Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A1S6, Canada, International Graduate Training Center in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Vancouver (BC), Canada, INRIA Grenoble Rhône-Alpes, Montbonnot 38334, France, Université de Lyon 1, Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR5558 F-69622 Villeurbanne, France and LaBRI, Université Bordeaux I, 33405 Talence, France.
Bioinformatics. 2013 Dec 1;29(23):2987-94. doi: 10.1093/bioinformatics/btt527. Epub 2013 Sep 24.
Recent progress in ancient DNA sequencing technologies and protocols has lead to the sequencing of whole ancient bacterial genomes, as illustrated by the recent sequence of the Yersinia pestis strain that caused the Black Death pandemic. However, sequencing ancient genomes raises specific problems, because of the decay and fragmentation of ancient DNA among others, making the scaffolding of ancient contigs challenging.
We show that computational paleogenomics methods aimed at reconstructing the organization of ancestral genomes from the comparison of extant genomes can be adapted to correct, order and orient ancient bacterial contigs. We describe the method FPSAC (fast phylogenetic scaffolding of ancient contigs) and apply it on a set of 2134 ancient contigs assembled from the recently sequenced Black Death agent genome. We obtain a unique scaffold for the whole chromosome of this ancient genome that allows to gain precise insights into the structural evolution of the Yersinia clade.
最近在古 DNA 测序技术和方案方面的进展导致了整个古代细菌基因组的测序，正如最近引起黑死病大流行的鼠疫耶尔森菌菌株的测序所示。 然而，由于古 DNA 的衰变和碎片化等原因，测序古代基因组会引发一些特定的问题，这使得古基因组的支架构建具有挑战性。
我们表明，旨在通过比较现存基因组来重建祖先基因组结构的计算古基因组学方法可以被改编来纠正、排序和定向古代细菌的基因组。 我们描述了方法 FPSAC（快速组装古基因组）并将其应用于最近测序的黑死病病原体基因组中组装的 2134 个古代基因组。 我们得到了这个古代基因组的整个染色体的唯一支架，这使得我们能够深入了解耶尔森菌属的结构进化。
