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

ABSTRACT:

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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. •

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SUBMITTER: Blischak PD 

PROVIDER: S-EPMC4259454 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature