154 research outputs found
Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa
The hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents. It evolved in Australia where it is found over a wide range of habitat types and is an ecologically important species. Limited genomic resources are currently available for this species, thus our understanding of its evolutionary history and ecological adaptation is restricted. Here, we present a comprehensive transcriptome dataset for future genomic studies into this species.We performed Illumina sequencing of cDNA prepared from leaf tissue collected from seven populations of D. viscosa ssp. angustissima and spatulata distributed along an environmental gradient in South Australia. Sequenced reads were assembled to provide a transcriptome resource. Contiguous sequences (contigs) were annotated using BLAST searches against the NCBI non-redundant database and gene ontology definitions were assigned. Single nucleotide polymorphisms were detected for the establishment of a genetic marker set. A comparison between the two subspecies was also carried out.Illumina sequencing returned 268,672,818 sequence reads, which were de novoassembled into 105,125 contigs. Contigs with significant BLAST alignments (E value < 1e(-5))numbered at 44,191, with 38,311 of these having their most significant hits to sequences from land plant species. Gene Ontology terms were assigned to 28,440 contigs and KEGG analysis identified 146 pathways that the gene products from 5,070 contigs are potentially involved in. The subspecies comparison identified 8,494 fixed SNP differences across 3,979 contiguous sequences, indicating a level of genetic differentiation between them. Across all samples, 248,235 SNPs were detected.We have established a significant genomic data resource for D. viscosa,providing a comprehensive transcriptomic reference. Genetic differences among morphologically distinct subspecies were found. A wide range of putative gene regions were identified along with a large set of variable SNP markers, providing a basis for studies into the evolution and ecological adaptation of D. viscosa.Matthew J. Christmas, Ed Biffin and Andrew J. Low
Unconventional magnetic order on the hyperhoneycomb Kitaev lattice in -Li2IrO3: full solution via magnetic resonant x-ray diffraction
The recently-synthesized iridate -LiIrO has been proposed as a
candidate to display novel magnetic behavior stabilized by frustration effects
from bond-dependent, anisotropic interactions (Kitaev model) on a
three-dimensional "hyperhoneycomb" lattice. Here we report a combined study
using neutron powder diffraction and magnetic resonant x-ray diffraction to
solve the complete magnetic structure. We find a complex, incommensurate
magnetic order with non-coplanar and counter-rotating Ir moments, which
surprisingly shares many of its features with the related structural polytype
"stripyhoneycomb" -LiIrO, where dominant Kitaev interactions
have been invoked to explain the stability of the observed magnetic structure.
The similarities of behavior between those two structural polytypes, which have
different global lattice topologies but the same local connectivity, is
strongly suggestive that the same magnetic interactions and the same underlying
mechanism governs the stability of the magnetic order in both materials,
indicating that both - and -LiIrO are strong candidates
to realize dominant Kitaev interactions in a solid state material.Comment: 14 pages, 9 figure
Targeted capture to assess neutral genomic variation in the narrow-leaf hopbush across a continental biodiversity refugium
The Adelaide geosyncline, a mountainous region in central southern Australia, is purported to be an important continental refugium for Mediterranean and semi-arid Australian biota, yet few population genetic studies have been conducted to test this theory. Here, we focus on a plant species distributed widely throughout the region, the narrow-leaf hopbush, Dodonaea viscosa ssp. angustissima, and examine its genetic diversity and population structure. We used a hybrid-capture target enrichment technique to selectively sequence over 700 genes from 89 individuals across 17 sampling locations. We compared 815 single nucleotide polymorphisms among individuals and populations to investigate population genetic structure. Three distinct genetic clusters were identified; a Flinders/Gammon ranges cluster, an Eastern cluster, and a Kangaroo Island cluster. Higher genetic diversity was identified in the Flinders/Gammon Ranges cluster, indicating that this area is likely to have acted as a refugium during past climate oscillations. We discuss these findings and consider the historical range dynamics of these populations. We also provide methodological considerations for population genomics studies that aim to use novel genomic approaches (such as target capture methods) on non-model systems. The application of our findings to restoration of this species across the region are also considered.Matthew J. Christmas, Ed Biffin, Martin F. Breed & Andrew J. Low
Non-coplanar and counter-rotating incommensurate magnetic order stabilized by Kitaev interactions in -Li2IrO3
Materials that realize Kitaev spin models with bond-dependent anisotropic
interactions have long been searched for, as the resulting frustration effects
are predicted to stabilize novel forms of magnetic order or quantum spin
liquids. Here we explore the magnetism of -LiIrO, which has the
topology of a 3D Kitaev lattice of inter-connected Ir honeycombs. Using
resonant magnetic x-ray diffraction we find a complex, yet highly-symmetric
incommensurate magnetic structure with non-coplanar and counter-rotating Ir
moments. We propose a minimal Kitaev-Heisenberg Hamiltonian that naturally
accounts for all key features of the observed magnetic structure. Our results
provide strong evidence that -LiIrO realizes a spin Hamiltonian
with dominant Kitaev interactions.Comment: 10 pages, 7 figure
A new spin-anisotropic harmonic honeycomb iridate
The physics of Mott insulators underlies diverse phenomena ranging from high
temperature superconductivity to exotic magnetism. Although both the electron
spin and the structure of the local orbitals play a key role in this physics,
in most systems these are connected only indirectly --- via the Pauli exclusion
principle and the Coulomb interaction. Iridium-based oxides (iridates) open a
further dimension to this problem by introducing strong spin-orbit
interactions, such that the Mott physics has a strong orbital character. In the
layered honeycomb iridates this is thought to generate highly spin-anisotropic
interactions, coupling the spin orientation to a given spatial direction of
exchange and leading to strongly frustrated magnetism. The potential for new
physics emerging from such interactions has driven much scientific excitement,
most recently in the search for a new quantum spin liquid, first discussed by
Kitaev \cite{kitaev_anyons_2006}. Here we report a new iridate structure that
has the same local connectivity as the layered honeycomb, but in a
three-dimensional framework. The temperature dependence of the magnetic
susceptibility exhibits a striking reordering of the magnetic anisotropy,
giving evidence for highly spin-anisotropic exchange interactions. Furthermore,
the basic structural units of this material suggest the possibility of a new
family of structures, the `harmonic honeycomb' iridates. This compound thus
provides a unique and exciting glimpse into the physics of a new class of
strongly spin-orbit coupled Mott insulators.Comment: 12 pages including bibliography, 5 figure
Direct Evidence for Dominant Bond-directional Interactions in a Honeycomb Lattice Iridate Na2IrO3
Heisenberg interactions are ubiquitous in magnetic materials and have been
prevailing in modeling and designing quantum magnets. Bond-directional
interactions offer a novel alternative to Heisenberg exchange and provide the
building blocks of the Kitaev model, which has a quantum spin liquid (QSL) as
its exact ground state. Honeycomb iridates, A2IrO3 (A=Na,Li), offer potential
realizations of the Kitaev model, and their reported magnetic behaviors may be
interpreted within the Kitaev framework. However, the extent of their relevance
to the Kitaev model remains unclear, as evidence for bond-directional
interactions remains indirect or conjectural. Here, we present direct evidence
for dominant bond-directional interactions in antiferromagnetic Na2IrO3 and
show that they lead to strong magnetic frustration. Diffuse magnetic x-ray
scattering reveals broken spin-rotational symmetry even above Neel temperature,
with the three spin components exhibiting nano-scale correlations along
distinct crystallographic directions. This spin-space and real-space
entanglement directly manifests the bond-directional interactions, provides the
missing link to Kitaev physics in honeycomb iridates, and establishes a new
design strategy toward frustrated magnetism.Comment: Nature Physics, accepted (2015
Genomics-based phylogenetic and population genetic analysis of global samples confirms Halophila johnsonii Eiseman as Halophila ovalis (R.Br.) Hook.f.
Halophila johnsonii is an endangered seagrass species that is restricted to the southeast coast of Florida, United States. Its taxonomic status has been called into question, in particular, given the close morphological and genetic similarity of H. johnsonii and the widely distributed and morphologically variable Halophila ovalis, which is largely restricted to the Indo-Pacific region. While a close relationship to H. ovalis is uncontroversial, it remains uncertain whether H. johnsonii represents a distinct lineage or is a recent introduction to the Florida region. Given the conservation status of H. johnsonii, distinguishing these alternatives has important implications for the management of the species and its habitat. Here, we develop molecular data sets for samples of H. johnsonii and H. ovalis including DNA sequences, genome-wide SNPs and microsatellites with the view to resolving the affinities of H. johnsonii with respect to the wider H. ovalis complex. Phylogenetic hypotheses based upon plastid (∼18000 bp) and low copy nuclear DNA (∼6500 bp) sequences derived from hybrid capture, along with 990 genome-wide ddRAD SNPs consistently resolved H. johnsonii within H. ovalis. Specifically, we found a close affinity between H. johnsonii and H. ovalis sampled from the east coast of Africa. In addition, Halophila specimens collected in Antigua, which are within the range of morphological variation typical for H. ovalis, are virtually identical to H. johnsonii and the East African H. ovalis samples based upon DNA sequence analyses and these group together using Bayesian clustering analyses of microsatellites and ddRAD SNPs. We conducted population genetic analyses using large number of H. johnsonii samples collected over a 17-year period. Genotypic data generated through microsatellites and ddRAD SNPs revealed genetic uniformity for all 132 H. johnsonii samples across the Indian River Lagoon, Florida, while samples of H. ovalis from Antigua shared the same genotype as H. johnsonii. We conclude that the lack of genetic diversity and the absence of sexual reproduction strongly indicates that the total range of H. johnsonii is actually one clone that is closely related to populations in Africa and Antigua and may be derived from a recent introduction from one of those regions.Michelle Waycott, Kor-jent van Dijk, Ainsley Calladine, Eric Bricker and Ed Biffi
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