From 684b986bd409b754e5944aa7351b6359f50a1fab Mon Sep 17 00:00:00 2001 From: Charles Date: Fri, 3 Jul 2020 13:19:11 +0900 Subject: [PATCH] =?utf8?q?Caf=C3=A9?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- biblio/18563158.mdwn | 18 ++++++++++++++++++ tags/synteny.mdwn | 2 ++ 2 files changed, 20 insertions(+) create mode 100644 biblio/18563158.mdwn diff --git a/biblio/18563158.mdwn b/biblio/18563158.mdwn new file mode 100644 index 00000000..44150dc8 --- /dev/null +++ b/biblio/18563158.mdwn @@ -0,0 +1,18 @@ +[[!meta title="The amphioxus genome and the evolution of the chordate karyotype."]] +[[!tag chromosome synteny]] + +Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, +Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, +Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka +J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, +Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, +Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar +DS. + +Nature. 2008 Jun 19;453(7198):1064-71. doi:10.1038/nature06967 + +The amphioxus genome and the evolution of the chordate karyotype. + +[[!pmid 18563158 desc="17 ancestral chordate chromosomes."]] + +“We estimate that the haploid amphioxus genome contains 21,900 protein-coding loci. [...] The observed heterozygosity shows correlations at short distances that decay on scales greater than ∼1 kb, indicating extensive recombination in the population. [...] Wwe reconstructed the gene complements of 17 linkage groups (that is, proto-chromosomes) of the last common chordate ancestor. [...] This analysis shows that most of the human genome (112 segments spanning 2.68 Gb, or 95% of the euchromatic genome) was affected by large-scale duplication events on the vertebrate stem before the bony vertebrate radiation (that is, the teleost/tetrapod split), and that nearly all of the ancient chordate chromosomes were quadruplicated. [...] Allowing for a range of nearly parsimonious reconstructions of 2R, we estimate that the bony vertebrate ancestor had between 37 and 49 chromosomes.” diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn index 83c8fa61..9bd08b3a 100644 --- a/tags/synteny.mdwn +++ b/tags/synteny.mdwn @@ -9,6 +9,8 @@ were enriched near CTCF-binding events. distribution follows a power law and explain it with a model that requires breakpoints to be in open regions (ENCODE) interacting with each other (Hi-C). +The ancestral chordate has 17 chromosomes according to [[Putnam and coll, 2008|biblio/18563158]]. + The ancestral amniote has 49 chromosomes according to [[Sacerdot and coll., 2018|biblio/30333059]]. [[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints -- 2.47.3