BBGD: an online database for blueberry genomic data

Background  

Blueberry is a member of the Ericaceae family, which also includes closely related cranberry and more distantly related rhododendron, azalea, and mountain laurel. Blueberry is a major berry crop in the United States, and one that has great nutritional and economical value. Extreme low temperatures, however, reduce crop yield and cause major losses to US farmers. A better understanding of the genes and biochemical pathways that are up- or down-regulated during cold acclimation is needed to produce blueberry cultivars with enhanced cold hardiness. To that end, the blueberry genomics database (BBDG) was developed. Along with the analysis tools and web-based query interfaces, the database serves both the broader Ericaceae research community and the blueberry research community specifically by making available ESTs and gene expression data in searchable formats and in elucidating the underlying mechanisms of cold acclimation and freeze tolerance in blueberry.     

RNAcentral: A vision for an international database of RNA sequences

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.     

IntergenicDB: a database for intergenic sequences

A whole genome contains not only coding regions, but also non-coding regions. These are located between the end of a given coding region and the beginning of the following coding region. For this reason, the information about gene regulation process underlies in intergenic regions. There is no easy way to obtain intergenic regions from current available databases. IntergenicDB was developed to integrate data of intergenic regions and their gene related information from NCBI databases. The main goal of INTERGENICDB is to offer friendly database for intergenic sequences of bacterial genomes.

Availability

http://intergenicdb.bioinfoucs.com/     

Analysis of bacterial communities in sponges and coral inhabiting Red Sea,using barcoded 454 pyrosequencing

Microbial communities are linked with marine sponge are diverse in their structure and function. Our understanding of the sponge-associated microbial diversity is limited especially from Red Sea in Saudi Arabia where few species of sponges have been studied. Here we used pyrosequencing to study two marine sponges and coral species sampled from Obhur region from Red sea in Jeddah. A total of 168 operational taxonomic units (OTUs) were identified from Haliclona caerulea, Stylissa carteri and Rhytisma fulvum. Taxonomic identification of tag sequences of 16S ribosomal RNA revealed 6 different bacterial phyla and 9 different classes. A proportion of unclassified reads were was also observed in sponges and coral sample. We found diverse bacterial communities associated with two sponges and a coral sample. Diversity and richness estimates based on OUTs revealed that sponge H. caerulea had significantly high bacterial diversity. The identified OTUs showed unique clustering in three sponge samples as revealed by Principal coordinate analysis (PCoA). Proteobacteria (88–95%) was dominant phyla alonwith Bacteroidetes, Planctomycetes, Cyanobacteria, Firmicutes and Nitrospirae. Seventeen different genera were identified where genus Pseudoalteromonas was dominant in all three samples. This is first study to assess bacterial communities of sponge and coral sample that have never been studied before to unravel their microbial communities using 454-pyrosequencing method.     

A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley

The genomes of barley and wheat, two of the world's most important crops, are very large and complex due to their high content of repetitive DNA. In order to obtain a whole-genome sequence sample, we performed two runs of 454 (GS20) sequencing on genomic DNA of barley cv. Morex, which yielded approximately 1% of a haploid genome equivalent. Almost 60% of the sequences comprised known transposable element (TE) families, and another 9% represented novel repetitive sequences. We also discovered high amounts of low-complexity DNA and non-genic low-copy DNA. We identified almost 2300 protein coding gene sequences and more than 660 putative conserved non-coding sequences. Comparison of the 454 reads with previously published genomic sequences suggested that TE families are distributed unequally along chromosomes. This was confirmed by in situ hybridizations of selected TEs. A comparison of these data for the barley genome with a large sample of publicly available wheat sequences showed that several TE families that are highly abundant in wheat are absent from the barley genome. This finding implies that the TE composition of their genomes differs dramatically, despite their very similar genome size and their close phylogenetic relationship.     

Genetic analysis of freezing tolerance in blueberry (Vaccinium section Cyanococcus)

An understanding of the genetic control of freezing tolerance (FT) in woody perennials is important for the effective selection and development of plants with a broader climatic adaptation. This study was undertaken to examine the inheritance and gene action of FT in segregating populations of a woody perennial blueberry (Vaccinium, section Cyanococcus). Two backcross populations were derived from interspecific hybrids of the diploid species Vaccinium darrowi and Vaccinium caesariense, which are widely divergent in their FT. The bud FTs of uniformly cold acclimated plants of parental, F₁, and two backcross populations were evaluated with a laboratory controlled freeze-thaw regime, followed by a visual assessment of injury. FT (LT₅₀) was defined as the temperature causing 50% of the flower buds to be injured. Data indicate that the two parents were homozygous for genes for low or high FT. Freezing-tolerance values of the parental and F₁ populations indicate that freeze-sensitivity is a partially dominant trait. Results from reciprocal crosses revealed that there was no significant maternal influence on freezing tolerance. Parental phenotypes were fully recovered in 40–42 plants of each testcross population, suggesting that FT is determined by relatively few genes. The degree of dominance and an analysis of generation means revealed that FT in blueberry is controlled largely by additive gene effects and, to a lesser degree, by dominance gene effects. Testing of various genetic models indicated that FT inheritance can be adequately explained by a simple additive-dominance model; however, two epistatic models involving additive-additive and dominance-dominance interactions also fit the data. Received: 25 May 1999 / Accepted: 16 June 1999     

454测序技术在微生物生态学研究中的应用

以Sanger法(双脱氧核苷酸末端终止法)为代表的第1代测序技术由于其成本高、速度慢、通量低等不足,满足不了大规模测序的要求.进入21世纪后,以Roche 454为代表的第2代测序技术诞生了,454测序法作为一种高通量的测序方法,近年来已被广泛应用于微生物生态学研究中.介绍了该测序技术的原理和操作步骤,结合本实验室的研...     

ChSeq: A database of chameleon sequences

Chameleon sequences (ChSeqs) refer to sequence strings of identical amino acids that can adopt different conformations in protein structures. Researchers have detected and studied ChSeqs to understand the interplay between local and global interactions in protein structure formation. The different secondary structures adopted by one ChSeq challenge sequence‐based secondary structure predictors. With increasing numbers of available Protein Data Bank structures, we here identify a large set of ChSeqs ranging from 6 to 10 residues in length. The homologous ChSeqs discovered highlight the structural plasticity involved in biological function. When compared with previous studies, the set of unrelated ChSeqs found represents an about 20‐fold increase in the number of detected sequences, as well as an increase in the longest ChSeq length from 8 to 10 residues. We applied secondary structure predictors on our ChSeqs and found that methods based on a sequence profile outperformed methods based on a single sequence. For the unrelated ChSeqs, the evolutionary information provided by the sequence profile typically allows successful prediction of the prevailing secondary structure adopted in each protein family. Our dataset will facilitate future studies of ChSeqs, as well as interpretations of the interplay between local and nonlocal interactions. A user‐friendly web interface for this ChSeq database is available at prodata.swmed.edu/chseq .     

一个植物分类数据库

本文介绍了一个苔藓植物分类数据库的设计及其结构,是使用ＶｉｓｕａｌＢａｓｉｃ４０,以中国苔藓植物的标本,学名,分布,文献,分类性状等为基本资料,以打印标签、名录、文献索引,构成分类性状的原始数据矩阵,并与数量分类程序,以及ＤＥＬＴＡ,ＰＡＵＰ和ＣＬＵＳＴＡＮ等应用程序的连结为目标进行开发的。其基本构想是在这样一个框架之下,逐渐积累中国苔藓植物的基本资料,能够完成大部分的标本室和分类学工作,并在使用过程中进一步扩展和完善其结构和功能,从而为中国苔藓植物的研究提供极大的便利。     

Microscopic examination of spatial transcriptome using Seq-Scope

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野生蓝莓和花青素提取物对高脂饮食小鼠肠道菌群的影响

【目的】研究野生蓝莓和花青素提取物对高脂饮食小鼠肠道菌群的影响。【方法】采用高脂饲料喂养C57BL/6小鼠,同时膳食补充野生蓝莓或花青素提取物,将25只无菌小鼠分为5组:正常对照组(Normal chow diet,NCD),普通饲料+10 g/100 g蓝莓组(NCD+BB),高脂饲料组(High-fat diet,HFD),高脂饲料+10 g/100 g蓝莓组(HFD+BB),高脂饲料+20 mg/100 g花青素组(HFD+ACN),饲养10周,每周对其食物摄入量、能量摄入量以及体重进行测定,并运用DGGE方法对小鼠肠道菌群结构变化进行动态监测。【结果】各实验组食物摄入量无显著性差异,HFD+BB组和HFD+ACN组能量摄入量均明显高于NCD+BB组。虽然HFD+BB组体重增加最为明显,但10周末时HFD+BB组体重与其他各组无显著差异。随着实验的进行,HFD组、HFD+BB组和HFD+ACN组肠道微生物多样性发生明显变化。HFD+BB组与NCD组菌群差异最大,HFD+ACN组与NCD组肠道菌群DGGE图谱相似性系数明显高于HFD组,对优势条带测序结果显示膳食补充蓝莓或花青素提取物可明显降低肥胖相关细菌Firmicutes的数量。【结论】蓝莓和花青素提取物可改善由高脂饮食引起的肠道微生态失调,调节肠道菌群结构,具有潜在的减肥消脂功能。