AI Article Synopsis
- Next-generation sequencing is producing vast genomic data, but analyzing it for phylogenetic reconstruction is challenging, especially for non-model organisms due to difficulties in genome assembly and alignment.
- The new Assembly and Alignment-Free (AAF) method allows phylogenetic trees to be created directly from unassembled genome data, addressing issues like sequencing errors and incomplete data through sophisticated mathematical models.
- Testing the AAF method on 12 mammal genomes and 21 tropical tree genomes demonstrates its ability to work effectively with low-coverage data, paving the way for phylogenomic studies in non-model species.
Article Abstract
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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501066 | PMC |
| http://dx.doi.org/10.1186/s12864-015-1647-5 | DOI Listing |
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