Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system for this population and subsequent development of high-resolution genetic map. An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation. This is useful for accurate mRNA abundance and detection of expression QTL (eQTLs) in mapping populations. Deep RNA-Seq of two Brassica rapa genotypes-R500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)-using eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads. A total of 330,995 SNPs were identified in transcribed regions between the two genotypes with an average frequency of one SNP in every 200 bases. The deep RNA-Seq reassembled Brassica rapa transcriptome identified 44,239 protein-coding genes. Compared with current gene models of B. rapa, we detected 3537 novel transcripts, 23,754 gene models had structural modifications, and 3655 annotated proteins changed. Gaps in the current genome assembly of B. rapa are highlighted by our identification of 780 unmapped transcripts. All the SNPs, annotations, and predicted transcripts can be viewed at http://phytonetworks.ucdavis.edu/

Measurement of e + e − → ωη ′ cross sections at s = 2. 000 to 3. 080 GeV

We measured the Born cross sections for the process e+e− → ωη′ at 22 center-of-mass energies from 2.000 to 3.080 GeV with the BESIII detector at the BEPCII collider. We observed a resonant structure with a statistical significance of 9.6σ. A Breit-Wigner fit determines its mass to be MR = (2153 ± 30 ± 31) MeV/c2 and its width to be ΓR = (167 ± 77 ± 7) MeV, where the first uncertainties are statistical and the second are systematic

Search for the semi-muonic charmonium decay J/ψ → D − μ + ν μ + c. c

Using (10087 ± 44) × 106J/ψ events collected with the BESIII detector at the BEPCII e+e− storage ring at the center-of-mass energy of s = 3.097 GeV, we present a search for the rare semi-muonic charmonium decay J/ψ → D−μ+νμ + c.c.. Since no significant signal is observed, we set an upper limit of the branching fraction to be B (J/ψ → D−μ+νμ + c.c.) < 5.6 × 10−7 at 90% confidence level. This is the first search for the weak decay of charmonium with a muon in the final state

Observation of the semileptonic decays D 0 → K S 0 π − π 0 e + ν e and D + → K S 0 π + π − e + ν e

By analyzing e+e− annihilation data corresponding to an integrated luminosity of 2.93 fb−1 collected at a center-of-mass energy of 3.773 GeV with the BESIII detector, the first observation of the semileptonic decays D0→KS0π−π0e+νe and D+→KS0π+π−e+νe is reported. In the hypothesis that all events correspond to K1(1270) decays, the branching fractions are measured to be BD0→K11270−→KS0π−π0e+νe=1.69−0.46+0.53±0.15×10−4 and BD+→K¯112700→KS0π+π−e+νe=1.47−0.40+0.45±0.14×10−4 with statistical significance of 5.4σ and 5.6σ, respectively. When combined with measurements of the K1(1270) → K+π−π decays, the absolute branching fractions are determined to be BD0→K11270−e+νe=1.08−0.13−0.10+0.14+0.08±0.21×10−3 and BD+→K¯112700e+νe=1.70−0.23+0.26±0.13±0.35×10−3. The first and second uncertainties are statistical and systematic, respectively, and the third uncertainties originate from the assumed branching fractions of the K1(1270) → Kππ decays

Measurement of the e + e − → K S 0 K L 0 π 0 cross sections from s = 2. 000 to 3. 080 GeV

Based on e+e− collision data collected at center-of-mass energies from 2.000 to 3.080 GeV by the BESIII detector at the BEPCII collider, a partial wave analysis is performed for the process e+e− → KS0KL0π0. The results allow the Born cross sections of the process e+e− → KS0KL0π0, as well as its subprocesses e+e− → K∗(892)0K¯0 and K2∗(1430)0K¯0 to be measured. The Born cross sections for e+e− → KS0KL0π0 are consistent with previous measurements by BaBar, but with substantially improved precision. The Born cross section lineshape of the process e+e−K∗(892)0K¯0 is consistent with a vector meson state around 2.2 GeV with a significance of 3.2σ. A Breit-Wigner fit determines its mass as MY = (2164.7 ± 9.1 ± 3.1) MeV/c2 and its width as ΓY = (32.4 ± 21.0 ± 1.8) MeV

Search for ∆S = 2 nonleptonic hyperon decays Ω − → Σ 0 π − and Ω − → nK −

Using (27.12 ± 0.14) × 108ψ(3686) events collected by the BESIII detector at the center-of-mass energy of s = 3.686 GeV, we search for the first time for two nonleptonic hyperon decays that change strangeness by two units, Ω− → Σ0π− and Ω− → nK−. No significant signal is observed. The upper limits on their decay branching fractions are determined to be B(Ω− → Σ0π−) < 5.4 × 10−4 and B(Ω− → nK−) < 2.4 × 10−4 at the 90% confidence level

Measurement of Born cross section of e + e − → Σ + Σ ¯ − at center-of-mass energies between 3.510 and 4.951 GeV

Using 24.1 fb−1 of e+e− collision data collected with the BESIII detector at the BEPCII collider, the Born cross sections and effective form factors of the e+e−→Σ+Σ¯− reaction are measured. The measurements are performed at center-of-mass energies ranging from 3.510 to 4.951 GeV. No significant evidence for the decay of the charmonium(-like) states, ψ(3770), ψ(4040), ψ(4160), Y(4230), Y(4360), ψ(4415), and Y(4660), into a Σ+Σ¯− final state is observed. Consequently, upper limits for the products of the branching fractions and the electronic partial widths at the 90% confidence level are reported for these decays

Observation of ψ (3686) → Ω − K + Ξ ¯ 0 + c. c

Using (27.12 ± 0.14) × 108ψ(3686) events collected with the BESIII detector at BEPCII, the decay of ψ(3686) →Ω−K+Ξ¯0 + c.c. is observed for the first time. The branching fraction of this decay is measured to be Bψ3686→Ω−K+Ξ¯0+c.c. = (2.78 ± 0.40 ± 0.18) × 10−6, where the first uncertainty is statistical and the second is systematic. Possible baryon excited states are searched for in this decay, but no evident intermediate state is observed with the current sample size

Measurements of K S 0 - K L 0 asymmetries in the decays Λ c + → p K L, S 0, p K L, S 0 π + π − and p K L, S 0 π 0

Using e+e− annihilation data sets corresponding to an integrated luminosity of 4.5 fb−1, collected with the BESIII detector at center-of-mass energies between 4.600 and 4.699 GeV, we report the first measurements of the absolute branching fractions BΛc+→pKL0 = (1.67 ± 0.06 ± 0.04)%, BΛc+→pKL0π+π− = (1.69 ± 0.10 ± 0.05)%, and BΛc+→pKL0π0 = (2.02 ± 0.13 ± 0.05)%, where the first uncertainties are statistical and the second systematic. Combining with the known branching fractions of Λc+→pKS0, Λc+→pKS0π+π−, and Λc+→pKS0π0, we present the first measurements of the KS0-KL0 asymmetries RΛc+KS, L0X=BΛc+→KS0X−BΛc+→KL0XBΛc+→KS0X+BΛc+→KL0X in charmed baryon decays: RΛc+pKS, L0=−0.025±0.031, RΛc+pKS, L0π+π−=−0.027±0.048 and RΛc+pKS, L0π0=−0.015±0.046. No significant asymmetries with statistical significance are observed