the genome of the swiss mascot: bos taurus aka the cow!

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

Author: nyoko

Post on 12-Feb-2016




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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; - PowerPoint PPT Presentation


  • 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 (2X) assembly;Only 11 are of good quality (>=7X): human, mouse, rat, dog, horse, chimpanzee, orangutan, guinea pig, opossum, platypus andnow bovine.

  • 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

  • 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 L1 Dominette 01449. The source of the BAC library DNA was Hereford bull L1 Domino 99375, the sire of the former animal. Whose genome is it by the way?So who is right?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 seriously2.87 Gb genome in 29 autosomal and the X and Y chromosomes;They found 22000 protein-coding genes. Which is probably, like for human, a over-prediction. The number is probably nearer 20000.

  • Orthologs across mammalsThey estimate that 14345 protein-coding genes are common to all mammals. The analysis was carried out on 7 species;Almost 17000 are common between human and cow.

  • Niu* genes in cowThere 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); beta-defensins (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.

  • 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 similaritiesThe 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

  • VariationsCattle were domesticated about 10000 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 40000 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 (UniGe) and Alexandre Reymond (UniLa) also participated in the genome analysis.

  • So we can do:No! Sorry: meuuuh

  • And in Swiss-ProtWe currently have 5659 bovine entries;Bovine is number 6 in our statistics and the 4th mammal (after rat with 7365 entries);4667 entries are linked to one of the two main large scale full length mRNA 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).