Domestic Pig's Genome Sequenced

choi

(1) This week, Nature has a cover story on this topic.

current issue of Nature
http://www.nature.com/nature/journal/v491/n7424/index.html
("Bringing Home the Bacon")

Note:
(a) Click "About the cover" underneath the cover, to read the synopsis.
(b) Bring home the bacon. The Phrase Finder, undated.
http://www.phrases.org.uk/meanings/bring-home-the-bacon.html

(2) Alison Abbott, Pig Geneticists Go the Whole Hog; Genome will benefit farmers and medical researchers. Nature, 491: 315–316.
http://www.nature.com/news/pig-g ... e-whole-hog-1.11801

Note:
(a) The (2), in News section, precedes the article ((3) below) in print. You do not have to read (2), before reading (3). In fact, you need not read (3) at all, just read the quotation and notation made by me in (3).
(b) Go the whole hog. The Phrase Finder, undated.
http://www.phrases.org.uk/meanings/go-the-whole-hog.html
(c) Duroc (pig)
http://en.wikipedia.org/wiki/Duroc_(pig)
(d) Regarding the binomial nomenclature: "Sus scrofa."
(i) wild boar
http://en.wikipedia.org/wiki/Wild_boar
(Sus scrofa; "The species includes many subspecies. It is the wild ancestor of the domestic pig")
(ii) domestic pig
http://en.wikipedia.org/wiki/Domestic_pig
(Sus scrofa domesticus; also swine or hog; "traces its ancestry to the wild boar; it is considered a subspecies of the wild boar or a distinct species in its own right")
(e) Regarding the pig's name "TJ Tabasco."
(i) As a male initials, TJ usually stands for "Thomas Joseph."
(ii) Tabasco (disambiguation)
http://en.wikipedia.org/wiki/Tabasco_(disambiguation)
(the brand name of a chili sauce, made of "Tabasco pepper," which originates in a Mexican state of that name)


(3) Groenen MAM et al, Analyses of Pig Genomes Provide Insight Into Porcine Demography and Evolution. Nature, 49: 393–398 (Nov 15, 2012).
http://www.nature.com/nature/jou ... ll/nature11622.html

Quote:

"[abstract:] Wild pigs emerged in South East Asia [5.3–3.5 Myr, or million years, ago] and subsequently spread across Eurasia. Then, beginning ~10,000 years ago, pigs were domesticated in multiple locations across Eurasia. * * * [text:] Phylogenomic analyses of complete genome sequences from these wild boars and six domestic pigs revealed distinct Asian and European lineages (Supplementary Fig. 23) that split during the mid-Pleistocene 1.6–0.8 Myr ago (Calabrian stage, Frantz, L. A. F. et al., manuscript submitted). Colder climates during the Calabrian glacial intervals probably triggered isolation of populations across Eurasia. Admixture analyses (Supplementary Information) within Eurasian Sus scrofa disclosed gene flow between the northern Chinese and European populations consistent with pig migration across Eurasia, between Europe and northern China, throughout the Pleistocene. Our demographic analysis on the whole-genome sequences of European and Asian wild boars (Fig. 3) revealed an increase in the European population after pigs arrived from China.

"[abstract:] Pigs have the largest repertoire of functional olfactory receptor genes * * * [text:] Another significant porcine genome expansion is the olfactory receptor gene family. We identified 1,301 porcine olfactory receptor genes and 343 partial olfactory receptor genes20. The fraction of pseudogenes within these olfactory receptor sequences (14%) is the lowest observed in any species so far. This large number of functional olfactory receptor genes most probably reflects the strong reliance of pigs on their sense of smell while scavenging for food.

Note:
(a)
(i) Due to evolution, some genes were duplicated incorrectly, or inactivated. These genes are called psudogenes, because their sequences suggest being a gene but in fact are not functional.
(ii) If a gene mutates, the function may remain the same (when the mutation is silent), change in intensity (enhance or decrease) or in purpose If, on the other hand, a gene is duplicated (or multiplied) before a copy of the gene mutates, both original function and new change may co-exist, which might be a safer route in evolution.
(b) porcine (adj; Latin porcinus, from noun porcus pig):
"of, relating to, or suggesting swine"
http://www.merriam-webster.com/dictionary/porcine
(c) Pleistocene
en.wikipedia.org/wiki/Pleistocene
(the geological epoch which lasted from about 2,588,000 to 11,700 years ago; the Pleistocene is divided into four stages or ages, the Gelasian, Calabrian [1.8 to 0.78 million years ago], Ionian and Tarantian)

(i) The Calabrian stage is named after
Calabria
http://en.wikipedia.org/wiki/Calabria
("Calabria was first settled by Italic Oscan-speaking tribes. Two of these tribes were the Oenotrians (roughly translated into the "vine-cultivators") and the Itali. Greek contact with the latter resulted in Calabria taking the name of the tribe and was the first region to be called Italy (Italia)")
(ii) Michelle Fabio, History of Calabria. Bleeding Espresso; Savor simplicity one sip at a time, undated. bleedingespresso.com/calabria/history-of-calabria
("The name “Calabria” wouldn’t come until the reign of the Byzantines. * * * The Byzantines are credited with giving Calabria her name from the term “kalos-bruo” meaning 'fertile earth'”)
(iii) Stolen Figs: And Other Adventures in Calabria - Page 21 - Google Books Result
books.google.com/books?isbn=1429966068
Mark Rotella, Stolen Figs; And other adventures in Calabria. North Point Press (2003) at page 21
http://books.google.com/books?id ... alabria&f=false
("Calabria. The Byzantine Greeks named her--from the hyphenated term kalo-bruo, whcih means 'fertile earth'")


(4) Niimura Y and Nei M, Extensive Gains and Losses of Olfactory Receptor Genes in Mammalian Evolution. PLoS ONE, 2: e708 (2007).
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933591/

, whose Table 1 lists numbers of functional olfactory genes for each species (the numbers were minimal at the time of publication because draft genome sequences of various species were incompete).

Order.....................Species........Functional genes
Monotremata.........Platypus........265
Marsupialia.............Opossum....1,188
Cetartiodactyla.......Cow...............970
Carnivora...............Dog...............811
Rodentia................Mouse.........1,035
..............................Rat.............1,207
Primates.................Macaque.......309
.............................Human...........387