Small RNA是生命活動重要的調控因子,短小的序列長度(如microRNA一般在18-30nt之間);種類繁多, siRNA(小干擾RNA ), microRNA(微小RNA),還有其他一些種類的小RNA,如piRNA(蛋白互作小RNA),snRNA(小核RNA),snoRNA(核仁小RNA)等種類;幾乎存在于所有的生物體中;在基因表達調控、生物個體發(fā)育、代謝及疾病的發(fā)生等過程中發(fā)揮著重要作用。
De novo 測序也叫基因組從頭測序,不需要任何基因序列信息即可對某個物種進行測序。通過對基因組序列未知或沒有近源物種基因組信息的某個物種,對其不同長度基因組DNA片段及其文庫進行序列測定,用生物信息學的分析方法對序列進行拼接、組裝,從而獲得該物種的基因組序列圖譜。目前廣泛應用于從頭解析未知物種的基因組序列、基因組成、進化特點等。
革命性的第三代測序 ---全長轉錄組,微生物基因組,基因組de novo 第三代基因測序技術又被為 “Single Molecule Real Time (SMRTTM) DNA Sequencing”(單分子實時DNA測序技術),該方法基于納米孔的單分子讀取技術,不需要擴增即可快速讀取序列。目前,Pacific Biosciences 公司已經(jīng)成功推出了商業(yè)化的第三代測序儀PacBio RS平臺,使得第三代測序正式走入人們的視角。 技術優(yōu)勢: ? 更長的測序讀長 (平均讀長可超過10000 bp,有超過50%的讀長大于14000 bp),可大幅提高定位準確性及拼接效率,有利于闡釋基因組所發(fā)生的變異以及大尺度結構重排等信息并發(fā)現(xiàn)其相關的生物學意義。? 單分子實時檢測,模板制備時無需PCR擴增,每一條模板鏈都可獲得相應序列信息,數(shù)據(jù)覆蓋均勻,準確;可以檢測稀有變異;? 可同時獲得動力學信息,可進行甲基化等修飾堿基的直接測定;? 覆蓋深度幾乎不受序列中GC/AT含量差異的影響;? 從樣本制備到獲取序列信息簡便快捷; 參考文獻Donald S, Hagen T, Fabian G, et al. A single-molecule long-read survey of the human transcriptome [J]. Nature biotechnology, 2013.Flusberg B A, Webster D R, Lee J H, , et al. Direct detection of DNA methylation during single-molecule,real-time sequencing [J]. Nat Method, 2010.Chin C...
The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive...
An overview of our assembly strategy is shown in Figure 1. We started with a SOAPdenovo- based de novo assembly of Illumina sequence data from human HapMap sample NA12878, which had a contig N50 of 11.1 kb and a scaffold N50 of 590 kb after filtering for scaffolds that were at least 3 kb in length (...
Transposable elements and expression of retrotransposons Long terminal repeat (LTR) retrotransposons were identified using structural criteria10,11. About 44% of the assembly was accounted for by TEs (Supplementary Table 8 ). LTR retrotransposons were the most abundant of these elements, repres...
Winter dormancy is a well known mechanism adopted by temperate plants, to mitigate the chilling temperature of winters. However, acquisition of sufficient chilling during winter dor-mancy ensures the normal phenological traits in subsequent growing period. Thus, low tem-perature appears to play cruc...
Whole genome protein families were classified by InterProScan analysis (Jones et al., 2014). The peptidase families were identified by BLASTP searching against MEROPS peptidase database release 9.12 with a cuto? e-value of 1e-20 (Rawlings et al., 2014). The transporters were classified on the b...