Complementary DNA sequencing: expressed sequence tags and human genome project

Automated partial DNA sequencing was conducted on more than 600 randomly selected human brain complementary DNA (cDNA) clones to generate expressed sequence tags (ESTs). ESTs have applications in the discovery of new human genes, mapping of the human genome, and identification of coding regions in genomic sequences. Of the sequences generated, 337 represent new genes, including 48 with significant similarity to genes from other organisms, such as a yeast RNA polymerase II subunit; Drosophila kinesin, Notch, and Enhancer of split; and a murine tyrosine kinase receptor. Forty-six ESTs were mapped to chromosomes after amplification by the polymerase chain reaction. This fast approach to cDNA characterization will facilitate the tagging of most human genes in a few years at a fraction of the cost of complete genomic sequencing, provide new genetic markers, and serve as a resource in diverse biological research fields.     

Environmental genome shotgun sequencing of the Sargasso Sea

We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.     

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.     

水稻种质资源萌发期与孕穗期耐冷性鉴定

目的筛选耐寒性水稻品种。方法以广泛代表性的14个亚洲国家187个水稻核心种质为研究对象,根据种内群体关系和地理位置将其分为4个平行组;分别对4个平行组的三叶期幼苗进行4 ℃低温处理,时间梯度设为24、36、48和60 h,7 d缓苗期后统计其秧苗黄叶率并鉴定耐寒等级。结果根据黄叶率百分比可以精准鉴定水稻的5个耐寒等级,且粳稻的耐寒性普遍比籼稻强。11个强耐寒品种主要分布于高纬度或高海拔地区。4 ℃处理24和36 h后的黄叶率在不同品种间呈现丰富多样性,该耐寒处理方式获得的表型性状适合全基因组关联分析。结论品种之间耐寒性的差异不仅由遗传因素决定,还与其地理分布和当地种植策略相关。本研究初步筛选出11个苗期耐寒水稻品种,可为耐寒种质资源的遗传改良和分子育种提供参考。     

基于家系基因组测序对骡基因组结构多样性分析

为分析马(Equus caballus)和驴(Equus asinus)杂交后两套结构和功能完善的独立基因组在骡基因组中整合后的结构多样性,本研究以马属动物三成员家系的全基因组序列为研究对象,分别以纯血马基因组和驴基因组为参考,识别驴、马和骡的InDel、SNP和CNV;通过生物信息分析,分析骡的de novo SNP及其突变频率、识别骡特异性CNV,并进行功能分析。结果显示:1)驴、马和骡分别获得100.01、103.78和114.36 Gb 的高质量Illumina基因组测序数据。2)以纯血马基因组为参考,识别的InDels、SNPs和CNVs分别为402 533~2 110 786、5 012 403~23 819 055和2 126~3 761;以驴基因组为参考,识别的InDels、SNPs和CNVs分别为527 351~2 279 875、3 212 499~23 549 224和3 572~7 812。3)骡de novo SNPs分别为555和419,其突变频率为1.72×10^-7~2.21×10^-7。4)获得骡特异性CNVs分别为396和859,总长度分别为2.15和3.77 Mb。5)变异相关基因主要和机体的免疫及癌症过程相关。综上,骡基因组发生了高频率的de novo SNPs和特异性CNVs,这些结构变异可能对马和驴异种杂交不相容以及骡的遗传适应性具有重要意义,为进一步开展马和驴异种杂交的遗传基础及其分子机制的研究提供候选遗传位点。     

牛全基因组测序研究进展

牛作为反刍动物的代表,具有独特的生物学特征和重要的哺乳动物进化地位,是人类生产活动的重要工具和肉、奶等物质需求的主要来源。近10年来,牛全基因组研究取得了很多重要的进展,为解释牛的生物学特征和加快品种的分子育种进程发挥了重要作用,文章重点介绍了牛全基因组测序的相关研究成果,以及测序工作完成后的研究进展,讨论了牛全基因组测序工作的机遇、研究重点,以及今后面临的挑战。     

Single-molecule DNA sequencing of a viral genome

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.     

The dog genome: survey sequencing and comparative analysis

A survey of the dog genome sequence (6.22 million sequence reads; 1.5x coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (>25%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. Mutation rates, conserved synteny, repeat content, and phylogeny can be compared among human, mouse, and dog. A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog.