From: Charles Date: Thu, 31 Oct 2019 04:46:13 +0000 (+0900) Subject: Café X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=ee66431445119a15f4f1a240c003f724cd18f795;p=setup%2F.git Café --- diff --git a/biblio/25209798.mdwn b/biblio/25209798.mdwn new file mode 100644 index 00000000..f95f9b7a --- /dev/null +++ b/biblio/25209798.mdwn @@ -0,0 +1,23 @@ +[[!meta title="Gibbon genome and the fast karyotype evolution of small apes."]] +[[!tag chromosome synteny evolution]] + +Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, +Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, +Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, +Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, +Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, +Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, +Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, +Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, +O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann +GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, +Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan +SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, +Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, +Rogers J, Wilson RK, Gibbs RA. + +Nature. 2014 Sep 11;513(7517):195-201. doi:10.1038/nature13679 + +Gibbon genome and the fast karyotype evolution of small apes. + +[[!pmid 25209798 desc=""“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.” “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.” “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”]] diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn index 6dd88e5b..4ece1256 100644 --- a/tags/synteny.mdwn +++ b/tags/synteny.mdwn @@ -1,6 +1,11 @@ [[!meta title="pages tagged synteny"]] -[[Renschler and coll, (2019)|biblio/31601616]] found 20 synteny breakpoints +[[Carbone and coll. (2014)|biblio/25209798]] found 96 gibbon–human synteny +breakpoints (~30 per Gb), associated with segmental duplication or Alu element +enrichment. They often bore signatures of non-homology based mechanisms, and +were enriched near CTCF-binding events. + +[[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B compartment” “Overlaps of TAD boundaries and SB breakpoints in all comparisons are highly significant”