Phylogenetics and comparative analysis of the mitochondrial genomes of three violet‐ringed octopuses

Similar morphological characters and little molecular data of Amphioctopus rex, A. neglectus and A. cf. ovulum resulted in their unknown phylogenetic statuses and equivocal relationships. In this study, the complete mitochondrial genomes of these three species collected in Chinese waters were sequenced and compared with each other to clarify the relationships among them. The lengths of the mitochondrial genomes varied from 15,646 bp to 15,814 bp, and the A + T content and GC skew for protein‐coding genes showed little variation. In contrast, both a dendrogram based on codon usage and the gene arrangements of the three octopuses showed that A. rex was more closely related to A. neglectus than to A. cf. ovulum. Five data sets and two methods (maximum likelihood and Bayesian inference) were utilized for the first time to explore the phylogenetic relationships among these three species in Octopodidae. The results indicated that a data set combining protein‐coding genes and RNA genes (PR) was optimal for analysing the relationships among 43 cephalopods. All of the phylogenetic trees divided the cephalopods into 10 taxa and supported the monophyly of Oegopsida, Myopsida, Sepiidae and Octopodidae. In this study, Idiosepiidae was classified as sister to Sepiolidae. Trees constructed using all data sets robustly supported the monophyly of the genus Amphioctopus. Notably, A. rex was more closely related to A. neglectus than to A. cf. ovulum, although these three species share the characteristic of violet rings on dark ocelli.     

菌落PCR在大规模基因组测序中的应用

一种利用菌落直接PCR扩增DNA并用于测序的实验方法.通过对引物的设计和菌液浓度控制,使PCR反应后的内容物对测序干扰减到最小.与传统的测序过程比较,它省去了抽提模板DNA一步,节省了大量时间和实验成本.另外此方法可对BAC亚克隆库构建时由连接转化过程中导致的假阳性起筛选和鉴定作用.采用该法成功测定了籼稻（Oryza sativa indica）广陆矮4号的L3173号BAC DNA全长序列（约100 kb）,GenBank登录号：AL512542.     

小麦及其近缘种中基因组特异性DNA重复序列的研究进展

本文对小麦族植物中基因组特异性DNA重复序列的分类、基本特征、分离和鉴定方法、在小麦遗传改良中的应用以及未来研究的发展趋势进行了简述。综合已有的研究结果可以看出基因组特异性DNA重复序列是小麦族植物基因组特异性形成的重要构成部分。对基因组特异性DNA重复序列的研究是认识小麦族植物基因组的有效途径之一,基因组特异性DNA重复序列的应用将进一步促进小麦族植物分子细胞遗传学和普通小麦遗传改良研究的进展。 Advances in Studies of Genome-Specific Repetitive DNA Sequences in Wheat and Related Species BAI Jian-rong1,2,JIA Xu1,WANG Dao-wen1 1.The State Key Laboratory of Plant Cell and Chromosome Engineering,Institute of Genetics and Developmental Biology,The Chinese Academy of Sciences,Beijing 100101,China; 2.Crop Genetics Institute,Shanxi Academy of Agricultural Sciences,Taiyuan 030031,China Abstract:In this paper we review recent advances in studies of several aspects of genome specific repetitive DNA sequences in wheat and related species.The available results demonstrate that genome specific repetitive DNA sequences are important components of genome specificity in wheat and related species.Research on genome specific repetitive DNA sequences is essential to the elucidation of genome function.The application of genome specific repetitive DNA sequences will aid molecular cytogenetic studies in wheat and related species and contributes to genetic improvement of common wheat. Key words：wheat;genome specific repetitive DNA sequence;chromosome     

Nuclear DNA content estimates in multicellular green, red and brown algae: phylogenetic considerations

BACKGROUND AND AIMS: Multicellular eukaryotic algae are phylogenetically disparate. Nuclear DNA content estimates have been published for fewer than 1 % of the described species of Chlorophyta, Phaeophyta and Rhodophyta. The present investigation aims to summarize the state of our knowledge and to add substantially to our database of C-values for theses algae. METHODS: The DNA-localizing fluorochrome DAPI (4', 6-diamidino-2-phenylindole) and RBC (chicken erythrocyte) standard were used to estimate 2C values with static microspectrophotometry. KEY RESULTS: 2C DNA contents for 85 species of Chlorophyta range from 0.2-6.1 pg, excluding the highly polyploidy Charales and Desmidiales with DNA contents of up to 39.2 and 20.7 pg, respectively. 2C DNA contents for 111 species of Rhodophyta range from 0.1-2.8 pg, and for 44 species of Phaeophyta range from 0.2-1.8 pg. CONCLUSIONS: New availability of consensus higher-level molecular phylogenies provides a framework for viewing C-value data in a phylogenetic context. Both DNA content ranges and mean values are greater in taxa considered to be basal. It is proposed that the basal, ancestral genome in each algal group was quite small. Both mechanistic and ecological processes are discussed that could have produced the observed C-value ranges.     

Regulation of DNA double-strand break repair pathway choice

DNA double-strand breaks （DSBs） are critical lesions that can result in cell death or a wide variety of genetic alterations including largeor small-scale deletions, loss of heterozygosity, translocations, and chromosome loss. DSBs are repaired by non-homologous end-joining （NHEJ） and homologous recombination （HR）, and defects in these pathways cause genome instability and promote tumorigenesis. DSBs arise from endogenous sources including reactive oxygen species generated during cellular metabolism, collapsed replication forks, and nucleases, and from exogenous sources including ionizing radiation and chemicals that directly or indirectly damage DNA and are commonly used in cancer therapy. The DSB repair pathways appear to compete for DSBs, but the balance between them differs widely among species, between different cell types of a single species, and during different cell cycle phases of a single cell type. Here we review the regulatory factors that regulate DSB repair by NHEJ and HR in yeast and higher eukaryotes. These factors include regulated expression and phosphorylation of repair proteins, chromatin modulation of repair factor accessibility, and the availability of homologous repair templates. While most DSB repair proteins appear to function exclusively in NHEJ or HR, a number of proteins influence both pathways, including the MRE11/RAD50/NBS1（XRS2） complex, BRCA1, histone H2AX, PARP-1, RAD18, DNA-dependent protein kinase catalytic subunit （DNA-PKcs）, and ATM. DNA-PKcs plays a role in mammalian NHEJ, but it also influences HR through a complex regulatory network that may involve crosstalk with ATM, and the regulation of at least 12 proteins involved in HR that are phosphorylated by DNA-PKcs and/or ATM.     

ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs

Polyploidy is ubiquitous and its consequences are complex and variable. A change of ploidy level generally influences genetic diversity and results in morphological, physiological and ecological differences between cells or organisms with different ploidy levels. To avoid cumbersome experiments and take advantage of the less biased information provided by the vast amounts of genome sequencing data, computational tools for ploidy estimation are urgently needed. Until now, although a few such tools have been developed, many aspects of this estimation, such as the requirement of a reference genome, the lack of informative results and objective inferences, and the influence of false positives from errors and repeats, need further improvement. We have developed ploidyfrost , a de Bruijn graph-based method, to estimate ploidy levels from whole genome sequencing data sets without a reference genome. ploidyfrost provides a visual representation of allele frequency distribution generated using the ggplot2 package as well as quantitative results using the Gaussian mixture model. In addition, it takes advantage of colouring information encoded in coloured de Bruijn graphs to analyse multiple samples simultaneously and to flexibly filter putative false positives. We evaluated the performance of ploidyfrost by analysing highly heterozygous or repetitive samples of Cyclocarya paliurus and a complex allooctoploid sample of Fragaria × ananassa. Moreover, we demonstrated that the accuracy of analysis results can be improved by constraining a threshold such as Cramér's V coefficient on variant features, which may significantly reduce the side effects of sequencing errors and annoying repeats on the graphical structure constructed.     

辽东丁香完整叶绿体基因组的结构与特征

为获得辽东丁香（Syringa villosa subsp. wolfii）叶绿体全基因组的基本特征,采用高通量测序技术分析了其叶绿体基因组序列信息,并讨论其系统演化位置。结果表明：（1）辽东丁香叶绿体基因组全长156 517 bp,具有典型的四分体结构;具有131个功能基因,包括36个tRNA基因、8个rRNA基因和87个蛋白质编码基因。（2）该叶绿体基因组蛋白编码区的总密码子偏好性（RSCU）分析显示,RSCU值>1的密码子有31个,其中以A/U碱基结尾的有21个;RSCU值<1的密码子有34个,其中以G/C碱基结尾的密码子有22个。（3）在辽东丁香的叶绿体基因组中,检测出334个散在重复序列,包括170个正向重复序列和164个回文重复序列;检测到227个SSR位点,其中226个位点成功设计出PCR引物。（4）最大似然法构建系统进化树分析显示,辽东丁香与云南丁香（S. yunnanensis）亲缘关系最近。本研究通过对辽东丁香叶绿体基因组重复序列、IR边界、系统发育等进行分析,为辽东丁香后续的分子标记开发、系统发育分析、物种资源鉴定评价、DNA条形码开发等提供参考。     

The Alarmone (p)ppGpp Regulates Primer Extension by Bacterial Primase

Primase is an essential component of the DNA replication machinery, responsible for synthesizing RNA primers that initiate leading and lagging strand DNA synthesis. Bacterial primase activity can be regulated by the starvation-inducible nucleotide (p)ppGpp. This regulation contributes to a timely inhibition of DNA replication upon amino acid starvation in the Gram-positive bacterium Bacillus subtilis. Here, we characterize the effect of (p)ppGpp on B. subtilis DnaG primase activity in vitro. Using a single-nucleotide resolution primase assay, we dissected the effect of ppGpp on the initiation, extension, and fidelity of B. subtilis primase. We found that ppGpp has a mild effect on initiation, but strongly inhibits primer extension and reduces primase processivity, promoting termination of primer extension. High (p)ppGpp concentration, together with low GTP concentration, additively inhibit primase activity. This explains the strong inhibition of replication elongation during starvation which induces high levels of (p)ppGpp and depletion of GTP in B. subtilis. Finally, we found that lowering GTP concentration results in mismatches in primer base pairing that allow priming readthrough, and that ppGpp reduces readthrough to protect priming fidelity. These results highlight the importance of (p)ppGpp in protecting replisome integrity and genome stability in fluctuating nucleotide concentrations upon onset of environmental stress.