Dataset Information

Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci.

ABSTRACT: UNLABELLED: PREMISE OF THE STUDY:We developed and tested primers for 218 nuclear loci for studying population genetics, phylogeography, and genome evolution in bryophytes. • METHODS AND RESULTS:We aligned expressed sequence tags (ESTs) from Ceratodon purpureus to the Physcomitrella patens genome sequence, and designed primers that are homologous to conserved exons but span introns in the P. patens genome. We tested these primers on four isolates from New York, USA; Otavalo, Ecuador; and two laboratory isolates from Austria (WT4 and GG1). The median genome-wide nucleotide diversity was 0.008 substitutions/site, but the range was large (0-0.14), illustrating the among-locus heterogeneity in the species. • CONCLUSIONS:These loci provide a valuable resource for finely resolved, genome-wide population genetic and species-level phylogenetic analyses of C. purpureus and its relatives.

SUBMITTER: McDaniel SF

PROVIDER: S-EPMC4105291 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci.

McDaniel Stuart F SF van Baren Marijke J MJ Jones Kelly S KS Payton Adam C AC Quatrano Ralph S RS

Applications in plant sciences 20130328 4

<h4>Unlabelled</h4><h4>Premise of the study</h4>We developed and tested primers for 218 nuclear loci for studying population genetics, phylogeography, and genome evolution in bryophytes. •<h4>Methods and results</h4>We aligned expressed sequence tags (ESTs) from Ceratodon purpureus to the Physcomitrella patens genome sequence, and designed primers that are homologous to conserved exons but span introns in the P. patens genome. We tested these primers on four isolates from New York, USA; Otavalo, ...[more]

PMID: 25202534

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Project description:BACKGROUND: Exon-primed intron-crossing (EPIC) markers have three advantages over anonymous genomic sequences in studying evolution of natural populations. First, the universal primers designed in exon regions can be applied across a broad taxonomic range. Second, the homology of EPIC-amplified sequences can be easily determined by comparing either their exon or intron portion depending on the genetic distance between the taxa. Third, having both the exon and intron fragments could help in examining genetic variation at the intraspecific and interspecific level simultaneously, particularly helpful when studying species complex. However, the paucity of EPIC markers has hindered multilocus studies using nuclear gene sequences, particularly in teleost fishes. RESULTS: We introduce a bioinformatics pipeline for developing EPIC markers by comparing the whole genome sequences between two or more species. By applying this approach on five teleost fishes whose genomes were available in the Ensembl database http://www.ensembl.org, we identified 210 EPIC markers that have single-copy and conserved exon regions with identity greater than 85% among the five teleost fishes. We tested 12 randomly chosen EPIC markers in nine teleost species having a wide phylogenetic range. The success rate of amplifying and sequencing those markers varied from 44% to 100% in different species. We analyzed the exon sequences of the 12 EPIC markers from 13 teleosts. The resulting phylogeny contains many traditionally well-supported clades, indicating the usefulness of the exon portion of EPIC markers in reconstructing species phylogeny, in addition to the value of the intron portion of EPIC markers in interrogating the population history. CONCLUSIONS: This study illustrated an effective approach to develop EPIC markers in a taxonomic group, where two or more genome sequences are available. The markers identified could be amplified across a broad taxonomic range of teleost fishes. The phylogenetic utility of individual markers varied according to intron size and amplifiability. The bioinformatics pipelines developed are readily adapted to other taxonomic groups.

Project description:Background and aimsDioecy and sexual dimorphism occur in many terrestrial plant species but are especially widespread among the bryophytes. Despite the prevalence of dioecy in non-vascular plants, surprisingly little is known about how fine-scale sex-specific cell and leaf morphological traits are correlated with sex-specific physiology and population sex ratios. Such data are critical to understanding the inter-relationship between sex-specific morphological and physiological characters and how their relationship influences population structure. In this study, these data types were assessed to determine how they vary across three populations within one moss species and whether fine-scale morphological traits scale up to physiological and sex ratio characteristics.MethodsTwenty cell-, leaf- and canopy-level traits and two photochemical measurements were compared between sexes and populations of the dioecious moss Ceratodon purpureus . Field population-expressed sex ratios were obtained for the same populations.Key resultsMale and female plants differed in cell, leaf and photochemical measures. These sexual dimorphisms were female biased, with females having larger and thicker leaves and greater values for chlorophyll fluorescence-based, leaf photochemistry measurements than males. Female traits were also more variable than male traits. Interestingly, field population sex ratios were significantly male biased in two study populations and female biased in the third study population.ConclusionsThe results demonstrate that the larger morphology and the greater physiological output of female C. purpureus gametophytes compared with males occurs across populations and is likely to have significant effects on resource allocation and biotic interactions. However, this high level of dimorphism does not explain population sex ratio variation in the three study populations tested. This research lays the groundwork for future studies on how differential sex-specific variation in cell and leaf traits influences bryophyte plant fitness.

Dataset Information

Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci.

Publications

Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci.

Similar Datasets

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