Genomic tools development for Aquilegia: construction of a BAC-based physical map

<p>Abstract</p> <p>Background</p> <p>The genus <it>Aquilegia</it>, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. <it>Aquilegia </it>species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance.</p> <p>Results</p> <p>BAC-based genomic resources, including two BAC libraries, a physical map with anchored markers and BAC end sequences, were established from <it>A. formosa</it>. The physical map was composed of a total of 50,155 BAC clones in 832 contigs and 3939 singletons, covering 21X genome equivalents. These contigs spanned a physical length of 689.8 Mb (~2.3X of the genome) suggesting the complex heterozygosity of the genome. A set of 197 markers was developed from ESTs induced by drought-stress, or involved in anthocyanin biosynthesis or floral development, and was integrated into the physical map. Among these were 87 genetically mapped markers that anchored 54 contigs, spanning 76.4 Mb (25.5%) across the genome. Analysis of a selection of 12,086 BAC end sequences (BESs) from the minimal tiling path (MTP) allowed a preview of the <it>Aquilegia </it>genome organization, including identification of transposable elements, simple sequence repeats and gene content. Common repetitive elements previously reported in both monocots and core eudicots were identified in <it>Aquilegia </it>suggesting the value of this genome in connecting the two major plant clades. Comparison with sequenced plant genomes indicated a higher similarity to grapevine (<it>Vitis vinifera</it>) than to rice and <it>Arabidopsis </it>in the transcriptomes.</p> <p>Conclusions</p> <p>The <it>A. formosa </it>BAC-based genomic resources provide valuable tools to study <it>Aquilegia </it>genome. Further integration of other existing genomics resources, such as ESTs, into the physical map should enable better understanding of the molecular mechanisms underlying adaptive radiation and elaboration of floral morphology.</p

Additional file 10 of Genomic tools development for Aquilegia: construction of a BAC-based physical map

Authors’ original file for figure

Genomic tools development for Aquilegia: construction of a BAC-based physical map

Abstract Background The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance. Results BAC-based genomic resources, including two BAC libraries, a physical map with anchored markers and BAC end sequences, were established from A. formosa. The physical map was composed of a total of 50,155 BAC clones in 832 contigs and 3939 singletons, covering 21X genome equivalents. These contigs spanned a physical length of 689.8 Mb (~2.3X of the genome) suggesting the complex heterozygosity of the genome. A set of 197 markers was developed from ESTs induced by drought-stress, or involved in anthocyanin biosynthesis or floral development, and was integrated into the physical map. Among these were 87 genetically mapped markers that anchored 54 contigs, spanning 76.4 Mb (25.5%) across the genome. Analysis of a selection of 12,086 BAC end sequences (BESs) from the minimal tiling path (MTP) allowed a preview of the Aquilegia genome organization, including identification of transposable elements, simple sequence repeats and gene content. Common repetitive elements previously reported in both monocots and core eudicots were identified in Aquilegia suggesting the value of this genome in connecting the two major plant clades. Comparison with sequenced plant genomes indicated a higher similarity to grapevine (Vitis vinifera) than to rice and Arabidopsis in the transcriptomes. Conclusions The A. formosa BAC-based genomic resources provide valuable tools to study Aquilegia genome. Further integration of other existing genomics resources, such as ESTs, into the physical map should enable better understanding of the molecular mechanisms underlying adaptive radiation and elaboration of floral morphology

Additional file of Genomic tools development for Aquilegia: construction of a BAC-based physical map

Additional file of Genomic tools development for Aquilegia: construction of a BAC-based physical ma

Additional file of Genomic tools development for Aquilegia: construction of a BAC-based physical map

Additional file of Genomic tools development for Aquilegia: construction of a BAC-based physical ma

Additional file 3 of Genomic tools development for Aquilegia: construction of a BAC-based physical map

Additional file 3:Spread sheet of the detail sequence information of the overgo probes used in this study. The probes with the nomenclature of Aq_SR_ctg and AHOTEg were derived from drought stress ESTs, while the TC probes were from a list of genes potentially involved in anthocyanin biosynthesis or floral development. To generate the probes, marker sequences were processed through a pipeline composed of RepeatMasker, Cross-Match and Tandem Repeat Finder to remove low complex sequence regions before screening for overgo oligomers by OligoSpawn. (XLS 64 KB

Design of a new recoil separator for measurements of radiative capture reactions in astrophysics

The rates of proton- and alpha-capture reactions on unstable proton-rich nuclei are needed to understand the energy generation and element synthesis occurring in novae, X-ray bursts, and other explosions. Direct measurements of the cross sections of some of these reactions are now possible with radioactive beams and a recoil separator. A new device for such measurements, the Separator for CApture Reactions [SECAR], is being designed for use at the Facility for Rare Isotope Beams (FRIB). The specifications and preliminary conceptual design will be discussed along with plans for the first set of measurements. © 2010 American Institute of Physics

Unbound States of \u3csup\u3e32\u3c/sup\u3eCl relevant for Novae

The 31S(p,γ?)32Cl proton-capture reaction is expected to be the dominant breakout pathway of the SiP cycle, which is important for understanding nucleosynthesis in some novae [1]. At novae temperatures, the 31S(p,γ?)32Cl reaction rate is dominated by 31S+p resonances. Discrepancies in the 32Cl resonance energies were reported in previous measurements [1, 2]. We used the 32S(3He,t)32Cl charge-exchange reaction to produce unbound states in 32Cl and determine their excitation energies by detecting tritons at the focal plane of the Enge Spectrograph at the Yale University\u27s Wright Nuclear Structure Laboratory. Proton branching ratios were determined by detecting the decay protons coming from the residual 32Cl states using a silicon array in the spectrometer\u27s target chamber. The improved energy values of excited levels in 32Cl and measurements of the proton-branching ratios should significantly improve our understanding of the 31S(p,γ?)32Cl reaction rate. © Copyright owned by the author(s

Predictors of staging accuracy, pathologic nodal involvement, and overall survival for cT2N0 carcinoma of the esophagus

OBJECTIVE: Clinical T2N0 esophageal carcinoma is a heterogenous disease frequently complicated by inaccurate staging. Incorrect staging may lead to suboptimal treatment for patients with unidentified local-regionally advanced disease. Therapeutic options for these patients remain controversial. We sought to evaluate the outcomes of patients with cT2N0 who underwent esophagectomy as either primary therapy or after neoadjuvant treatment. METHODS: This was a multi-institutional collaboration of 26 high-volume esophageal centers. Patients with complete staging who underwent elective resection from 2002 to 2012 were included. Three treatment groups were identified; primary esophagectomy, preoperative chemotherapy, and preoperative chemoradiation (CXRT). Pretreatment variables were explored for independent predictors of long-term outcomes. The primary esophagectomy subgroup was evaluated for stage migration. RESULTS: In total, 767 patients were evaluated; 35% (268) had preoperative therapy (195 CXRT, 73 chemotherapy). Staging accuracy was 14% (70/499), with pT  0 in 39% (195). Preoperative treatment modality (none, CXRT, chemotherapy) was not identified as a predictor of outcome (median survival 63, 70, 71 months, respectively, P = .956). Longitudinal tumor length >3.25 cm was predictive of pN+ for the primary esophagectomy cohort as well as adenocarcinoma histology only (odds ratio 2.2 and 2.4, respectively, P < .001). CONCLUSIONS: Current treatment options for patients with cT2N0M0 do not reveal a comparative survival advantage to preoperative therapy. Pretreatment tumor length can identify a subgroup of patients at risk for understaging (pN+). The incidence of overstaging suggests that organ-sparing approaches (endoscopic resection) may play a future role in appropriately selected patients.status: publishe