Cow genome

[Oolon Colluphid]

Science Vol. 324. no. 5926, pp. 522 - 528 (24 April 2009)

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

The Bovine Genome Sequencing and Analysis Consortium et al.

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage.

The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes.

Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness.

Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs.

The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

http://www.sciencemag.org/content/vol324/issue5926/images/large/324_522_F1.jpeg


Fig. 1 Protein orthology comparison among genomes of cattle, dog, human, mouse, and rat (Bos taurus, Canis familiaris, Homo sapiens, Mus musculus, Rattus norvegicus, representing placental mammals), opossum (Monodelphis domestica, marsupial), and platypus (Ornithorhynchus anatinus, monotreme).

(A) The majority of mammalian genes are orthologous, with more than half preserved as single copies (dark blue); a few thousand have species-specific duplications (blue); another few thousand have been lost in specific lineages (orange). We also show those lacking confident orthology assignment (green), and those that are apparently lineage specific [unique (white)]. Placental-specific orthologs are shown in pink. Single- or multiple-copy genes were defined on the basis of representatives in human, bovine, or dog; mouse or rat; and opossum or platypus.

(B) Venn diagram showing shared orthologous groups (duplicated genes were counted as one) between laurasiatherians (cattle and dog), human, rodents (mouse and rat), and nonplacental mammals (opossum and platypus) on the basis of the presence of a representative gene in at least one of the grouped species [as in (A)].

(C) Distribution of ortholog protein identities between human and the other species for a subset of strictly conserved single-copy orthologs.

(D) A maximum likelihood phylogenetic tree using all single-copy orthologs supports the accepted phylogeny and quantifies the relative rates of molecular evolution expressed as the branch lengths.

[SteveF]

Interestingly, one of the team is this guy:

http://www.answersingenesis.org/docs/3726.asp

Behind this French YEC organisation:

http://www.aucommencement.net/

Funnily enough, here's a press release on the subject that's fairly evolution heavy and lists him as a contact:

http://www.international.inra.fr/press/cow_genome_sequence_provides_new_insights_on_bovin e_biology

[4321lynx]

Interestingly, one of the team is this guy:

http://www.answersingenesis.org/docs/3726.asp

Behind this French YEC organisation:

http://www.aucommencement.net/

Funnily enough, here's a press release on the subject that's fairly evolution heavy and lists him as a contact:

http://www.international.inra.fr/press/cow_genome_sequence_provides_new_insights_on_bovin e_biology

Googled his name --- Andre Eggen --- got 302,000 entries.
Proof you can be a great scientist & a major godbotherer/biblethumper at the same time.
No end to human rationalisation. As a friend said:"People are funny". He meant peculiar or strange.

And godbless'em, there's a "CreationistWiki" on the net. :bang:

Thanks for the links. Brushed-up my French a little bit. :D

[4321lynx]

Whilst we're on this subject.

How close are domesticated cattle in DNA to the various buffalo/bison around the world? Has anyone extracted any auroch DNA?

[DMB]

I found the interview linked to from the AIG article interesting. When he is talking about "the Church" in France, it appears to be a fundie Protestant kind of church that he has in mind. Of course, France is at base a Catholic country, so it is very misleading to talk in those terms.

[lpetrich]

Nice to see another genome sequenced in detail.

I've tried to find out about genome projects, but the lists of genome projects I've found are a confusing mess -- you have to look very closely at what's going on in each project. Is it the whole genome or EST's (Expressed Sequence Tags)? It is low coverage, a draft assembly, or completed?


GOLD: Genomes OnLine Database (http://www.genomesonline.org/)
NHGRI's Approved Sequencing Targets (http://www.genome.gov/10002154)
NCBI's Genome Projects (http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj)
JGI's Genome Projects (http://www.jgi.doe.gov/genome-projects/pages/projects.jsf)
International Sequencing Consortium (http://www.intlgenome.org/viewDatabase.cfm)


Phylogenetic coverage is still very patchy, however, with much sequencing effort concentrated in certain groups and not in closely-related ones.

[4321lynx]

Nice to see another genome sequenced in detail.

I've tried to find out about genome projects, but the lists of genome projects I've found are a confusing mess -- you have to look very closely at what's going on in each project. Is it the whole genome or EST's (Expressed Sequence Tags)? It is low coverage, a draft assembly, or completed?


GOLD: Genomes OnLine Database (http://www.genomesonline.org/)
NHGRI's Approved Sequencing Targets (http://www.genome.gov/10002154)
NCBI's Genome Projects (http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj)
JGI's Genome Projects (http://www.jgi.doe.gov/genome-projects/pages/projects.jsf)
International Sequencing Consortium (http://www.intlgenome.org/viewDatabase.cfm)


Phylogenetic coverage is still very patchy, however, with much sequencing effort concentrated in certain groups and not in closely-related ones.

Thank you. Will look through them soon.

[lpetrich]

Various sequencing labs also list genome projects; I'll concentrate on eukaryotic ones:

Washington University Genome Sequencing Center (http://genome.wustl.edu/genome_group_index.cgi)
Baylor College of Medicine Human Genome Sequencing Center (http://www.hgsc.bcm.tmc.edu/project-species-x-organisms.hgsc)
MIT/Harvard Broad Institute (http://www.broad.mit.edu/node/296)
The Institute for Genetic Research (TIGR) (http://www.tigr.org/tdb/euk/)
Agencourt: NHGRI (http://www.agencourt.com/services/experience/nhgri/index.php)
Berkeley Drosophila Genome Project (http://www.fruitfly.org/)
J. Craig Venter Intitute on Plant Genomes (http://www.jcvi.org/cms/research/groups/plant-genomics/)
Sanger Institute (http://www.sanger.ac.uk/Projects/)


TIGR has some drawings of tigers with some of its species, which made me think of a logo for it: a tiger playing with a giant ball of yarn, with one end unraveled as a double helix.


The patchiness of gene sequencing is partly due to the expense of doing so. A decade ago, the Human Genome Sequence was a major project, and there was some controversy over whether it was really worth doing. But in the years since then, sequencing technology has advanced enough to make sequencing of human-sized genomes much more easily feasible, and advances are likely to continue. But sequencers still have to decide which large organisms' genomes are worth sequencing, which will make the patchiness continue into the next decade.

As an illustration of the patchiness of the genome sequencing to date, over 20 Drosophila fruit-fly species and at least 10 Caenorhabditis nematode species have their genomes at various stages of sequencing, from accepted proposal from completion, comparable to the number for all other invertebrates combined.

This is because they are often used as model systems, and that is because they are easy to raise in the lab. Comparing close species can help show what makes them different -- adaptations? Premating or postmating isolation mechanisms? The latter would include female flies' pheromone making, male flies' ability to smell them, male flies' additional features like spotted wings, female flies' ability to recognize them, sperm-cell surface proteins, and egg-cell sperm-recognition proteins.


Looking more broadly and starting from our species, here are some ones in the sequencing pipeline:

Great Apes:
- Human, Homo sapiens
- Chimpanzee, Pan troglodytes
- Orangutan, Pongo abelii
Lesser Apes:
- Gibbon, Nomascus leucogenys
Old World Monkeys:
- Macaques, Macaca sp.
- Baboon, Papio hamadryas
New World Monkeys:
- Marmoset, Callithrix jacchus
- Squirrel Monkey, Saimiri sp.
Prosimians:
- Mouse Lemur, Microcebus murinus
- Bushbaby, Otolemur garnetti
- Tarsier, Tarsius syrichta

Rodents:
- Domestic Mouse, Mus musculus
- Domestic Rat, Rattus norvegicus
- Mouse, Peromyscus spp.
- Kangaroo Rat, Dipodomys sp.
- Squirrel, Spermophilis tridecemlineatus
- Guinea Pig, Cavia porcellus
Lagomorphs:
- Rabbit, Oryctolagus cuniculus
- Pika, Ochotona princeps

Other Euarchontoglires:
- Tree Shrew, Tupaia belangeri
- Flying Lemur, Dermoptera sp.
- Colugo, Cynocephalus volans
- Tenrec, Echinops telfairi

Carnivorans:
- Domestic Dog, Canis (lupus) familiaris
- Domestic Cat, Felis (sylvestris) catus
Cetartiodactyls:
- Domestic Bovine, Bos taurus
- Alpaca, Vicugna pacos
- Pig, Sus scrofa
- Bottlenose Dolphin, Tursiops truncatus
Bats:
- Microbat, Myotis lucifugus
- Megabat, Pteropus vampyrus
Other Laurasiatherians:
- Horse, Equus caballus
- Pangolin, Manis pentadactyla
- European Hedgehog, Erinaceus europeaus
- European Shrew, Sorex araneus

Xenarthrans:
- Nine-Banded Armadillo, Dasypus novemcinctus
- Sloth, Choloepus hoffmanni

Afrotherians:
- African Savannah Elephant, Loxodonta africana africana
- Hyrax, Procavia capensis
- Elephant Shrew, Elephantulus sp.

Marsupials:
- Tammar Wallaby, Macropus eugenii
- Lab Opossum, Monodelphis domestica

Monotremes:
- Duckbill Platypus, Ornithorhynchus anatinus

Birds:
- Chicken, Gallus gallus
- Zebra Finch, Zebrafinch Taeniopygia guttata
Reptiles:
- Anole Lizard, Anolis carolinensis
- Painted Turtle, Chrysemys picta
Amphibians:
- Clawed frog, Xenopus tropicalis

Lobe-finned Fish:
- Coelacanth, Latimeria spp.
Ray-finned Fish:
- Pufferfish, Fugu rubripes, Tetraodon nigroviridis
- Stickleback, Gasterosteus aculeatus
- Tilapia Cichlid, Oreochromis niloticus, ...
- Zebrafish, Danio rerio
Cartilaginous Fish:
- Elephant Shark, Callorhinchus milii
- Skate, Raja erinacea
Jawless Fish:
- Sea Lamprey, Petromyzon marinus
- Hagfish, Eptatretus burgeri

Invertebrate Chordates:
- Amphioxus, Branchiostoma floridae
- Sea Squirt, Ciona spp.
Other Deuterostomes:
- Acorn Worm, Saccoglossus kowalesvskii
- Sea Urchins, Strongylocentrotus spp., Allocentrotus fragilis

Dipterans:
- Fruit flies, Drosophila spp.
- Sand flies, Lutzomiya longipalpis, Phlebotomus papatasi
- Hessian fly, Mayetiola destructor
- Mosquitoes, Anopheles gambiae, Aedes aegyptii
Hymenopterans:
- Honeybee, Apis mellifera
- Bumblebee, Bombus terrestris
- Parasitioid Wasp, Nasonia spp.
Hemipterans:
- Pea Aphid, Acyrothosyphon pisum
- Chagas-carrier bug, Rhodnius prolixus
Other Insects:
- Cotton Bollworm Moth, Helicoverpa armigera
- Red Flour Beetle, Tribolium castaneum
- Body Louse, Pediculus humanus

Other Arthropods:
- Water Flea, Daphnia pulex
- Amphipod Crustacean, Jassa slatteryi
- Tick, Ixodes scapularis
- Honeybee Mite, Varroa destructor
- Horseshoe Crab, Limulus polyphemus
- Centipede, Strigamia maritima

Other Ecdysozoans:
- Tardigrade (Water Bear), Hypsibius dujardini
- Nematodes, Caenorhabditis spp., ...
- Priapulid Worm, Priapulus caudatus

Mollusks:
- Freshwater Snail, Biomphalaria glabrata
- Sea Slug, Aplysia californica

Other Lophotrochozoans:
- Planarian, Schmidtea mediterranea
- Blood fluke Schistosoma mansoni
- Tapeworms, Echinococcus multilocularis, Taenia solium

Cnidarians:
- Starlet Sea Anemone, Nematostella vectensis
- Freshwater Polyp, Hydra magnipapillata

Placozoan:
- Trichoplax adhaerens

This list is much more impressive than I'd first thought, it must be said. I've decided to stop here, since interpreting genome-project status can be difficult.

[Steviepinhead]

Great round-up, lpetrich!

Don't forget the Neanderthal project at Svante Paabo's lab. Even though the completion of the first pass of the first draft has been announced, we don't really have detailed results yet, so I'd consider that one still ongoing as well.