金华猪和大约克猪分娩后21d乳腺microRNAs的预测和差异研究

microRNAs(miRNAs)是一类单链小RNAs,是重要的基因表达调控因子,通过与靶基因的3'UTR序列互补来调控基因的表达。鉴定乳腺组织的miRNAs及其靶基因,对揭示miRNA在乳腺组织基因调控中的作用十分重要。本研究分别从分娩后21d金华和大约克母猪的乳腺组织中提取小RNA并构建各自的cDNA文库,通过Illumina Genome AnalyzerⅡx测序平台对它们进行高通量深度测序。将测序初始序列经过序列类型、长度、丰度的筛选得到比对序列,然后与已有的miRNA数据库、Genome和EST数据库进行比对。将两个猪种检测到的miRNA进行品种间差异性比较,并在差异性结果中选择相对丰度较高的前10个miRNA对其进行生物信息学分析。结果发现:金华猪乳腺组织的比对序列有9672024条,大约克猪6946905条;共检测到金华猪单一序列miRNA有848个,大约克猪683个;金华猪预测的新单一序列miRNA有369个,大约克猪231个;两个猪种间差异显著的miRNA有288个(P<0.01);相对丰度较高的前10个miRNA的靶基因有1829个,这些靶基因主要参与了抗原加工和呈递、Ⅰ型糖尿病、缝隙连接...     

Complete genome and phylogenetic analysis of bovine papillomavirus type 15 in Southern Xinjiang dairy cow

BackgroundBovine papilloma is a neoplastic disease caused by bovine papillomaviruses (BPVs), which were recently divided into 5 genera and at least 24 genotypes.ObjectivesThe complete genome sequence of BPV type 15 (BPV Aks-02), a novel putative BPV type from skin samples from infected cows in Southern Xinjiang China, was determined by collecting warty lesions, followed by DNA extraction and amplicon sequencing.MethodsDNA was analyzed initially by polymerase chain reaction (PCR) using the degenerate primers FAP59 and FAP64. The complete genome sequences of the BPV Aks-02 were amplified by PCR using the amplification primers and sequencing primers. Sequence analysis and phylogenetic analysis were performed using bio-informatic software.ResultsThe nucleotide sequence of the L1 open reading frame (ORF) of BPV Aks-02 was 75% identity to the L1 ORF of BPV-9 reference strain from GenBank. The complete genome consisted of 7,189 base pairs (G + C content of 42.50%) that encoded 5 early (E8, E7, E1, E2, and E4) and 2 late (L1 and L2) genes. The E7 protein contained a consensus CX₂CX₂₉CX₂C zinc-binding domain and a LxCxE motif. Among the different members of this group, the percentages of the complete genome and ORFs (including 5 early and 2 late ORFs) sequence identity of BPV Aks-02 were closer to the genus Xipapillomavirus 1 of the Xipapillomavirus genus. Phylogenetic analysis and sequence similarities based on the L1 ORF of BPV Aks-02 revealed the same cluster.ConclusionsThe results suggest that BPV type (BPV Aks-02) clustered with members of the Xipapillomavirus genus as BPV 15 and were closely related to Xipapillomavirus 1.     

水稻基因组序列研究进展

水稻是世界上最重要的粮食作物之一,是禾本科植物的模式植物。综述了基于图位克隆的水稻基因组序列,基因组大小为389 Mb,包括37 544个非转座因子相关蛋白的基因。95%的基因组序列被精确测定,包括全部的常染色质、2个完整的着丝点及6条完整的染色体。基因组中串联重复序列占14%,平均每Mb为51个SSR。SwaI光学限制性(酶切)图谱的构建使图距缩短了11%,使基因组大小变为382.17 Mb。