The unexpected depths of genome‐skimming data: A case study examining Goodeniaceae floral symmetry genes¹

Abstract

Premise of the study:The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae.Methods:Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes.Results:Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions.Discussion:Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

“…In the near future, as the number of fully assembled genomes steadily increase, the ability to use these for assembling genome skim data will increase. This may allow for increased assembly and utilisation of the nuclear and mitochondrial DNA [64] recovered from the genome skims, increasing the power and range of applications for the data.…”

Practical considerations for plant phylogenomics

“…However, when sequenced at a higher depth (2–3×), Berger et al. () have demonstrated that it is possible to extract low‐copy nuclear genes. Higher coverage is needed not only to ensure complete representation of low‐copy loci but also to overcome issues of sequencing error.…”

“…Often, genome skim data contain less than 1× coverage of the nuclear genome, making them inadequate for identification of nuclear genes. However, when sequenced at a higher depth (2-3×), Berger et al (2017) have demonstrated that it is possible to extract low-copy nuclear genes. Higher coverage is needed not only to ensure complete representation of low-copy loci but also to overcome issues of sequencing error.…”

Peer Review #2 of "Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies (v0.1)"

“…The process provides an extensive data set, capable of recovering high-copy fractions of total genomic DNA (organellar genomes, nuclear ribosomal DNA, and other multi-copy elements) through random shearing and inexpensive multiplexing (Berger et al, 2017;Matos-Maraví et al, 2018). The technique is potentially efficient for old museum material and ethanol-preserved specimens (Staats et al, 2013;Maddison and Cooper, 2014;Linard et al, 2016;Grandjean et al, 2017).…”