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生物信息學

技術平臺

  •  擁有包括Sun V880Sun V890,曙光EP480,曙光EP850-GF等多臺服務器,總存儲空間達到100TB,具有60個線程的同步計算能力和超過800GB的內存支持,擁有包括自行研發的GA-PlotVirtualGenome等軟件在內的一整套基因組學和分子進化所需的生物信息學軟件。 

 

   

技術人員

   10余位博士組成的強大科研團隊,配置專人對客戶進行全方面的跟蹤服務,在Nature、PNAS、PLoS ONE等國際權威刊物多次發表文章。

服務內容

    芯片生物信息學服務、全基因組生物信息學服務、蛋白質組生物信息學服務、其他如序列拼接、功能基因注釋分類等。

芯片生物信息學服務

    對基因芯片的表達譜數據進行預處理與歸一化分析,篩選顯著差異表達的基因,對差異表達的基因數據進行聚類分析,進行規模化的染色體定位分析和基于染色體和轉錄因子的轉錄調控分析,并結合基因分類數據庫和信號轉導數據庫進行基因的分類和注釋、相關代謝路徑和信號通路的分析。

全基因組生物信息學服務

    全基因組測序策略的實施,對獲得的全基因組序列進行深入細致的生物信息分析,也可以對客戶提供的全基因組序列進行分析。已完成超過31個全基因組生物信息學分析,研究成果發表于NaturePNASMolecular MicrobiologyJournal of BacteriologyPLoS ONE等國際權威刊物。

蛋白質組生物信息學服務

蛋白質的質譜分析,蛋白質分子三維結構構建、模板與活性分析。

其他生物信息學服務

根據客戶需要提供包括序列比對、探針設計、基因預測、蛋白質結構功能域預測等生物信息學服務。
生物信息學數據庫,包括序列數據庫、SNP數據庫、MLST數據庫等的構建與維護;
生物信息學培訓,包括序列拼接、基因組生物信息學分析、生物信息學數據庫的構建與維護、蛋白質生物信息學分析等。

成功案例

AbstractA high-density genetic map of papaya (Carica papaya L.) was constructed using microsatellite markers derived from BAC end sequences and whole-genome shot gun sequences. Fifty-four F2 plants derived from varieties AU9 and SunUp were used for linkage mapping. A total of 707 markers, including 706 microsatellite loci and the morphological marker fruit flesh color, were mapped into nine major and three minor linkage groups. The resulting map spanned 1069.9 cM with an average distance of 1.5 cM between adjacent markers. This sequence-based microsatellite map resolved the very large linkage group 2 (LG 2) of the previous high-density map using amplified fragment length polymorphism markers.  The nine major LGs of our map represent papaya’s haploid nine chromosomes with LG 1 of the sex chromosome being the largest. This map validates the suppression of recombination at the male-specific region of the Y chromosome (MSY) mapped on LG 1 and at potential centromeric regions of other LGs. Segregation distortion was detected in a large region on LG 1 surrounding the MSY region due to the abortion of the YY genotype and in a region of LG6 due to an unknown cause. This high-density sequencetagged genetic map is being used to integrate genetic and physical maps and to assign genome sequence scaffolds to papaya chromosomes. It provides a framework for comparative structural and evolutional genomic research in the order Brassicales.
AbstractAerobic methanotrophic bacteria consume methane as it diffuses away from methanogenic zones of soil and sediment. They act as a biofilter to reduce methane emissions to the atmosphere, and they are therefore targets in strategies to combat global climate change. No cultured methanotroph grows optimally below pH 5, but some environments with active methane cycles are very acidic. Here we describe an extremely acidophilic methanotroph that grows optimally at pH 2.0–2.5. Unlike the known methanotrophs, it does not belong to the phylum Proteobacteria but rather to the Verrucomicrobia, a widespread and diverse bacterial phylum that primarily comprises uncultivated species with unknown genotypes. Analysis of its draft genome detected genes encoding particulate methane monooxygenase that were homologous to genes found in methanotrophic proteobacteria. However, known genetic modules for methanol and formaldehyde oxidation were incomplete or missing, suggesting that the bacterium uses some novel methylotrophic pathways. Phylogenetic analysis of its three pmoA genes (encoding a subunit of particulate methane monooxygenase) placed them into a distinct cluster from proteobacterial homologues. This indicates an ancient divergence of Verrucomicrobia and Proteobacteria methanotrophs rather than a recent horizontal gene transfer of methanotrophic ability. The findings show that methanotrophy in the Bacteria is more taxonomically, ecologically and genetically diverse than previously thought, and that previous studies have failed to assess the full diversity of methanotrophs in acidic environments.
AbstractPapaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 33 draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica’s distinguishing morpho-physiological, medicinal and nutritional properties.
    AbstractCholera, caused by Vibrio cholerae, erupted globally from South Asia in 7 pandemics, but there were also local outbreaks between the 6th (1899–1923) and 7th (1961–present) pandemics. All the above are serotype O1, whereas environmental or invertebrate isolates are antigenically diverse. The pre 7th pandemic isolates mentioned above, and other minor pathogenic clones, are related to the 7th pandemic clone, while the 6th pandemic clone is in the same lineage but more distantly related, and non-pathogenic isolates show no clonal structure. To understand the origins and relationships of the pandemic clones, we sequenced the genomes of a 1937 prepandemic strain and a 6th pandemic isolate, and compared them with the published 7th pandemic genome. We distinguished mutational and recombinational events, and allocated these and other events, to specific branches in the evolutionary tree. There were more mutational than recombinational events, but more genes, and 44 times more base pairs, changed by recombination. We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7th pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed. We then used this to estimate the divergence date of the 6th and 7th pandemic clones to be about 1880. While there is a large margin of error, this is far more realistic than the 10,000–50,000 years ago estimated using the usual assumptions. We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes. There were also substantial changes in the major integron, attributed to gain of individual cassettes including copying from within, or loss of blocks of cassettes. The approaches used open up new avenues for analysing the origin and history of other important pathogens.
    AbstractMicrobes contribute to geochemical cycles in the ecosystem. They also play important roles in biodegradation and bioremediation of contaminated environments, and have great potential in energy conversion and regeneration. Up to date, at least 150 genomes of non-pathogenic microbes have been sequenced, of which, the majority are bacteria from various environments or of industrial uses. The emerging field ‘metagenomics’ in combination with the high-throughput sequencing technology offers opportunities to discover new functions of microbes in the environment on a large scale, and has become the ‘hot spot’ in the field of environmental microbiology. Seven genomes of bacteria from various extreme environments, including high temperature, high and low pressure, and extreme acidic regions, have been sequenced by researchers in China, leading to the discovery of metabolic pathways, genetic functions and new enzymes, which are related to the niches those bacteria occupy. These results were published in Nature, PNAS, Genome Research and other top international journals. In the meantime, several groups in China have started ‘metagenomics’ programs. The outcomes of these researches are expected to generate a considerable number of novel findings, taking Chinese researchers to the frontier of genomics for environmental and industrial microorganisms.
 
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