Dataset Information

New targets acquired: Improving locus recovery from the Angiosperms353 probe set.

ABSTRACT: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery. We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a 'mega353' target file, with each locus represented by 17-373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets. Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.

SUBMITTER: McLay TGB

PROVIDER: S-EPMC8312740 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

New targets acquired: Improving locus recovery from the Angiosperms353 probe set.

McLay Todd G B TGB Birch Joanne L JL Gunn Bee F BF Ning Weixuan W Tate Jennifer A JA Nauheimer Lars L Joyce Elizabeth M EM Simpson Lalita L Schmidt-Lebuhn Alexander N AN Baker William J WJ Forest Félix F Jackson Chris J CJ

Applications in plant sciences 20210614 7

<h4>Premise</h4>Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for a ...[more]

PMID: 34336399

Similar Datasets

Project description:Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns, but require the integration of the latest genomic information. This study provides a comprehensive workflow implemented in an R package (rePROBE) to assign the entire probes and to annotate the probe sets based on up-to-date genomic and transcriptomic information. The rePROBE package can be applied to available gene expression microarray platforms and addresses both public and custom databases. The revised probe assignment and updated probe-set annotation are applied to commercial microarrays available for different livestock species, i.e., chicken (Gallus gallus; ChiGene-1_0-st: 443,579 probes and 18,530 probe sets), pig (Sus scrofa; PorGene-1_1-st: 592,005 probes and 25,779 probe sets), and cattle (Bos Taurus; BovGene-1_0-st: 530,717 probes and 24,759 probe sets), as well as available for human (Homo sapiens; HuGene-1_0-st) and mouse (Mus musculus; HT_MG-430_PM). Using current species-specific transcriptomic information (RefSeq, Ensembl, and partially non-redundant nucleotide sequences) and genomic information, the applied workflow reveals 297,574 probes (15,689 probe sets) for chicken, 384,715 probes (21,673 probe sets) for pig, 363,077 probes (21,238 probe sets) for cattle, 481,168 probes (23,495 probe sets) for human, and 324,942 probes (32,494 probe sets) for mouse. These are representative of 12,641, 15,758, 18,046, 20,167, and 16,335 unique genes that are both annotated and positioned for chicken, pig, cattle, human, and mouse, respectively. Additionally, the workflow collects information on the number of single nucleotide polymorphisms (SNPs) within respective targeted genomic regions and thus provides a detailed basis for comprehensive analyses such as expression quantitative trait locus (eQTL) studies to identify quantitative and functional traits. The rePROBE R package is freely available at https://github.com/friederhadlich/rePROBE.

Dataset Information

New targets acquired: Improving locus recovery from the Angiosperms353 probe set.

Publications

New targets acquired: Improving locus recovery from the Angiosperms353 probe set.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets