GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified "baiting and iterative ...mapping" approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ).
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been ...clarified.
With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family.
Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments.
Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
Abstract
Distinct X-ray plateau and flare phases have been observed in the afterglows of gamma-ray bursts (GRBs), and most of them should be related to central engine activities. In this paper, we ...collect 174 GRBs with X-ray plateau phases and 106 GRBs with X-ray flares. There are 51 GRBs that overlap in the two selected samples. We analyze the distributions of the proportions of the plateau energy
E
plateau
and the flare energy
E
flare
relative to the isotropic prompt emission energy
E
γ
,iso
. The results indicate that they well meet the Gaussian distributions and the medians of the logarithmic ratios are ∼−0.96 and −1.39 in the two cases. Moreover, strong positive correlations between
E
plateau
(or
E
flare
) and
E
γ
,iso
with slopes of ∼0.95 (or ∼0.80) are presented. For the overlapping sample, the slope is ∼0.80. We argue that most of X-ray plateaus and flares might have the same physical origin but appear with different features because of the different circumstances and radiation mechanisms. We also test the applicabilities of two models, i.e., black holes surrounded by fractured hyperaccretion disks and millisecond magnetars, on the origins of X-ray plateaus and flares.
Since a substitution box (
S
-box) is the nonlinearity part of a symmetric key encryption scheme, it directly determines the performance and security level of the encryption scheme. Thus, generating
...S
-box with high performance and efficiency is attracting. This paper proposes a novel method to construct
S
-box using the complete Latin square and chaotic system. First, a complete Latin square is generated using the chaotic sequences produced by a chaotic system. Then an
S
-box is constructed using the complete Latin square. Performance analyses show that the
S
-box generated by our proposed method has a high performance and can achieve strong ability to resist many security attacks such as the linear attack, differential attack and so on. To show the efficiency of the constructed
S
-box, this paper further applies the
S
-box to image encryption application. Security analyses show that the developed image encryption algorithm is able to encrypt different kinds of images into cipher images with uniformly distributed histograms. Performance evaluations demonstrate that it has a high security level and can outperform several state-of-the-art encryption algorithms.
The advances accelerated by next‐generation sequencing and long‐read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of ...phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole‐genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole‐genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
This review highlights the major challenges faced by phylogenomic studies, including genomic conflict and orthology inference, and makes practical recommendations for the transformation from a few loci‐based analyses to large‐scale phylogenomics.
Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes ...from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated crown age is substantially earlier than that of unequivocal angiosperm fossils, and the difference is here termed the 'Jurassic angiosperm gap'. Our time-calibrated plastid phylogenomic tree provides a highly relevant framework for future comparative studies of flowering plant evolution.
Motivated by renewed evidence for new physics in b → sℓℓ transitions in the form of LHCb's new measurements of theoretically clean lepton-universality ratios and the purely leptonic Bs → μ+μ− decay, ...we quantify the combined level of discrepancy with the Standard Model and fit values of short-distance Wilson coefficients. A combination of the clean observables RK, RK*, and Bs → μ μ alone results in a discrepancy with the Standard Model at 4.0σ, up from 3.5σ in 2017. One-parameter scenarios with purely left-handed or with purely axial coupling to muons fit the data well and result in a ∼5σ pull from the Standard Model. In a two-parameter fit of new-physics contributions with both vector and axial-vector couplings to muons the allowed region is much more restricted than in 2017, principally due to the much more precise result on Bs → μ+ μ−, which probes the axial coupling to muons. Including angular observables data restricts the allowed region further. A by-product of our analysis is an updated average of BR (Bs → μ+ μ−) = ( 2.8 ± 0.3 ) × 10−9.
Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly ...impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades.
Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation.
We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.
Low‐cost, environment‐friendly aqueous Zn batteries have great potential for large‐scale energy storage, but the intercalation of zinc ions in the cathode materials is challenging and complex. ...Herein, the critical role of structural H2O on Zn2+ intercalation into bilayer V2O5·nH2O is demonstrated. The results suggest that the H2O‐solvated Zn2+ possesses largely reduced effective charge and thus reduced electrostatic interactions with the V2O5 framework, effectively promoting its diffusion. Benefited from the “lubricating” effect, the aqueous Zn battery shows a specific energy of ≈144 Wh kg−1 at 0.3 A g−1. Meanwhile, it can maintain an energy density of 90 Wh kg−1 at a high power density of 6.4 kW kg−1 (based on the cathode and 200% Zn anode), making it a promising candidate for high‐performance, low‐cost, safe, and environment‐friendly energy‐storage devices.
The co‐intercalation of H2O and Zn2+ as well as the “lubricating effect” of water in V2O5·nH2O is demonstrated, which enhances the rate capability and energy density of zinc batteries. A combination of an ultrahigh power density of 6.4 kW kg−1 and a high energy density of 144 Wh kg−1 is achieved in aqueous rechargeable zinc batteries.
The aim of the present study was to investigate the feasibility of resection based on the nerve and fibrous tissue (NFT) structures around the superior mesenteric artery (SMA) for resectable ...pancreatic adenocarcinoma (R-PDAC) patients.
NFTs around the SMA were classified into four "intensive NTFs area" with spreading the NFTs around the SMA and three SMA nerve plexus regions without branching nerves according to autopsy findings. Complete dissection of four "intensive NTFs areas" was performed by pre-exposing three SMA nerve plexus regions without branching nerves as "dissection-guiding points" with SMA nerve plexus preservation (NFT-based resection). Among 157 R-PDAC patients undergoing pancreaticoduodenectomy, surgical outcomes of 78 patients with NFT-based resection were compared with 59 patients with half-SMA nerve plexus dissection and 20 patients without NFTs dissection.
In the NFT-based resection group, 76.5% had tumor involvement and metastasis in each intensive NTFs area. Operative time, blood loss, and postoperative diarrhea rate were significantly lower in NFT-based resection than in half-SMA nerve plexus group (321 vs 390 min; P < .01, 228 vs 550 mL; P < .01, 5.1% vs 15.3%; P = .04, respectively). R0 rate and median overall survival significantly improved in NFT-based resection than in non-NFT dissection group (93.6% vs 65.0%; P < .01, 49.6 vs 23.6 months, P = .01).
NFT-based resection may become a novel method for R-PDAC patients.
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