Dataset Information

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

ABSTRACT: UNLABELLED: 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.

SUBMITTER: Blischak PD

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

REPOSITORIES: biostudies-literature

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

Blischak Paul D PD Wenzel Aaron J AJ Wolfe Andrea D AD

Applications in plant sciences 20141204 12

<h4>Unlabelled</h4><h4>Premise of the study</h4>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. •<h4>Methods</h4>Using both previously sequenced genomic libraries and our own low-coverage whole-genome shotgun sequencing libraries, we used the MAKE ...[more]

PMID: 25506519

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Project description:In many plant species, pollination syndromes predict the most effective pollinator. However, other floral visitors may also offer effective pollination services and promote mixed pollination systems. Several species of the species-rich Penstemon (Plantaginaceae) exhibit a suite of floral traits that suggest adaptation for pollination by both hymenopterans and hummingbirds. Transitions from the ancestral hymenopteran pollination syndrome to more derived hummingbird pollination syndrome may be promoted if the quantity or quality of visits by hummingbirds is increased and if the ancestral pollinator group performs less efficiently. The quantification of such shifts in pollination systems in the group is still limited. We aimed to investigate floral traits linked to this pollination syndrome in Penstemon gentianoides with flowers visited by bumblebees and hummingbirds.We investigated the floral biology, pollinator assemblages, breeding system and nectar production patterns of P. gentianoides inhabiting a temperate montane forest in central Mexico. Pollination experiments were also conducted to assess the pollinator effectiveness of bumblebees and hummingbirds.P. gentianoides flowers are protandrous, with 8-d male phase (staminate) flowers, followed by the ∼1-7 d female phase (pistillate phase). Flowers display traits associated with hymenopteran pollination, including purple flowers abruptly ampliate-ventricose to a broad throat with anthers and stigmas included, and long lifespans. However, the nectar available in the morning hours was abundant and dilute, traits linked to flowers with a hummingbird pollination syndrome. Two hummingbird species made most of the visits to flowers, Selasphorus platycercus (30.3% of all visits), followed by Archilochus colubris (11.3%). Bumblebees (Bombus ephippiatus, B. huntii and B. weisi) accounted for 51.8% of all recorded visits, but their foraging activity was restricted to the warmer hours. Hummingbirds made more foraging bouts and visited more flowers than hymenopteran species. Flowers experimentally pollinated by B. ephippiatus produced significantly more fruits than those pollinated by S. platycercus. However, there was no statistical difference in the number of seeds produced per fruit when a bumblebee or a hummingbird was the pollinator.We have shown that bumblebees and hummingbirds visit and pollinate P. gentianoides flowers. Despite floral traits resembling the hymenoptera pollination syndrome, flowers of P. gentianoides offer characteristic nectar rewards to flowers with a hummingbird pollination syndrome. Although pollination efficiency is higher among flowers visited by hymenoptera, the noteworthy percentage of fruit production and number of seeds per fruit derived from hummingbird pollination highlights the importance of hummingbirds as a functional group of pollinators that might have potential evolutionary consequences to the plants.

Dataset Information

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

Publications

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

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