Description
This track shows a multiple alignment of 447 mammalian genomes made with Cactus and constraint scores derived from it.
To build this track, the Zoonomia 241 alignment was used as a starting point, all primates and a few outdated
assemblies were removed and an alignment between 233 newly sequenced primates was added. See the Methods section below for details, and
also the publications by Kuderna et al. 2023 in the Reference section.
All alignments and operations on them were performed using the Cactus toolkit.
Data Access
Downloads for data in this track are available from the directory:
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 human 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. Missing sequence in any
assembly is highlighted in the track display by regions of yellow when zoomed
out and by Ns when displayed at base level. 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 human 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 human 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 human sequence at those
alignment positions relative to the longest non-human 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:
| Gene Track | Species |
| RefSeq Genes | Bos mutus, Canis lupus familiaris, Carlito syrichta, Cercocebus atys, Chinchilla lanigera, Colobus angolensis, Condylura cristata, Dipodomys ordii, Elephantulus edwardii, Eptesicus fuscus, Felis catus, Felis catus fca126, Fukomys damarensis, Homo sapiesn, Ictidomys tridecemlineatus, Macaca mulatta, Macaca nemestrina, Marmota marmota, Microtus ochrogaster, Miniopterus natalensis, Mus musculus, Mus pahari, Myotis brandtii, Myotis davidii, Myotis lucifugus, Odobenus rosmarus, Orcinus orca, Otolemur garnettii, Peromyscus maniculatus, Piliocolobus tephrosceles, Propithecus coquerelli, Pteropus alecto, Pteropus vampyrus, Rattus norvegicus, Rhinopithecus roxellana, Saimiri boliviensis, Sorex araneus, Sus scrofa, Theropithecus gelada, Tupaia chinensis |
| Ensembl Genes | Cavia aperea |
| Augustus Genes | Eidolon helvum, Pteronotus parnellii |
| no annotation | Acinonyx jubatus, Acomys cahirinus, Ailuropoda melanoleuca, Ailurus fulgens, Allactaga bullata, Allenopithecus nigroviridis, Allochrocebus lhoesti, Allochrocebus preussi, Allochrocebus solatus, Alouatta belzebul, Alouatta caraya, Alouatta discolor, Alouatta juara, Alouatta macconnelli, Alouatta nigerrima, Alouatta palliata, Alouatta puruensis, Alouatta seniculus, Ammotragus lervia, Anoura caudifer, Antilocapra americana, Aotus azarae, Aotus griseimembra, Aotus nancymaae, Aotus trivirgatus, Aotus vociferans, Aplodontia rufa, Arctocebus calabarensis, Artibeus jamaicensis, Ateles geoffroyi_a, Ateles geoffroyi_b, Ateles belzebuth, Ateles chamek, Ateles marginatus, Ateles paniscus, Avahi laniger, Avahi peyrierasi, Balaenoptera acutorostrata, Balaenoptera bonaerensis, Beatragus hunteri, Bison bison, Bos indicus, Bos taurus, Bubalus bubalis, Cacajao ayresi, Cacajao calvus, Cacajao hosomi, Cacajao melanocephalus, Callibella humilis, Callimico goeldii, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Camelus bactrianus, Camelus dromedarius, Camelus ferus, Canis lupus VD, Canis lupus dingo, Canis lupus orion, Capra aegagrus, Capra hircus, Capromys pilorides, Carollia perspicillata, Castor canadensis, Catagonus wagneri, Cavia porcellus, Cavia tschudii, Cebuella niveiventris, Cebuella pygmaea, Cebus albifrons, Cebus olivaceus, Cebus unicolor, Cephalopachus bancanus, Ceratotherium simum, Ceratotherium simum cottoni, Cercocebus chrysogaster, Cercocebus lunulatus, Cercocebus torquatus, Cercopithecus ascanius, Cercopithecus cephus, Cercopithecus diana, Cercopithecus hamlyni, Cercopithecus lowei, Cercopithecus albogularis, Cercopithecus mona, Cercopithecus neglectus, Cercopithecus nictitans, Cercopithecus petaurista, Cercopithecus pogonias, Cercopithecus roloway, Chaetophractus vellerosus, Cheirogaleus major, Cheirogaleus medius, Cheracebus lucifer, Cheracebus lugens, Cheracebus regulus, Cheracebus torquatus, Chiropotes albinasus, Chiropotes israelita, Chiropotes sagulatus, Chlorocebus aethiops, Chlorocebus pygerythrus, Chlorocebus sabaeus, Choloepus didactylus, Choloepus hoffmanni, Chrysochloris asiatica, Colobus guereza, Colobus polykomos, Craseonycteris thonglongyai, Cricetomys gambianus, Cricetulus griseus, Crocidura indochinensis, Cryptoprocta ferox, Ctenodactylus gundi, Ctenomys sociabilis, Cuniculus paca, Dasyprocta punctata, Dasypus novemcinctus, Daubentonia madagascariensis, Delphinapterus leucas, Desmodus rotundus, Dicerorhinus sumatrensis, Diceros bicornis, Dinomys branickii, Dipodomys stephensi, Dolichotis patagonum, Echinops telfairi, Elaphurus davidianus, Ellobius lutescens, Ellobius talpinus, Enhydra lutris, Equus asinus, Equus caballus, Equus przewalskii, Erinaceus europaeus, Erythrocebus patas, Eschrichtius robustus, Eubalaena japonica, Eulemur albifrons, Eulemur collaris, Eulemur coronatus, Eulemur flavifrons, Eulemur fulvus, Eulemur macaco, Eulemur mongoz, Eulemur rubriventer, Eulemur rufus, Eulemur sanfordi, Felis nigripes, Galago moholi, Galago senegalensis, Galagoides demidoff, Galeopterus variegatus, Giraffa tippelskirchi, Glis glis, Gorilla beringei, Gorilla gorilla, Graphiurus murinus, Hapalemur alaotrensis, Hapalemur gilberti, Hapalemur griseus, Hapalemur meridionalis, Hapalemur occidentalis, Helogale parvula, Hemitragus hylocrius, Heterocephalus glaber, Heterohyrax brucei, Hippopotamus amphibius, Hipposideros armiger, Hipposideros galeritus, Hoolock leuconedys, Hyaena hyaena, Hydrochoerus hydrochaeris, Hylobates abbotti, Hylobates agilis, Hylobates klossii, Hylobates pileatus, Hylobates muelleri, Hylobates pileatus, Hystrix cristata, Indri indri, Inia geoffrensis, Jaculus jaculus, Kogia breviceps, Lagothrix lagothricha, Lasiurus borealis, Lemur catta, Leontocebus fuscicollis, Leontocebus illigeri, Leontocebus nigricollis, Leontopithecus chrysomelas, Leontopithecus rosalia, Lepilemur ankaranensis, Lepilemur dorsalis, Lepilemur ruficaudatus, Lepilemur septentrionalis, Leptonychotes weddellii, Lepus americanus, Lipotes vexillifer, Lophocebus aterrimus, Loris lydekkerianus, Loris tardigradus, Loxodonta africana, Lycaon pictus, Macaca arctoides, Macaca assamensis, Macaca cyclopis, Macaca fascicularis, Macaca fuscata, Macaca leonina, Macaca maura, Macaca nigra, Macaca radiata, Macaca siberu, Macaca silenus, Macaca thibetana, Macaca tonkeana, Macroglossus sobrinus, Mandrillus leucophaeus, Mandrillus sphinx, Manis javanica, Manis pentadactyla, Megaderma lyra, Mellivora capensis, Meriones unguiculatus, Mesocricetus auratus, Mesoplodon bidens, Mico argentatus, Mico humeralifer, Mico schneideri, Microcebus murinus, Microgale talazaci, Micronycteris hirsuta, Miniopterus schreibersii, Miopithecus ogouensis, Mirounga angustirostris, Mirza zaza, Monodon monoceros, Mormoops blainvillei, Moschus moschiferus, Mungos mungo, Murina feae, Mus caroli, Mus spretus, Muscardinus avellanarius, Mustela putorius, Myocastor coypus, Myotis myotis, Myrmecophaga tridactyla, Nannospalax galili, Nasalis larvatus, Neomonachus schauinslandi, Neophocaena asiaeorientalis, Noctilio leporinus, Nomascus annamensis, Nomascus concolor, Nomascus gabriellae, Nomascus siki_a, Nomascus siki_b, Nyctereutes procyonoides, Nycticebus bengalensis, Nycticebus coucang, Nycticebus pygmaeus, Ochotona princeps, Octodon degus, Odocoileus virginianus, Okapia johnstoni, Ondatra zibethicus, Onychomys torridus, Orycteropus afer, Oryctolagus cuniculus, Otocyon megalotis, Otolemur crassicaudatus, Ovis aries, Ovis canadensis, Pan paniscus, Pan troglodytes, Panthera onca, Panthera pardus, Panthera tigris, Pantholops hodgsonii, Papio anubis, Papio cynocephalus, Papio hamadryas, Papio kindae, Papio papio, Papio ursinus, Paradoxurus hermaphroditus, Perodicticus ibeanus, Perodicticus potto, Perognathus longimembris, Petromus typicus, Phocoena phocoena, Piliocolobus badius, Piliocolobus gordonorum, Piliocolobus kirkii, Pipistrellus pipistrellus, Pithecia albicans, Pithecia chrysocephala, Pithecia hirsuta, Pithecia mittermeieri, Pithecia pissinattii, Pithecia pithecia, Pithecia vanzolinii, Platanista gangetica, Plecturocebus bernhardi, Plecturocebus brunneus, Plecturocebus caligatus, Plecturocebus cinerascens, Plecturocebus cupreus, Plecturocebus dubius, Plecturocebus grovesi, Plecturocebus hoffmannsi, Plecturocebus miltoni, Plecturocebus moloch, Pongo abelii, Pongo pygmaeus, Presbytis comata, Presbytis mitrata, Procavia capensis, Prolemur simus, Propithecus coronatus, Propithecus diadema, Propithecus edwardsi, Propithecus perrieri, Propithecus tattersalli, Propithecus verreauxi, Psammomys obesus, Pteronura brasiliensis, Puma concolor, Pygathrix cinerea, Pygathrix nigripes, Pygathrix nigripes, Rangifer tarandus, Rhinolophus sinicus, Rhinopithecus bieti, Rhinopithecus strykeri, Rousettus aegyptiacus, Saguinus bicolor, Saguinus geoffroyi, Saguinus imperator, Saguinus inustus, Saguinus labiatus, Saguinus midas, Saguinus mystax, Saguinus oedipus, Saiga tatarica, Saimiri cassiquiarensis, Saimiri macrodon, Saimiri oerstedii, Saimiri sciureus, Saimiri ustus, Sapajus apella, Sapajus macrocephalus, Scalopus aquaticus, Semnopithecus entellus, Semnopithecus hypoleucos, Semnopithecus johnii, Semnopithecus priam, Semnopithecus schistaceus, Semnopithecus vetulus, Sigmodon hispidus, Solenodon paradoxus, Spermophilus dauricus, Spilogale gracilis, Suricata suricatta, Symphalangus syndactylus, Tadarida brasiliensis, Tamandua tetradactyla, Tapirus indicus, Tapirus terrestris, Tarsius lariang, Tarsius wallacei, Thryonomys swinderianus, Tolypeutes matacus, Tonatia saurophila, Trachypithecus auratus, Trachypithecus crepusculus, Trachypithecus cristatus, Trachypithecus francoisi, Trachypithecus geei, Trachypithecus germaini, Trachypithecus hatinhensis, Trachypithecus laotum, Trachypithecus leucocephalus, Trachypithecus melamera, Trachypithecus obscurus, Trachypithecus phayrei, Trachypithecus pileatus, Tragulus javanicus, Trichechus manatus, Tupaia tana, Tursiops truncatus, Uropsilus gracilis, Ursus maritimus, Varecia rubra, Varecia variegata, Vicugna pacos, Vulpes lagopus, Xerus inauris, Zalophus californianus, Zapus hudsonius, Ziphius cavirostris
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Table 2. Gene tracks used for codon translation.
Methods
This alignment was created by making three edits (using Cactus) to the
241-way mammalian Zoonomia Cactus alignment
(
https://cglgenomics.ucsc.edu/data/cactus/).
- One additional cat genome, "Felis_catus_fca126" (GCA_018350175.1) was
added as a sister taxa to the existing "Felis_catus" species
- Five additional canine genomes were also added: canFam4,
"Canis_lupus_dingo" (GCA_003254725.1), "Canis_lupus_orion"
(GCA_905319855.2), "Nyctereutes_procyonoides" (GCA_905146905.1) and
"Otocyon_megalotis" (GCA_017311455.1). "Canis_lupus" from the Zoonomia
alignment was also renamed "Canis_lupus_VD" to reflect the fact that it
corresponds to a "village dog" and not "wolf" sample.
- The 43-species primates clade from the Zoonomia alignment was removed
and replaced with the 243-way primates alignment from Identification of
constrained sequence elements across 239 primate genomes, increasing the alignment by 200
additional primate species.
Phylogenic tree
The phylogenic tree was established by the research described
in A global catalog of whole-genome diversity from 233 primate
species.
Sequences
Table 1. Genome assemblies included in the 447-way Conservation track.
References
Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F
et al.
Identification of constrained sequence elements across 239 primate genomes.
Nature. 2023 Nov 29;.
DOI: 10.1038/s41586-023-06798-8; PMID: 38030727
Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J,
Rousselle M et al.
A global catalog of whole-genome diversity from 233 primate species.
Science. 2023 Jun 2;380(6648):906-913.
DOI: 10.1126/science.abn7829;
PMID: 37262161
Zoonomia Consortium.
A comparative genomics multitool for scientific discovery and conservation.
Nature. 2020 Nov;587(7833):240-245.
DOI: 10.1038/s41586-020-2876-6; PMID: 33177664; PMC: PMC7759459
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC et
al.
Dense sampling of bird diversity increases power of comparative genomics.
Nature. 2020 Nov;587(7833):252-257.
DOI: 10.1038/s41586-020-2873-9; PMID: 33177665; PMC: PMC7759463
Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J
et al.
Progressive Cactus is a multiple-genome aligner for the thousand-genome era.
Nature. 2020 Nov;587(7833):246-251.
DOI: 10.1038/s41586-020-2871-y; PMID: 33177663; PMC: PMC7673649
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