The genome of the Swiss mascot Bos taurus

The genome of the Swiss mascot: Bos taurus aka the cow!

Yet another mammalian genome? • After human, mouse and rat were “finished”, projects were initiated to sequence the genome of many mammalian species; • Ensembl currently contains information on 35 mammal genomes; • But most of them are low coverage (2 X) assembly; • Only 11 are of good quality (>=7 X): human, mouse, rat, dog, horse, chimpanzee, orangutan, guinea pig, opossum, platypus and…now bovine.

Sequencing was carried out at the Human Genome Sequencing Center at Baylor College of Medicine Started in 2004 and “completed” in April 2009. Most of the data was made available in 2007 (7. 1 X draft assembly).

Three papers were very recently published describing respectively, the genome, the variations in different breeds and a new algorithm used for an alternative (better) assembly of the genome

The genome paper attracted lots of publicity and hype about how the knowledge of the cow genome could help agriculture

Whose genome is it by the way? On some sites it says that the DNA comes from: Hereford bull L 1 Domino 99375, registration number 41170496 On other sites it says: The first cow genome to be sequenced was that of a Hereford cow named L 1 Dominette, shown here with her calf. So who is right? The combined strategy was a hybrid of a Whole Genome Shotgun (WGS) approach and a hierarchical (BAC clone) approach. The sequencing combines BAC shotgun reads with WGS reads from small insert libraries as well as BAC end sequences (BES). The DNA for the small insert WGS libraries was from white blood cells from the Hereford cow L 1 Dominette 01449. The source of the BAC library DNA was Hereford bull L 1 Domino 99375, the sire of the former animal. So its both Domino and Dominette, father and daughter!

Alas its an English-speaking cow they sequenced, not a Swiss one!

While in Switzerland we generally encounter….

And, of course our famous fighting cows from Herens!

And anyway because of cows we live a dangerous life in Switzerland: the next time you are hiking in the Alps, stop hugging those cows!!

More seriously… • 2. 87 Gb genome in 29 autosomal and the X and Y chromosomes; • They found 22’ 000 protein-coding genes. Which is probably, like for human, a overprediction. The number is probably nearer 20’ 000.

Orthologs across mammals • They estimate that 14’ 345 protein-coding genes are common to all mammals. The analysis was carried out on 7 species; • Almost 17’ 000 are common between human and cow.

Niu* genes in cow • There has been an extension of some gene families in cow such as: – Milk-specific proteins (caseins); – Expansion of bacterial-defense proteins: cathelicidins (10 in cow, 1 in human); betadefensins (106 versus 39) C-type lysozymes, etc; – Immunity proteins such as interferons betas (6 vs 1) and omegas (24 vs 1); – Reproduction: prolactin-related proteins. (*) Niu is Chinese for cow!

Why more genes for bacterial defense and immunity? • Maybe because the rumen of the cow is a factory full of bacteria and there is an increased risk of opportunistic infections; • Immunity may have been in positive selection because of the herd behavior that can promote rapid disease transmission.

Sequence similarities • The genome paper confirm something that Swiss-Prot annotators already were familiar with: while cow is more divergent than rodents to human, the sequence of orthologous proteins are more similar; • This is due to the rapid evolutionary rate of evolution in the rodent group (short life and lots of evolutionary pressure from the environment).

Phylogenetic trees of mammals based on genome sequences

Variations • Cattle were domesticated about 10’ 000 years ago; • Two sub-species were domesticated: Bos primigenius taurus (cow) and Bos primigenius indicus (zebu); • There are 800 different breeds and 1. 3 billion cow living with us on earth (and are responsible for 18% of greenhouse gases production); • A genome-wide survey of almost 40’ 000 SNPs reveal that domestication has left signatures of selection; • Diversity has decreased compared to the ancestral population, yet it is not so low as it could have been thought.

And did Switzerland play a role in this genome project? • The ortholog analysis was carried out by Evgeny Zdobonov, Evgenia Kriventseva, Thomas Junier from the Swiss Institute of Bioinformatics; • Stylianos Antonorakis (Uni. Ge) and Alexandre Reymond (Uni. La) also participated in the genome analysis.

So we can do: No! Sorry: meuuuh

And in Swiss-Prot • We currently have 5’ 659 bovine entries; • Bovine is number 6 in our statistics and the 4 th mammal (after rat with 7’ 365 entries); • 4’ 667 entries are linked to one of the two main large scale full length m. RNA projects (MGC and USDA); • Only 80 entries are linked to the genome because the CDSs have not been predicted and are only available in Ensembl so far. So all of these cases were manual “creations” to complete a specific sequence and/or isoform; • 92 entries are fragments (bovine was the target of many peptide sequencing studies).