Bromus tectorum
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ABSTRACT:
PROVIDER: PRJNA311072 | ENA |
REPOSITORIES: ENA
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Project description:To investigate phylogenetic relationships among and within major lineages of Bromus, with focus on Bromus sect. Bromus, we analyzed DNA sequences from two nuclear ribosomal (ITS, ETS) and two plastid (rpl32-trnLUAG , matK) regions. We sampled 103 ingroup accessions representing 26 taxa of B. section Bromus and 15 species of other Bromus sections. Our analyses confirm the monophyly of Bromus s.l. and identify incongruence between nuclear ribosomal and plastid data partitions for relationships within and among major Bromus lineages. Results support classification of B. pumilio and B. gracillimus within B. sect. Boissiera and B. sect. Nevskiella, respectively. These species are sister groups and are closely related to B. densus (B. sect. Mexibromus) in nrDNA trees and Bromus sect. Ceratochloa in plastid trees. Bromus sect. Bromopsis is paraphyletic. In nrDNA trees, species of Bromus sects. Bromopsis, Ceratochloa, Neobromus, and Genea plus B. rechingeri of B. sect. Bromus form a clade, in which B. tomentellus is sister to a B. sect. Genea-B. rechingeri clade. In the plastid trees, by contrast, B. sect. Bromopsis species except B. tomentosus form a clade, and B. tomentosus is sister to a clade comprising B. sect. Bromus and B. sect. Genea species. Affinities of B. gedrosianus, B. pulchellus, and B. rechingeri (members of the B. pectinatus complex), as well as B. oxyodon and B. sewerzowii, are discordant between nrDNA and plastid trees. We infer these species may have obtained their plastomes via chloroplast capture from species of B. sect. Bromus and B. sect. Genea. Within B. sect. Bromus, B. alopecuros subsp. caroli-henrici, a clade comprising B. hordeaceus and B. interruptus, and B. scoparius are successive sister groups to the rest of the section in the nrDNA phylogeny. Most relationships among the remaining species of B. sect. Bromus are unresolved in the nrDNA and plastid trees. Given these results, we infer that most B. sect. Bromus species likely diversified relatively recently. None of the subdivisional taxa proposed for Bromus sect. Bromus over the last century correspond to natural groups identified in our phylogenetic analyses except for a group including B. hordeaceus and B. interruptus.
| S-EPMC9526414 | biostudies-literature
Project description:Bromus biebersteinii is a perennial gramineous grass, which is mainly distributed in Southwest Asia. In our study, we obtained the complete chloroplast genome of B. biebersteinii and found it is 137,189 bp in length. The GC content of its whole chloroplast genome is 38.37%. Among the 134 unique genes in the circular genome, 38 tRNA, 8 rRNA and 88 protein-coding genes were successfully annotated. We constructed the Maximum likelihood (ML) tree with 12 species, and found that B. biebersteinii was phylogenetically close to Bromus vulgaris of the genus Bromus.
| S-EPMC8218841 | biostudies-literature
Project description:Background and aimsBromus tectorum (cheatgrass or downy brome) is an exotic annual grass that is dominant over large areas of former shrubland in western North America. To flower in time for seed production in early summer, B. tectorum plants generally require vernalization at winter temperatures, either as imbibed seeds or as established seedlings.MethodsVariation in response to increasing periods of vernalization as seeds or seedlings for progeny of ten full-sib families from each of four B. tectorum populations from contrasting habitats was studied.Key resultsAs vernalization was increased from 0 to 10 weeks, the proportion of plants flowering within 20 weeks increased, weeks to initiation of flowering decreased, and seed yield per plant increased, regardless of whether plants were vernalized as seeds or seedlings. Most of the variation was accounted for by differences among populations. Plants of the warm desert population flowered promptly even without vernalization, while those of the cold desert, foothill and montane populations showed incremental changes in response variables as a function of vernalization period. Populations differed in among-family variance, with the warm desert population generally showing the least variance and the cold desert population the most. Variation among populations and among families within populations decreased as vernalization period increased, whereas the non-genetic component of variance showed no such pattern.ConclusionsVariation in vernalization response was found to be adaptively significant and apparently represents the result of contrasting selection regimes on a range of founder genotypes.
| S-EPMC4242293 | biostudies-literature
Project description:<p>X-linked Dystonia-Parkinsonism (XDP) is a long-standing quandary in human disease genetics. XDP is predominantly observed on Panay island in the Philippines. This study is one of the first of its kind to interrogate an unsolved Mendelian disorder by integrating genome and transcriptome assembly methods using Illumina, 10X Genomics, Pacific Biosciences, and Agilent genome targeting technologies. These data provide strong evidence for a pathogenic link between a noncoding SVA retrotransposon and XDP. We demonstrate that this Mendelian disorder is associated with a sine-VNTR-Alu (SVA) retrotransposon that inserted into the TAF1 gene and is shared by all XDP probands, yet never observed in controls from worldwide populations. Transcriptome assembly in iPSC-derived neural stem cells (NSCs) and neurons revealed that this SVA caused aberrant splicing and significant intron retention, which was negatively correlated with TAF1 expression. Remarkably, CRISPR/Cas9 excision of the SVA rescued the aberrant transcriptional signature and normalized expression of TAF1 in patient-derived NSCs.</p>
| phs001525 | dbGaP
Project description:BackgroundGlobal change produces pervasive negative impacts on biodiversity worldwide. Land use change and biological invasions are two of the major drivers of global change that often coexist; however, the effects of their interaction on natural habitats have been little investigated. In particular, we aimed to analyse whether the invasion of an introduced grass (Bromus tectorum; cheatgrass) along roads verges and the disturbance level in the natural surrounding habitat interact to influence the degree of B. tectorum invasion in the latter habitats in north-western Patagonia.MethodsAlong six different roads, totalling approximately 370 km, we set two 50 m × 2 m sampling plots every 5 km (73 plots in total). One plot was placed parallel to the road (on the roadside) and the other one perpendicular to it, towards the interior of the natural surrounding habitat. In each plot, we estimated the B. tectorum plant density in 1 m2 subplots placed every 5 m. In the natural habitat, we registered the vegetation type (grassy steppe, shrub-steppe, shrubland, and wet-meadow) and the disturbance level (low, intermediate, and high). Disturbance level was visually categorized according to different signs of habitat degradation by anthropogenic use.ResultsB. tectorum density showed an exponential decay from roadsides towards the interior of natural habitats. The degree of B. tectorum invasion inside natural habitats was positively related to B. tectorum density on roadsides only when the disturbance level was low. Shrub-steppes, grassy steppes and shrublands showed similar mean density of B. tectorum. Wet-meadows had the lowest densities of B. tectorum. Intermediate and highly disturbed environments presented higher B. tectorum density than those areas with low disturbance.DiscussionOur study highlights the importance of the interaction between road verges and disturbance levels on B. tectorum invasion in natural habitats surrounding roads of north-western Patagonia, particularly evidencing its significance in the invasion onset. The importance of invasion in road verges depends on disturbance level, with better conserved environments being more resistant to invasion at low levels of B. tectorum density along road verges, but more susceptible to road verges invasion at higher levels of disturbance. All the habitats except wet-meadows were invaded at a similar degree by B. tectorum, which reflects its adaptability to multiple habitat conditions. Overall, our work showed that synergies among global change drivers impact native environments favouring the invasion of B. tectorum.
| S-EPMC6120438 | biostudies-literature
Project description:Bromus Inermis Leyss 1761 is a perennial herb with large yield and famous for its high nutritional value and long utilization season. The study of B. inermis chloroplast (cp) genome provides an important basis for the study of chloroplast genetic engineering and system evolution. Its cp genome was 137,153 bp in length, containing a pair of inverted repeated (IR) regions (21,699 bp), separated by a large single copy region (LSC) of 81,137 bp, and a small single copy (SSC) region of 12,618 bp. Moreover, a total of 129 functional genes were annotated, including 83 mRNA, 38 tRNA genes, and 8 rRNA genes. The phylogenetic relationships of 15 species indicated that B. inermis was closely related to Bromus biebersteinii. This study might contribute to provide a theoretical basis for species identification and biological research.
| S-EPMC8462858 | biostudies-literature