Sequence. Plants join the genome sequencing bandwagon

An international consortium announced this week that it has finished the first genome sequence of a higher plant. For plant biologists, the eagerly awaited genome of this small weed, Arabidopsis thaliana, offers a window into the genetic makeup of all plants, including key crops. And it's a clear window indeed, as the six international sequencing teams on three continents have produced a genome sequence that is more complete than that of any multicellular organism which has been published to date. Through this window, they are seeing for the first time that plants may be much more complex than many biologists have imagined.     

Enrichment of gene-coding sequences in maize by genome filtration

Approximately 80% of the maize genome comprises highly repetitive sequences interspersed with single-copy, gene-rich sequences, and standard genome sequencing strategies are not readily adaptable to this type of genome. Methodologies that enrich for genic sequences might more rapidly generate useful results from complex genomes. Equivalent numbers of clones from maize selected by techniques called methylation filtering and High C0t selection were sequenced to generate approximately 200,000 reads (approximately 132 megabases), which were assembled into contigs. Combination of the two techniques resulted in a sixfold reduction in the effective genome size and a fourfold increase in the gene identification rate in comparison to a nonenriched library.     

Genomics. Public-private project to deliver mouse genome in 6 months

Research on the mouse genome lurched into the fast lane last week, as private donors joined the U.S. government to step on the gas. A public-private consortium announced on 6 October that it's kicking $58 million into a new fund that will pay to sequence the DNA of the "black six" (C57BL/6J) strain of laboratory mouse. The consortium aims to produce a draft version of the genome by the end of February.     

2022 年 3 期目录

  目的  木棉是我国南方地区重要的观赏植物,研究不同时期花蕾和花朵的花瓣基因表达差异,揭示花色变异的遗传调控机制,为建立花色定向育种技术提供科学依据。  方法  以木棉不同发育时期深红色花和黄色花的花瓣为研究对象,利用Illumina HiSeqTM 4000开展转录组测序;分别采用DESeq2和Kyoto Encyclopedia of Genes and Genomes（KEGG）数据库进行差异表达基因鉴定和通路富集分析。  结果  测序共获得75 190个单基因,4 772个单基因能被公共数据库注释;基因功能富集分析显示,基因主要富集在基本功能预测、信号转导机制和转录后修饰、蛋白折叠、分子伴侣等通路。共获得不同时期差异表达基因10 397个,显著富集在29个生物学通路,主要包括光合作用、代谢和植物激素信号转导通路等。其中,参与苯丙烷生物合成通路的差异表达基因有72个,参与类胡萝卜素、黄酮类生物合成通路和苯丙氨酸代谢通路的差异表达基因分别为25个,这些通路和基因均与花青素的生物合成相关;另有4个差异表达基因显著富集在甜菜碱的生物合成通路中。qRT-PCR数据验证了转录组数据的可靠性。  结论  （1）光合作用、代谢、植物激素信号转导、黄酮类生物合成、苯丙烷生物合成、苯丙氨酸代谢及能量代谢等通路相关基因可能参与花瓣的发育过程。（2）黄酮类生物合成通路相关基因在深红色花发育的花蕾中期与花朵期显著高表达,可能是花色呈现红色的主要原因。（3）类胡萝卜素生物合成通路的关键合成酶基因的部分家族成员在黄色花发育的花蕾期和花蕾中期显著高表达,可能是导致花色呈现黄色的主要原因。      

40株新城疫病毒全基因组的比较研究

利用作者单位测得的和从GenBank检索得到的40株新城疫病毒(NDV)全基因组序列,采用SMS、DNAStar等生物信息分析软件,比较分析NDV全基因组的基本特征和分子进化规律.结果表明: 40株NDV全基因组核酸序列长度有3种:15186、15192、15198 nt,均符合6倍数规律;基因组A T含量占53%～54%,C G含量占46%左右;NDV基因组前三分之一(4500 nt前)序列存在高GC含量区,特别是在大约1200～2400 nt区域,GC含量最高达到69%;F基因片段构建的分子进化树显示,40株NDV划分为两大类(ClassⅠ,ClassⅡ),基因组长度为15198 nt的毒株属于ClassⅠ,其余的属于ClassⅡ;ClassⅡ毒株又分为基因Ⅰ～Ⅶ型,这些已测序的毒株中没有基因Ⅷ和Ⅸ型;病毒6个基因CDS序列构建的进化树显示,各基因进化基本保持一致,仅少数毒株存在差异,可能与病毒分子的基因重组有关.     

Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. O?mycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known o?mycete avirulence genes.     

Global identification of human transcribed sequences with genome tiling arrays

Elucidating the transcribed regions of the genome constitutes a fundamental aspect of human biology, yet this remains an outstanding problem. To comprehensively identify coding sequences, we constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome. Transcribed sequences were located across the genome via hybridization to complementary DNA samples, reverse-transcribed from polyadenylated RNA obtained from human liver tissue. In addition to identifying many known and predicted genes, we found 10,595 transcribed sequences not detected by other methods. A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins.     

基于序列功能注释的蛋白质相互作用预测方法研究

蛋白质-蛋白质相互作用(PPI)是大多数细胞过程和生物功能的基础.该研究基于蛋白质功能注释方法(FNM)首次提出了结合蛋白的重要性的方法、结构域相互作用、基因本体论注释序列和注释;然后融合不同的策略,分别建立了3种方法结合的蛋白质序列特征与FNM功能注释功能.利用蛋白质相互作用预测构建蛋白质相互作用网络是进一步理解蛋白质功能的必要前提,也是理解细胞新陈代谢及复杂疾病形成发生的基础和关键.     

螺旋藻基因组中糖苷酶类基因的序列分析

在NCBI基因组数据库中可检索到3个钝顶螺旋藻藻株、1个极大螺旋藻藻株、1个盐泽螺旋藻藻株和1个螺旋藻属未定种的藻株基因组序列。6个螺旋藻基因组序列来源的糖苷酶基因共计32个,编码蛋白含260~1 084个氨基酸,BLAST序列比对显示,与非螺旋藻种属来源的已知序列的相似性在49%~84%之间。系统进化分析表明,32个糖苷酶基因聚类成8个簇,另有3个基因分别单独构成进化分支。酶学功能预测显示,这些糖苷酶基因分别属于8个糖苷酶家族(GH3、GH9、GH13、GH23、GH25、GH38、GH57、GH104),具有8种糖苷酶催化活性(纤维素酶、溶菌酶、α-甘露糖苷酶、α-淀粉酶、普鲁兰酶、1,4-α-葡聚糖分支酶、肽聚糖结合功能、β-葡萄糖苷酶)。     

新疆褐牛产奶和繁殖性状候选基因功能注释

基于新疆褐牛产奶和繁殖性状全基因组关联分析研究结果,对候选基因进行生物信息学功能分析,进一步筛选出与新疆褐牛产奶和繁殖性状显著相关的关键基因。根据关联分析结果中显著单核苷酸多肽位点的物理位置共找到55个候选基因,其中49个基因可在数据库中检索到相应功能注释信息。GO分类结果显示,这些基因涉及代谢、转录等30个GO条目;KEGG代谢通路富集分析结果显示,候选基因富集于7个通路中,其中基因数最多的是Wnt信号通路和钙黏素信号通路。通过查阅各候选基因相关研究进展和相关基因的生物学功能、生理生化分析,发现对产奶性状候选基因中的CDH2、GABRG2和繁殖性状候选基因中的EPRS基因可进行下一步的基因功能研究。     

灰盖鬼伞基因组中微卫星序列的组成

本研究利用已公布的灰盖鬼伞基因组测序结果,对该真菌基因组中的微卫星(microsatellite)或简单重复序列(simplesequence repeats,SSRs)进行了系统分析。结果表明,在已公布的36.2 Mb的基因组序列中,共有7 859个SSR序列(长度大于15bp,匹配值大于80%)。SSR的碱基总数达143 kb,约占整个基因组碱基数的0.40%,平均4.61 kb中就有1个大于15 bp的SSR序列。其中数量最多的是3碱基SSR,数量达到3 033个,其次为6碱基重复序列(2 121个)、5碱基重复序列(1 820个),这3种SSR总数达6 974个,占SSR总数的84.9%,单碱基重复序列数量最少,仅有285个。与子囊菌中的稻瘟病菌和粗糙脉孢菌相比,灰盖鬼伞菌基因组中每百万碱基中的SSR数量和密度都较小。这些研究结果可为该担子菌基因组的特征描述、注释及分子标记的筛选提供基础信息。