides ratti Sep. 2014 strRat2/S. ratti ED321/GCA_001040885.1 MAF Net Microworm Panagrellus redivivus Feb. 2013 panRed1/WS240_Pred3/GCA_000341325.1 MAF Net A. ceylanicum Ancylostoma ceylanicum Mar. 2014 ancCey1/WS243_Acey_2013.11.30.genDNA/GCA_000688135.1 MAF Net N. americanus Necator americanus Dec. 2013 necAme1/WS242_N_americanus_v1/GCA_000507365.1 MAF Net Barber pole worm Haemonchus contortus Jul. 2013 haeCon2/WS239_Haemonchus_contortus_MHco3-2.0 MAF Net Pig roundworm Ascaris suum Sep. 2012 ascSuu1/GCA_000298755.1 MAF Net P. exspectatus Pristionchus exspectatus Mar. 2014 priExs1/WS243_P_exspectatus_v1 MAF Net P. pacificus Pristionchus pacificus Aug. 2014 priPac3/WS221_P_pacificus-v2 MAF Net M. hapla Meloidogyne hapla Sep. 2008 melHap1/WS210_M. hapla VW9 MAF Net M. incognita Meloidogyne incognita Feb. 2008 melInc2/WS245_M. incognita PRJEA28837 MAF Net Pine wood nematode Bursaphelenchus xylophilus Nov. 2011 burXyl1/WS229_B. xylophilus Ka4C1 MAF Net Dog heartworm Dirofilaria immitis Sep. 2013 dirImm1/WS240_D. immitis v2.2 MAF Net Eye worm Loa loa Jul. 2012 loaLoa1/WS235_L_loa_Cameroon_isolate/GCA_000183805.3 MAF Net O. volvulus Onchocerca volvulus Nov. 2013 oncVol1/WS241_O_volvulus_Cameroon_v3/GCA_000499405.1 MAF Net Filarial worm Brugia malayi May. 2014 bruMal2/WS244_B_malayi-3.1 MAF Net Trichinella Trichinella spiralis Jan. 2011 triSpi1/WS225_Trichinella_spiralis-3.7.1/GCA_000181795.2 MAF Net Whipworm Trichuris suis Jul. 2014 triSui1/WS243_T. suis DCEP-RM93M male/GCA_000701005.1 MAF Net
Table 1. Genome assemblies included in the 26-way Conservation track.
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 $organism 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.
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:
Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:
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 $organism sequence at those alignment positions relative to the longest non-$organism 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:
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.
Table 2. Gene tracks used for codon translation.
Gene Track Species 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 annotations Threadworm/S. ratti no annotation Pig roundworm/A. suum
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.
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.
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.
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).
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".
This track was created using the following programs:
The phylogenetic tree is based on Kiontke et al. (2007).
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