Herbarium genomics is proving promising as next‐generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired‐end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different Angiosperm families, 73 of which were from herbarium material with ages up to 146 years old. For 84 specimens, a sufficient number of paired‐end reads were generated (in total 9.4 × 1012 nucleotides), yielding successful plastome assemblies for 74 specimens. Those derived from herbarium specimens have lower fractions of plastome‐derived reads compared with those from fresh and silica‐gel‐dried specimens, but total herbarium assembly lengths are only slightly shorter. Specimens from wet‐tropical conditions appear to have a higher number of contigs per assembly and lower N50 values. We find no significant correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost‐effective (compared with Sanger sequencing or plastome‐enrichment approaches), and can be performed with limited sample destruction.
BackgroundCopper is an important heavy metal pollutant, with strong toxicity and great harm, which is easy to accumulate in the plant body and is difficult for degradation. This paper adopts medium culture method, taking “Zheng Dan 958” maize seedlings as sample materials. With different copper ion concentration gradients for the simulation of metal copper stress on maize seedlings, it explored the effects on the membrane structure (POD activity, MDA content, membrane permeability) and root activity.ResultsPOD activity increases dramatically when the copper concentration is over 10 μmol/L. MDA content increases sharply when the copper concentration is over 1000 μmol/L, showing a rising trend. Membrane permeability increases greatly when the copper concentration is over 100 μmol/L. Root activity decreases significantly when the copper concentration is 100 μmol/L, showing a clear downward trend.ConclusionsThe copper concentration of 1000 μmol/L has exceeded the maize seedling tolerance to copper, and the activities of protective enzymes of maize seedlings are inhibited. Cell membrane lipid peroxidation has caused serious damage on the structure and function of membrane. Structure of root cells of maize seedling is also damaged, reducing the root activity, so the maize is irreversible hurt.Electronic supplementary materialThe online version of this article (doi:10.1186/s40529-014-0047-5) contains supplementary material, which is available to authorized users.
Lettuce (Lactuca sativa L.) belongs to the genus Lactuca L. and is an important vegetable worldwide. Over the past decades, there have been many controversies about the phylogeny of Lactuca species due to their complex and diverse morphological characters and insufficient molecular sampling. In this study we provide the most extensive molecular phylogenetic reconstruction of Lactuca, including African wild species, using two chloroplast genes (ndhF and trnL-F). The sampling covers nearly 40 % of the total endemic African Lactuca species and 34 % of the total Lactuca species. DNA sequences from all the subfamilies of Asteraceae in Genebank and those generated from Lactuca herbarium samples were used to establish the affiliation of Lactuca within Asteracaeae. Based on the subfamily tree, we selected 33 ndhF sequences from 30 species and 79 trnL-F sequences from 48 species to infer relationships within the genus Lactuca using randomized axelerated maximum likelihood and Bayesian inference analyses. Biogeographical, chromosomal and morphological character states were reconstructed over the Bayesian tree topology. We conclude that Lactuca contains two distinct phylogenetic clades-the crop clade and the Pterocypsela clade. Other North American, Asian and widespread species either form smaller clades or mix with the Melanoseris species. The newly sampled African endemic species probably should be treated as a new genus.
Background Anteromedial cortex-to-cortex reduction is a key parameter for stable reconstruction of the fracture fragments during the intertrochanteric fracture fixation. This paper introduces the oblique fluoroscopic projection as a novel method to evaluate the quality of anteromedial cortical apposition. Methods Three proximal femur specimens were marked with steel wires along five anatomic landmarks: Greater trochanter, Lesser trochanter, Intertrochanteric line, Anterolateral tubercle and the Anteromedial cortical line. After obtaining the standard femoral neck AP and lateral fluoroscopic images, the C-arm was rotated by every 5°increments until a clear tangential view of the antero-medial-inferior corner cortex was observed. 98 cases of intertrochanteric hip fractures were enrolled from April 2018 to October 2019. After fixation with the nails, the intra-operative anteromedial cortex reduction quality was evaluated from the AP, the true lateral, and the new anteromedial oblique fluoroscopic images. The fluoroscopic results were compared with the post-operative 3D-CT reconstruction images. Results The specimen study showed that internal rotation of the C-arm to approximately 30 ° can remove all the obscure shadows and clearly display the antero-medial-inferior cortical tangent line. Clinically,the positive, neutral and negative apposition of different cortices via intra-operative fluoroscopic images showed79, 19 and 0 cases of medial cortical apposition in AP views; 2, 68 and 28 cases of anterior cortices in lateral views;and 22, 51 and 25cases of anteromedial cortical apposition in oblique views respectively. The post-operative 3D-CT reconstruction images revealed that the final anteromedial cortical contact was noted in 62 cases (63.3%), and lost in 36 cases (36.7%). The overall coincidence rate between intra-operative fluoroscopy and post-operative 3D-CT was 63.3% (62/98) in AP view,79.6% (78/98) in lateral view, and 86.7% (85/98) in oblique view(p < 0.001). Negative cortical apposition in oblique view was highly predictive of a final loss of cortical support on 3D CT (24/25 cases, 96%).And non-negative cortical apposition in oblique view was highly associated with true cortical support on 3D CT images (61/73 cases, 83.6%) (p < 0.001). Conclusions Besides the AP and lateral projections, an anteromedial oblique view of 30° certifies to be a very useful means for evaluation of the fracture reduction quality of anteromedial cortical apposition.
As important post-translational modifications, protein cysteine modifications (PCMs) occurring at cysteine thiol group play critical roles in the regulation of various biological processes in eukaryotes. Due to the rapid advancement of high-throughput proteomics technologies, a large number of PCM events have been identified but remain to be curated. Thus, an integrated resource of eukaryotic PCMs will be useful for the research community. In this work, we developed an integrative database for protein cysteine modifications in eukaryotes (iCysMod), which curated and hosted 108 030 PCM events for 85 747 experimentally identified sites on 31 483 proteins from 48 eukaryotes for 8 types of PCMs, including oxidation, S-nitrosylation (-SNO), S-glutathionylation (-SSG), disulfide formation (-SSR), S-sulfhydration (-SSH), S-sulfenylation (-SOH), S-sulfinylation (-SO2H) and S-palmitoylation (-S-palm). Then, browse and search options were provided for accessing the dataset, while various detailed information about the PCM events was well organized for visualization. With human dataset in iCysMod, the sequence features around the cysteine modification sites for each PCM type were analyzed, and the results indicated that various types of PCMs presented distinct sequence recognition preferences. Moreover, different PCMs can crosstalk with each other to synergistically orchestrate specific biological processes, and 37 841 PCM events involved in 119 types of PCM co-occurrences at the same cysteine residues were finally obtained. Taken together, we anticipate that the database of iCysMod would provide a useful resource for eukaryotic PCMs to facilitate related researches, while the online service is freely available at http://icysmod.omicsbio.info.
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