reference-free comparative genomics of 174 chloroplastsreference-free比较基因组学174叶绿体.pdfVIP

Reference-Free Comparative Genomics of 174 Chloroplasts 1,2 3 4 5 1,6 3 Chai-Shian Kua , Jue Ruan , John Harting , Cheng-Xi Ye , Matthew R. Helmus , Jun Yu , Charles H. Cannon1,4* 1 Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China, 2 Graduate School of the Chinese Academy of Sciences, Beijing, People’s Republic of China, 3 The CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China, 4 Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America, 5 Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America, 6 Amsterdam Global Change Institute, Vrije Universiteit, Amsterdam, The Netherlands Abstract Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ,18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes