Paramecium genome survey: a pilot project

A consortium of laboratories undertook a pilot sequencing project to gain insight into the genome of Paramecium. Plasmid-end sequencing of DNA fragments from the somatic nucleus together with similarity searches identified 722 potential protein-coding genes. High gene density and uniform small intron size make random sequencing of somatic chromosomes a cost-effective strategy for gene discovery in this organism.     

Parasites are GO

The Malaria Genome Sequencing Consortium Meeting was held on 5–6 June 2001 in Cambridge, UK, and was followed by a workshop discussing the generation of new parasite-specific gene ontology (GO) terms. Present at the meeting, which focused primarily on malaria, were representatives from the research community, the sequencing centres, including the Sanger Centre (Cambridge, UK) and The Institute for Genome Research (TIGR; Rockville, MD, USA), the European Bioinformatics Institute (EBI; Cambridge, UK), Plasmo DB and the GO consortium (Cambridge, UK).     

The sheep genome reference sequence: a work in progress

Until recently, the construction of a reference genome was performed using Sanger sequencing alone. The emergence of next-generation sequencing platforms now means reference genomes may incorporate sequence data generated from a range of sequencing platforms, each of which have different read length, systematic biases and mate-pair characteristics. The objective of this review is to inform the mammalian genomics community about the experimental strategy being pursued by the International Sheep Genomics Consortium (ISGC) to construct the draft reference genome of sheep (Ovis aries). Component activities such as data generation, sequence assembly and annotation are described, along with information concerning the key researchers performing the work. This aims to foster future participation from across the research community through the coordinated activities of the consortium. The review also serves as a ‘marker paper’ by providing information concerning the pre-publication release of the reference genome. This ensures the ISGC adheres to the framework for data sharing established at the recent Toronto International Data Release Workshop and provides guidelines for data users.     

Computational comparison of two mouse draft genomes and the human golden path

Background  

The availability of both mouse and human draft genomes has marked the beginning of a new era of comparative mammalian genomics. The two available mouse genome assemblies, from the public mouse genome sequencing consortium and Celera Genomics, were obtained using different clone libraries and different assembly methods.     

Comparative genomics of medaka and fugu

A small freshwater fish medaka (Oryzias latipes) has been one of the most attractive experimental systems for research in genetics and developmental biology. We have formed an international consortium Medaka Genome Initiative (MGI) to collect and share various information and resources on medaka. The MGI has set an ambitious goal aiming at the complete sequencing of the medaka genome and as a feasibility study we have begun sequencing one particular chromosome, linkage group 22 (LG22) of 22 Mb in size. Initial sequence analysis revealed unique features of the medaka genome in comparison to fugu genome.     

Genome size estimates for two important freshwater molluscs, the zebra mussel (Dreissena polymorpha) and the schistosomiasis vector snail (Biomphalaria glabrata).

The haploid genome sizes of two important molluscs were assessed by Feulgen image analysis densitometry. The genome size of the zebra mussel (Dreissena polymorpha), a prolific invader of North American lakes, was estimated to be 1C = 1.70 +/- 0.03 pg, and that of the freshwater snail Biomphalaria glabrata, the predominant intermediate vector of the human parasite Schistosoma mansoni, was estimated at 0.95 +/- 0.01 pg. These estimates will be important in future efforts in molluscan genomics, which at present lags far behind work being carried out with vertebrate and arthropod models. B. glabrata in particular, which has one of the smallest known gastropod genomes, is recommended as a highly suitable target for future genome sequencing.     

Decoding the oak genome: public release of sequence data,assembly, annotation and publication strategies

The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole‐genome shotgun (WGS) approach, without the use of costly and time‐consuming methods, such as fosmid or BAC clone‐based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS‐FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired‐end and mate‐pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired‐end reads and contaminants detected, resulting in a total of 17 910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.     

The promise of a protist: the Dictyostelium genome project

The genome of Dictyostelium discoideum is being sequenced by an international consortium and is scheduled for completion in the next few years. The sequence will accelerate research into a number of phenomena carried out by these versatile soil amoebae, providing insight into analogous processes that operate in a wide range of eukaryotes. These include the dynamic regulation of the cytoskeleton during chemotaxis, intercellular communication during multicellular development and the intracellular growth of bacterial pathogens. The current state of the genome project is summarized and the challenges of sequencing a genome with unusually low guanine and cytosine content and with a bimodal base composition distribution are discussed. The prospects for functional analyses at the genomic scale are also considered. Electronic Publication     

我国启动重大入侵害虫苹果蠹蛾基因组测序

苹果蠹蛾Cydia pomonella (L.)属鳞翅目卷蛾科,具有极强的适应性和抗逆能力,是仁果类果树的毁灭性害虫。1953年首次在我国新疆库尔勒发现,并迅速扩散危害,1987年随旅客携带物传入甘肃敦煌,造成了重大经济损失,是我国重点防控的检疫对象。近日,由中国农业科学院植物保护研究所、南京农业大学等科研单位联合启动了苹果蠹蛾的基因组测序工作。研究团队对苹果蠹蛾进行了10余代的纯化,建立了纯化品系。利用流式细胞分析和小片段文库前期测序等方法,对苹果蠹蛾基因组进行了初步的基因组前期分析。结果显示,苹果蠹蛾基因组大小约为650 Mb, 17-mer和SNP分析显示杂合度大约在0.3%-0.6%之间。经协商拟定了详细的全基因组鸟枪法测序方案后,基因组测序已经全面启动。苹果蠹蛾的基因组测序,对阐明其入侵机制、抗逆机理及防控等研究具有重要的推动意义。     

Euchromatic and heterochromatic compositional properties emerging from the analysis of Solanum lycopersicum BAC sequences

The consortium responsible for the sequencing of the tomato (Solanum lycopersicum) genome initially focused on the sequencing of the euchromatic regions using a BAC-by-BAC strategy. We analyzed the compositional features of the whole collection of BAC sequences publically available. This analysis highlights specific peculiarities of heterochromatic and euchromatic BACs, in particular: the whole BAC collection has i) a large variability in repeat and gene content, ii) a positive and significant correlation of LTR retrotransposons of the Gypsy class with the repeat content and iii) the preferential location of the SINEs (short interspersed nuclear elements) in BAC sequences showing a low repeat content. Our results point out a typical design of the tomato chromosomes and pave the way for further investigations on the relationship between DNA primary structure and chromatin organization in Solanaceae genomes.     

耐盐菌Staphylococcus sp. YZ-1和Bacillus cereus CC-1的Cr(VI)脱毒特性与机理

[背景]高盐含铬废水的去除过程中,Cr(Ⅵ)还原菌是研究者关注的重点,但目前对耐盐菌株的Cr(Ⅵ)脱毒特性及机理的分析仍较少。[目的]比较两株耐盐菌株的Cr(Ⅵ)移除特性,并区分Cr(Ⅵ)耐受机制的差异;通过基因组测序分析,从基因层面推测铬耐受相关基因;构建铬还原菌的混菌体系,考察两者对去除污染物的协同作用。[方法]从青海茶卡盐湖分离耐盐菌Staphylococcus sp.YZ-1,与Bacillus cereus CC-1进行基础特性和Cr(Ⅵ)去除性能的比较,并通过全基因组序列的分析验证特性测试的结果。[结果]两株菌都具有铬移除特性,但CC-1的铬移除效率更高,在初始Cr(Ⅵ)浓度为0.1 mmol/L情况下,CC-1能在12h内移除95.3%的Cr(Ⅵ),而YZ-1只能移除40.1%。在进一步实验中发现YZ-1只能对Cr(Ⅵ)进行还原,将其转化为可溶的有机态Cr(Ⅲ),而CC-1能同时对Cr(Ⅵ)进行还原和吸附。全基因组分析发现YZ-1具有编码外排泵蛋白的基因和编码NAD(P)H氧化还原酶的基因,而CC-1具有编码铬转运蛋白ChrA和细胞色素C氧化还原酶的基因。两株菌的混菌体系在处理含Cr(Ⅵ)、Te(Ⅳ)的废水时,菌群能将还原产物聚集成团并沉淀到底部。[结论]菌株YZ-1和CC-1均为耐盐铬还原菌,但YZ-1中的铬还原酶为诱导型酶,CC-1则为组成型酶。基因组数据分析鉴别出两者可能同时存在多种铬耐受机制相关编码基因。混合菌群可以结合YZ-1的自絮凝特性和两者均有的Te(Ⅳ)/Cr(Ⅵ)还原活性,具有潜在的实用价值。     

Stem cells in biology and disease - ESTOOLS International Symposium

ESTOOLS was the first EU-funded project entirely devoted to the study of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). The final meeting of the consortium took place in Lisbon from 26 to 28 May 2010 and gathered 298 researchers from 27 countries. A dense programme of scientific sessions and outreach activities and an ethics workshop gave an all-round overview of the challenges, perspectives and ethical issues of this exciting field. The ESTOOLS consortium was launched in 2006 as a 4-year EU-funded 6th Framework (FP6) project, with a total funding of 12 million euro. The project has been the largest European consortium devoted to the study of human ESCs, teaming up 21 research groups in 10 countries. After the discovery of human induced pluripotent stem cells (iPSCs) by Shinya Yamanaka and James Thomson in 2007, the consortium opened a new workpackage dedicated to this groundbreaking field, and became the first to devote EU funding to study human iPSCs. The Lisbon meeting marked the end of the consortiums funding cycle, but it was more than a wrap-up of its overall work and achievements, providing a showcase of cutting-edge research in human pluripotent stem cells, with the participation of international leaders in the field.     

GO‐FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO‐FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass‐roots organization formed to advance the annotation of newly assembled genomes of domesticated and non‐model organisms ( www.faang.org ). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org . In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO‐FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta‐data analysis standards were established.     

Cephalopod genomics: A plan of strategies and organization

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this white paper.     

Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome

The Swine Genome Sequencing Consortium (SGSC) was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC's mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP) that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA), presentations demonstrated that a human-pig comparative map has been completed, BAC fingerprint contigs (FPC) for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG) shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3x coverage of BACs comprising the MTP and 3x of the WG-shotgun libraries will be used to develop a draft 6x coverage of the pig genome.