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!
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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 (gt7X) human, mouse,
  rat, dog, horse, chimpanzee, orangutan, guinea
  pig, opossum, platypus andnow bovine.

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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
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The genome paper attracted lots of publicity and
hype about how the knowledge of the cow genome
could help agriculture
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Whose genome is it by the way?
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 L1
Dominette 01449. The source of the BAC library
DNA was Hereford bull L1 Domino 99375, the sire
of the former animal.
So its both Domino and Dominette, father and
daughter!
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Alas its an English-speaking cow they sequenced,
not a Swiss one!
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While in Switzerland we generally encounter.
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And, of course our famous fighting cows from
Herens!
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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!!
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More seriously

• 2.87 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.

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Orthologs across mammals

• They 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.

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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)
  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.

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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.

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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).

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Phylogenetic trees of mammals based on genome
sequences
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Variations

• Cattle 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.

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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.

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So we can do
No! Sorry meuuuh
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And in Swiss-Prot

• We 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).