scholarly journals NEW MOLECULAR MARKERS IN Hydrangea AND THEIR USEFULLNESS IN EVALUATING DIVERSITY, VERIFYING HYBRIDS, AND UNCOVERING GENES

HortScience ◽  
2005 ◽  
Vol 40 (3) ◽  
pp. 881b-881
Author(s):  
Tim Rinehart ◽  
Sandy Reed
Keyword(s):  
Species Diversity ◽  
Large Scale ◽  
Sequence Data ◽  
Issr Markers ◽  
Future Research ◽  
Species Variation ◽  
Marker Assisted Breeding ◽  
Dna Sequence Data ◽  
Hydrangea Macrophylla ◽  
Limited Usefulness

Hydrangea popularity and use in the landscape has expanded rapidly in recent years with the addition of remontant varieties. Most cultivars in production belong to the species Hydrangea macrophylla but H. paniculata, H. arborescens, H. serrata, H. aspera, H. heteromalla, H. integrifolia, H. anomala, H. seemanii, and H. quercifolia are also commercially available. In addition to species diversity there is high intra-species variation, particularly in H. macrophylla, which includes mopheads, lacecaps, French, Japanese, dwarf, and variegated varieties. Relatively little is known about the genetic background or combinability of these plants. DNA sequence data, genome size, RAPD, AFLP, and ISSR markers have been used for taxonomic identification and to estimate diversity within the genus. All of these methods have limited usefulness in a large scale breeding program. We recently established microsatellite markers for Hydrangea and evaluated their utility for estimating species diversity and identifying cultivars within H. macrophylla and H. paniculata. We also verified an inter-specific cross between H. macrophylla and H. paniculata using these markers. Future research includes marker assisted breeding, particularly with respect to remontant flowering traits.

scholarly journals Self-organizing Clustering: Non-hierarchical Clustering for Large Scale DNA Sequence Data

2007 ◽  
Vol 3 ◽  
pp. 193-197 ◽  
Author(s):  
Kou Amano ◽  
Hiroaki Ichikawa ◽  
Hidemitsu Nakamura ◽  
Hisataka Numa ◽  
Kaoru Fukami-Kobayashi ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Hierarchical Clustering ◽  
Large Scale ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Self Organizing

scholarly journals Sequence variation aware genome references and read mapping with the variation graph toolkit

2017 ◽  
Author(s):  
Erik Garrison ◽  
Jouni Sirén ◽  
Adam M. Novak ◽  
Glenn Hickey ◽  
Jordan M. Eizenga ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Large Scale ◽  
De Novo ◽  
Sequence Data ◽  
Variant Calling ◽  
Read Mapping ◽  
Dna Sequence Data ◽  
Suffix Arrays ◽  
Improved Accuracy ◽  
Reference Genomes

AbstractReference genomes guide our interpretation of DNA sequence data. However, conventional linear references are fundamentally limited in that they represent only one version of each locus, whereas the population may contain multiple variants. When the reference represents an individual’s genome poorly, it can impact read mapping and introduce bias. Variation graphs are bidirected DNA sequence graphs that compactly represent genetic variation, including large scale structural variation such as inversions and duplications.1 Equivalent structures are produced by de novo genome assemblers.2,3 Here we present vg, a toolkit of computational methods for creating, manipulating, and utilizing these structures as references at the scale of the human genome. vg provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays,4 with improved accuracy over alignment to a linear reference, creating data structures to support downstream variant calling and genotyping. These capabilities make using variation graphs as reference structures for DNA sequencing practical at the scale of vertebrate genomes, or at the topological complexity of new species assemblies.

scholarly journals A Show of Character—a further response to Wiley et al.

Zootaxa ◽  
2011 ◽  
Vol 2946 (1) ◽  
pp. 29 ◽  
Author(s):  
ANTHONY C. GILL ◽  
RANDALL D. MOOI
Keyword(s):  
Dna Sequence ◽  
Large Scale ◽  
Sequence Data ◽  
Molecular Data ◽  
Scientific Rigor ◽  
Dna Sequence Data ◽  
Phylogenetic Hypotheses ◽  
Alternative Relationships

Wiley et al. (2011) begin their critique of our paper (Mooi & Gill, 2010) with an assertion: “we need to make itclear that the foundation of their arguments rests not on scientific rigor, but rather on opinions about the re-classification of fishes using molecular data. This bias is the reason that they only targeted researchers who proposed changes in the higher-level taxonomy of fishes using phylogenetic hypotheses based on DNA sequence data (Miya et al. 2007, Smith & Craig 2007, Thacker 2009). In criticizing these studies, they do not suggest any alternative relationships or provide any counter evidence to the proposed relationships.” And on page 8, they apparently read our thoughts (aside from the title, none of the words in quotations was written by us in that context) and concluded: “Mooi & Gill entitled their paper “A crisis in fish systematics” because they long for the days when “real” ichthyologists found “meaningful” characters and “true” relationships.” Finally (p. 9), they contend that “Mooi & Gill’s various studies are usually focused on Johnson & Patterson’s (1993: 555) “disparate twigs of the [percomorph] tree,” whereas the explicit studies they criticize are large-scale and taxon rich datasets that have not otherwise been analyzed in Percomorpha.”

scholarly journals SSR Markers for Accelerated Hydrangea Breeding and Hybrid Verification

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1102B-1102
Author(s):  
Timothy Rinehart ◽  
Sandra Reed ◽  
Brian Scheffler
Keyword(s):  
Species Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Genetic Background ◽  
Interspecific Cross ◽  
Future Research ◽  
Marker Assisted Breeding

Hydrangea popularity and use in the landscape has expanded rapidly in recent years with the addition of remontant varieties. Relatively little is known about the genetic background or combinability of these plants. We recently established microsatellite markers for hydrangea and evaluated their utility for estimating species diversity and identifying cultivars. We also verified an interspecific cross using these markers. Future research includes marker assisted breeding, particularly with respect to remontant flowering traits.

scholarly journals Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)

2018 ◽  
Vol 66 (2) ◽  
pp. 115 ◽  
Author(s):  
Timothy J. Page ◽  
Mark I. Stevens ◽  
Mark Adams ◽  
Ralph Foster ◽  
Alejandro Velasco-Castrillón ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Total Evidence ◽  
Future Research ◽  
Limited Data ◽  
Dna Sequence Data ◽  
Species Being ◽  
North Western ◽  
Systematic Framework

Australia was once thought to be a biodiversity desert when considering the subterranean world; however, recent work has revealed a fascinating collection of cave creatures, many with surprising biogeographic histories. This has especially been so in the karstic regions of north-western Australia (Cape Range peninsula, Barrow Island, Pilbara), which is home not only to a diverse collection of subterranean invertebrates, but also to the continent’s only known underworld-adapted vertebrates, which includes the cave fish in the genus Milyeringa. These cave gudgeons have recently been in a state of taxonomic flux, with species being both split and lumped, but this was done with limited data (incomplete geographic sampling and no nuclear DNA sequence data). Therefore, we have revisited the systematic status of Milyeringa in a total-evidence molecular approach by integrating all existing data (mitochondrial, allozymes) with new DNA sequences from nuclear and mitochondrial loci and new multilocus allozyme data. Our conclusion, that there are two species, matches the most recent taxonomic treatment, with Milyeringa veritas present on both the eastern and western sides of the Cape Range peninsula, and Milyeringa justitia on Barrow Island. This has implications for future research in the linked fields of biogeography and conservation.

scholarly journals Data Attribution from Download to Publication

2018 ◽  
Vol 2 ◽  
pp. e26060
Author(s):  
Pamela Soltis
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Sequence Data ◽  
Research Process ◽  
Global Biodiversity Information Facility ◽  
Data Set ◽  
Dna Sequence Data ◽  
Large Scale Data ◽  
Data Tracking ◽  
Biodiversity Information

Digitized natural history data are enabling a broad range of innovative studies of biodiversity. Large-scale data aggregators such as Global Biodiversity Information facility (GBIF) and Integrated Digitized Biocollections (iDigBio) provide easy, global access to millions of specimen records contributed by thousands of collections. A developing community of eager users of specimen data – whether locality, image, trait, etc. – is perhaps unaware of the effort and resources required to curate specimens, digitize information, capture images, mobilize records, serve the data, and maintain the infrastructure (human and cyber) to support all of these activities. Tracking of specimen information throughout the research process is needed to provide appropriate attribution to the institutions and staff that have supplied and served the records. Such tracking may also allow for annotation and comment on particular records or collections by the global community. Detailed data tracking is also required for open, reproducible science. Despite growing recognition of the value and need for thorough data tracking, both technical and sociological challenges continue to impede progress. In this talk, I will present a brief vision of how application of a DOI to each iteration of a data set in a typical research project could provide attribution to the provider, opportunity for comment and annotation of records, and the foundation for reproducible science based on natural history specimen records. Sociological change – such as journal requirements for data deposition of all iterations of a data set – can be accomplished using community meetings and workshops, along with editorial efforts, as were applied to DNA sequence data two decades ago.

scholarly journals Temporal lags and overlap in the diversification of weevils and flowering plants

2009 ◽  
Vol 106 (17) ◽  
pp. 7083-7088 ◽  
Author(s):  
Duane D. McKenna ◽  
Andrea S. Sequeira ◽  
Adriana E. Marvaldi ◽  
Brian D. Farrell
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Divergence Times ◽  
Resource Tracking ◽  
Crown Group ◽  
Dna Sequence Data ◽  
Angiosperm Diversification ◽  
History Of ◽  
Fossil Data ◽  
Diversification Event

The extraordinary diversity of herbivorous beetles is usually attributed to coevolution with angiosperms. However, the degree and nature of contemporaneity in beetle and angiosperm diversification remain unclear. Here we present a large-scale molecular phylogeny for weevils (herbivorous beetles in the superfamily Curculionoidea), one of the most diverse lineages of insects, based on ≈8 kilobases of DNA sequence data from a worldwide sample including all families and subfamilies. Estimated divergence times derived from the combined molecular and fossil data indicate diversification into most families occurred on gymnosperms in the Jurassic, beginning ≈166 Ma. Subsequent colonization of early crown-group angiosperms occurred during the Early Cretaceous, but this alone evidently did not lead to an immediate and major diversification event in weevils. Comparative trends in weevil diversification and angiosperm dominance reveal that massive diversification began in the mid-Cretaceous (ca.112.0 to 93.5 Ma), when angiosperms first rose to widespread floristic dominance. These and other evidence suggest a deep and complex history of coevolution between weevils and angiosperms, including codiversification, resource tracking, and sequential evolution.

Assessment of the order Rhodymeniales (Rhodophyta) from British Columbia using an integrative taxonomic approach reveals overlooked and cryptic species diversity

Botany ◽  
2018 ◽  
Vol 96 (6) ◽  
pp. 359-383 ◽  
Author(s):  
Gina V. Filloramo ◽  
Gary W. Saunders
Keyword(s):  
British Columbia ◽  
Species Diversity ◽  
Dna Sequence ◽  
Sequence Data ◽  
The Novel ◽  
Additional Species ◽  
Dna Sequence Data ◽  
Species Groups ◽  
Taxonomic Approach ◽  
Genetic Species

Molecular-assisted alpha taxonomy using COI-5P and rbcL-3P was employed to reassess species diversity for the Rhodymeniales (Rhodophyta) in British Columbia. A total of 563 collections from British Columbia were resolved as 16 genetic species groups, whereas 13 were previously reported. Collections attributed to Botryocladia pseudodichotoma from British Columbia were resolved as distinct from collections of that species from California (type locality) and were assigned to Botryocladia hawkesii sp. nov. DNA sequence data also resolved an additional species of Fryeella. Although two species of Gloiocladia were recognized, genetic analyses resolved three: G. fryeana, G. laciniata, and Gloiocladia vigneaultii sp. nov. Data also resolved Gloiocladia media comb. nov. from California. For the genus Rhodymenia, where two species were expected, DNA sequence data resolved four. Both R. californica and R. pacifica were confirmed in British Columbia, whereas some collections field-identified as R. californica were genetically distinct and assigned to the novel species, Rhodymenia bamfieldensis sp. nov. Some collections initially identified as R. pacifica were assigned to the resurrected species R. rhizoides. Anatomical development for the monospecific genus Minium was also reassessed owing to that taxon’s assignment to the Fryeellaceae. Our investigation clarified the number of rhodymenialean species in British Columbia and resolved taxonomic and distributional uncertainties associated with some of these taxa.

scholarly journals Ploidy Variation and Genetic Diversity in Dichroa

HortScience ◽  
2010 ◽  
Vol 45 (2) ◽  
pp. 208-213 ◽  
Author(s):  
Timothy A. Rinehart ◽  
Brian E. Scheffler ◽  
Sandra M. Reed
Keyword(s):  
Genetic Diversity ◽  
Dna Sequence ◽  
Genetic Background ◽  
Sequence Data ◽  
Taxonomic Revision ◽  
Intergeneric Hybrids ◽  
High Genetic Diversity ◽  
Dna Sequence Data ◽  
Hydrangea Macrophylla ◽  
Close Genetic Relationship

Recent evidence suggests a close genetic relationship between Hydrangea macrophylla (Thunb.) Ser. and D. febrifuga Lour., which supports previous morphological and DNA sequence data. This relationship was confirmed by the production of fertile intergeneric hybrids. We characterize the genetic diversity of available D. febrifuga plants, both cultivars and wild-collected taxa, as breeding material to improve H. macrophylla. Relatively high genetic diversity is seen among D. febrifuga, which splits into two main clusters. We also document considerable differences in genome size when compared with previously characterized D. febrifuga. Dichroa versicolor (Fortune) D.R. Hunt plants were also included and data suggest that D. versicolor could be a hybrid between H. macrophylla and D. febrifuga, similar to the intergeneric hybrids produced by recent breeding efforts. Because native H. macrophylla plants do not overlap extensively with D. febrifuga populations, we tested Hydrangea indochinensis Merr. as a possible parent because endemic H. indochinensis populations overlap regions where D. febrifuga and D. versicolor have been collected. However, results suggest that H. indochinensis does not share a genetic background with D. versicolor. Taxonomic revision of Dichroa is warranted, especially because we document several more intergeneric hybrids from self-sown, open-pollinated sources.

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