An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data
文献类型：期刊论文
| 作者 | Fan, Huan ; Ives, Anthony R. ; Surget-Groba, Yann ; Cannon, Charles H. |
| 刊名 | BMC GENOMICS
 |
| 出版日期 | 2015 |
| 卷号 | 16页码:- |
| 关键词 | k-mers Phylogenomics Homoplasy Alignment-free Assembly-free |
| ISSN号 | 1471-2164 |
| 中文摘要 | Background: Next-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction of genomic data remains difficult because de novo assembly for non-model genomes and multi-genome alignment are challenging. Results: To greatly simplify the analysis, we present an Assembly and Alignment-Free (AAF) method (https://sourceforge.net/projects/aaf-phylogeny) that constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. Using mathematical calculations, models of sequence evolution, and simulated sequencing of published genomes, we address both evolutionary and sampling issues caused by direct reconstruction, including homoplasy, sequencing errors, and incomplete sequencing coverage. From these results, we calculate the statistical properties of the pairwise distances between genomes, allowing us to optimize parameter selection and perform bootstrapping. As a test case with real data, we successfully reconstructed the phylogeny of 12 mammals using raw sequencing reads. We also applied AAF to 21 tropical tree genome datasets with low coverage to demonstrate its effectiveness on non-model organisms. Conclusion: Our AAF method opens up phylogenomics for species without an appropriate reference genome or high sequence coverage, and rapidly creates a phylogenetic framework for further analysis of genome structure and diversity among non-model organisms. |
| 原文出处 | 10.1186/s12864-015-1647-5 |
| 语种 | 英语 |
| 公开日期 | 2015-08-11 |
| 源URL | [http://ir.xtbg.org.cn/handle/353005/9210]  |
| 专题 | 西双版纳热带植物园_动植物关系组 |
| 推荐引用方式 GB/T 7714 | Fan, Huan,Ives, Anthony R.,Surget-Groba, Yann,et al. An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data[J]. BMC GENOMICS,2015,16:-. |
| APA | Fan, Huan,Ives, Anthony R.,Surget-Groba, Yann,&Cannon, Charles H..(2015).An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data.BMC GENOMICS,16,-. |
| MLA | Fan, Huan,et al."An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data".BMC GENOMICS 16(2015):-. |
入库方式： OAI收割
来源：西双版纳热带植物园
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。