The excess of 5′ introns in eukaryotic genomes

In this work, 21 completely sequenced eukaryotic genomes were analyzed using an intragene comparison approach. We found that all of these genomes show a significant 5′-biased distribution of introns of protein-coding genes. Our findings are different from previous studies based on the intergene method, where introns are biased towards the 5′ end of genes only in intron-poor genomes, but are evenly distributed in intron-rich genomes. In addition, by analyzing the patterns of intron distribution of a set of well-compiled housekeeping genes from human and their respective orthologs identified by a bidirectional best BLAST hit method from the other genomes, we found that the trend of 5′-biased intron positions of the set of housekeeping genes for each genome is much more skewed than that of all genes of the same genome, and rarely if any of the housekeeping genes examined have an extremely 3′-biased position distribution in which all introns of a gene are located only at the 3′ portion of the gene. The most parsimonious explanation for our findings may be the model in which intron loss is caused by homologous recombination between the genomic copy of a gene and a reverse transcriptase product of a spliced mRNA

Search for C=+C=+ charmonium and XYZ states in e+e−→γ+He^+e^-\to \gamma+ H at BESIII

Within the framework of nonrelativistic quantum chromodynamics, we study the production of $C=+$ charmonium states $H$ in $e^+e^-\to \gamma~+~H$ at BESIII with $H=\eta_c(nS)$ (n=1, 2, 3, and 4), $\chi_{cJ}(nP)$ (n=1, 2, and 3), and $^1D_2(nD)$ (n=1 and 2). The radiative and relativistic corrections are calculated to next-to-leading order for $S$ and $P$ wave states. We then argue that the search for $C=+$ $XYZ$ states such as $X(3872)$, $X(3940)$, $X(4160)$, and $X(4350)$ in $e^+e^-\to \gamma~+~H$ at BESIII may help clarify the nature of these states. BESIII can search $XYZ$ states through two body process $e^+e^-\to \gamma H$, where $H$ decay to $J/\psi \pi^+\pi^-$, $J/\psi \phi$, or $D \bar D$. This result may be useful in identifying the nature of $C=+$ $XYZ$ states. For completeness, the production of $C=+$ charmonium in $e^+e^-\to \gamma +~H$ at B factories is also discussed.Comment: Comments and suggestions are welcome. References are update

Understanding the e+e−→D(∗)+D(∗)−e^+e^-\to D^{(*)+}D^{(*)-} processes observed by Belle

We calculate the production cross sections for $D^{*+}D^{*-}$, $D^+D^{*-}$ and $D^+D^-$ in $e^+e^-$ annihilation through one virtual photon in the framework of perturbative QCD with constituent quarks. The calculated cross sections for $D^{*+}D^{*-}$ and $D^+D^{*-}$ production are roughly in agreement with the recent Belle data. The helicity decomposition for $D^{*}$ meson production is also calculated. The fraction of the $D^{*\pm}_LD^{*\mp}_T$ final state in $e^+e^-\to D^{*+}D^{*-}$ process is found to be 65%. The fraction of $DD^*_T$ production is 100% and $DD^*_L$ is forbidden in $e^+e^-$ annihilation through one virtual photon. We further consider $e^+e^-$ annihilation through two virtual photons, and then find the fraction of $DD^{*}_T$ in $e^+e^-\to DD^{*}$ process to be about 91%.Comment: 8 pages, 2 figure

BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes

<p>Abstract</p> <p>Background</p> <p>Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest.</p> <p>Description</p> <p>BPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ) and Unweighted Pair-Group Method using Arithmetic averages (UPGMA). Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint.</p> <p>Conclusion</p> <p>BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by annotations make BPhyOG a powerful web server for genomic and genetic studies. It is freely available at <url>http://cmb.bnu.edu.cn/BPhyOG</url>.</p