Data from: Gene prediction and annotation in Penstemon (Plantaginaceae): a workflow for marker development from extremely low-coverage genome sequencing

Premise of the study: Penstemon (Plantaginaceae) is a large and diverse
genus endemic to North America. However, determining the phylogenetic
relationships among its 280 species has been difficult due to its recent
evolutionary radiation. The development of a large, multilocus data set
can help to resolve this challenge. Methods: Using both previously
sequenced genomic libraries and our own low-coverage whole-genome shotgun
sequencing libraries, we used the MAKER2 Annotation Pipeline to identify
gene regions for the development of sequencing loci from six extremely
low-coverage Penstemon genomes (∼0.005×−0.007×). We also compared this
approach to BLAST searches, and conducted analyses to characterize
sequence divergence across the species sequenced. Results: Annotations and
gene predictions were successfully added to more than 10,000 contigs for
potential use in downstream primer design. Primers were then designed for
chloroplast, mitochondrial, and nuclear loci from these annotated
sequences. MAKER2 identified longer gene regions in all six Penstemon
genomes when compared with BLASTN and BLASTX searches. The average level
of sequence divergence among the six species was 7.14%. Discussion:
Combining bioinformatics tools into a workflow that produces annotations
can be useful for creating potential phylogenetic markers from thousands
of sequences even when genome coverage is extremely low and reference data
are only available from distant relatives. Furthermore, the output from
MAKER2 contains information about important gene features, such as exon
boundaries, and can be easily integrated with visualization tools to
facilitate the process of marker development.