Open Collections

Allen, Julie M; Huang, Daisie I.; Cronk, Quentin C; Johnson, Kevin P

<b>Abstract</b><br/>Background: Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a single library of paired-end reads: aTRAM, automated Target Restricted Assembly Method. The aTRAM pipeline uses a reference sequence, BLAST, and an iterative approach to target and locally assemble the genes of interest. Results: Our results demonstrate that aTRAM rapidly assembles genes across distantly related taxa. In comparative tests with a closely related taxon, aTRAM assembled the same sequence as reference-based and de novo approaches taking on average < 1 min per gene. As a test case with divergent sequences, we assembled >1,000 genes from six taxa ranging from 25 – 110 million years divergent from the reference taxon. The gene recovery was between 97 – 99% from each taxon. Conclusions: aTRAM can quickly assemble genes across distantly-related taxa, obviating the need for draft genome assembly of all taxa of interest. Because aTRAM uses a targeted approach, loci can be assembled in minutes depending on the size of the target. Our results suggest that this software will be useful in rapidly assembling genes for phylogenomic projects covering a wide taxonomic range, as well as other applications. The software is freely available: http://www.github.com/juliema/aTRAM; <b>Usage notes</b><br /><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">Alignments from Pediculus schaeffi assemblies</h4><div class="o-metadata__file-description">This zip file contains folders with alignments from the assembly of Pediculus schaeffi genes using aTRAM, reference-based and de novo approaches. The alignments include each of these assemblies compared with the reference species Pediculus humanus as well as to each of the other assembly methods.</div><div class="o-metadata__file-name">DRYAD_PedSchaeffi_Data.zip</br></div></div><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">Alignments from aTRAM assemblies across taxa</h4><div class="o-metadata__file-description">Alignments of 1,107 aTRAM gene assemblies from six taxa. Each gene and each taxon is aligned to the reference sequence of Pediculus humanus.</div><div class="o-metadata__file-name">DRYAD_AllTaxon_Alignments.zip</br></div></div>

Dataset

2020-06-24

This dataset is made available under a Creative Commons CC0 license with the following additional/modified terms and conditions: CC0 Waiver

https://doi.org/10.5683/SP2/OZURMJ

https://creativecommons.org/publicdomain/zero/1.0/